INTRAOPERATIVE ALIGNMENT ASSESSMENT SYSTEM AND METHOD

RELATED APPLICATIONS

[0001] This application claims priority to United States provisional application Ser. No. 62/528,390, filed on July 3 ^rd , 2017, the entire contents of which are incorporated herein by reference.

BACKGROUND

[0002] Current tools limit a surgeon's ability to quickly and accurately assess the intraoperative alignment of their patient's spine, especially after the spine has been manipulated during a correction. In addition, most of the state-of-the-art options introduce or rely on excessive radiation exposure, inadequate visualization of anatomical landmark(s) of interest, and lengthy disruptions to the surgical workflow.

SUMMARY

[0003] Some embodiments include a method of analyzing and providing a patient's spinal alignment information and therapeutic device data. In some embodiments, the method can comprise obtaining initial patient data, and acquiring spinal alignment contour information. In some embodiments, the method can comprise assessing localized anatomical features of the patient, and obtaining anatomical region data. In some embodiments, the method can include analyzing the localized anatomy and therapeutic device location and contouring. In some embodiments, the method can output localized anatomical analyses and therapeutic device contouring data on a display.

DESCRIPTION OF THE DRAWINGS

[0004] FIG. 1 illustrates a system for assessing spinal alignment, local anatomy biomechanics, rod contours, and active contouring of a rod, as well as initialization of fiducials and interactive displays of various outputs in accordance with some embodiments of the invention.

[0005] FIG. 2A shows a representation of a body-surface-mountable fiducial patch in accordance with some embodiments of the invention. [0006] FIG. 2B displays the radiopaque elements of the fiducial patch of FIG. 2A as would be visible on an x-ray image of a patient with the patch applied in accordance with some embodiments of the invention.

[0007] FIG. 3A displays a vertebra with a bone-mounted fiducial fastened to the bone in accordance with some embodiments of the invention.

[0008] FIG. 3B shows an assembly view of a vertebra with a bone-mounted fiducial and top fiducial for coupling to the bone-mounted fiducial in accordance with some embodiments of the invention.

[0001] FIG. 3C shows a vertebra with a bone-mounted fiducial coupled with a top fiducial in accordance with some embodiments of the invention.

[0002] FIG. 4A illustrates an assembly or operation process for a skin-surface-mounted fiducial being applied to a patient's posterior skin as they are positioned prone on an operative table in accordance with some embodiments of the invention.

[0003] FIG. 4B illustrates a sample lateral radiograph of skin fiducials applied to an anatomical model in accordance with some embodiments of the invention.

[0004] FIG. 4C illustrates the sample lateral radiograph of FIG. 4B with annotated vectors in accordance with some embodiments of the invention.

[0005] FIG. 4D illustrates a C-arm based mount a type of an x-ray imaging system that can be utilized for image acquisition and subsequent initialization of fiducial markers in accordance with some embodiments of the invention.

[0006] FIG. 4E illustrates a sample x-ray image of a spine-fiducial pair from a different imaging angle from that of FIGS. 4A and 4B in accordance with some embodiments of the invention.

[0007] FIG. 4F illustrates the sample x-ray image of FIG. 4E including annotated vectors in accordance with some embodiments of the invention.

[0008] FIG. 4G illustrates 3D axes relative to the fiducial origin point onto which displacement vectors drawn over each of the 2D x-rays are able to be added based on input or calculated angle between each x-ray image plane in accordance with some embodiments of the invention.

[0009] FIG. 4H illustrates a system and method of localizing the fiducial in 3D tracking camera coordinates in accordance with some embodiments of the invention.

[0010] FIG. 41 displays the axes of a 3D-acquisition system with which the unique location and pose of the fiducial was registered as of FIG. 4H in accordance with some embodiments of the invention.

[0011] FIG. 5 A illustrates an optical tracking system in accordance with some embodiments of the invention.

[0012] FIG. 5B illustrates an ultrasound probe equipped with a tracked dynamic reference frame in accordance with some embodiments of the invention.

[0013] FIG. 5C illustrates an assembly or process view of a patient's skin surface overlying a cross-sectional view of a vertebra as a representation of a particular region of bony anatomy that could be registered to a skin-mounted fiducial in accordance with some embodiments of the invention.

[0014] FIG. 6 A illustrates an assembly or process view for applying a skin-mounted fiducial and its associated over-the drape fiducial in accordance with some embodiments of the invention.

[0015] FIG. 6B illustrates an assembly view of a skin-mounted fiducial and its associated over-the-drape mating fiducial in accordance with some embodiments of the invention.

[0016] FIG. 6C illustrates one embodiment of a skin-mounted fiducial applied to an anatomical phantom in a region that is outside the surgical site but located over regions of underlying anatomy for which their location within 3D-tracking coordinates is desired to be known in accordance with some embodiments of the invention.

[0017] FIG. 6D illustrates an embodiment of a skin-mounted fiducial mating with its over-the-drape fiducial across a surgical drape/towel in accordance with some embodiments of the invention. [0018] FIG. 7 illustrates an assembly view of a fiducial in accordance with some embodiments of the invention.

[0019] FIG. 8 illustrates an assembly view of a fiducial in accordance with some embodiments of the invention.

[0020] FIG. 9A illustrates an assembled skin-surface fiducial with mating top surface fiducial in accordance with some embodiments of the invention.

[0021] FIG. 9B illustrates an assembly view of the fiducial of FIG. 9 A in accordance with some embodiments of the invention.

[0022] FIG. 10A illustrates a 3D-trackable probe equipped with a rigidly attached trackable dynamic reference frame in accordance with some embodiments of the invention.

[0023] FIG. 10B illustrates a close-up perspective of an actuating tip and variable height selection depth stops of the probe of FIG. 10A in accordance with some embodiments of the invention.

[0024] FIG. IOC illustrates receptacles designed to mate with the probe of FIGS. 10A- 10B in accordance with some embodiments of the invention.

[0025] FIG. 10D illustrates the probe of FIG. 10A mated with a particular receptacle of FIG. IOC in accordance with some embodiments of the invention.

[0026] FIG. 10E illustrates the probe of FIG. 10A mated with a receptacle designed to mate with a different height selector of the probe than shown in FIG. 10D in accordance with some embodiments of the invention.

[0027] FIG. 10F illustrates an assembly view of a portion of a probe in accordance with some embodiments of the invention.

[0028] FIG. 10G illustrates a partially assembled view of the probe of FIG. 10F in accordance with some embodiments of the invention.

[0029] FIG. 11A illustrates a top perspective assembly view of a skin surface fiducial mated with an over-the-drape fiducial that contains three or more tracked markers in accordance with some embodiments of the invention. [0030] FIG. 11B illustrates a side perspective assembly view of the fiducial of FIG. 11A accordance with some embodiments of the invention.

[0031] FIG. 12 illustrates a representation of a tracked dynamic reference frame in accordance with some embodiments of the invention.

[0032] FIG. 13 illustrates a sample cross-sectional CT scan view of a spine in accordance with some embodiments of the invention.

[0033] FIG. 14A illustrates a tool equipped with a tracked dynamic reference frame in accordance with some embodiments of the invention.

[0034] FIGS. 14B-14C illustrate the tool of FIG. 14A in different arrangements in accordance with some embodiments of the invention.

[0035] FIGS. 15A-15C shows a probe equipped with a tracked dynamic reference frame (DRF) in various configurations in accordance with some embodiments of the invention.

[0036] FIG. 16 illustrates a rotary encoder in accordance with some embodiments of the invention.

[0037] FIG. 17A illustrates a pulley-gear system for use with the encoder of FIG. 16 in accordance with some embodiments of the invention.

[0038] FIG. 17B illustrates a gear of the pulley-gear system of FIG. 17A in accordance with some embodiments of the invention.

[0039] FIG. 18A illustrates a perspective view of a cord spool for use in the pulley-gear system of FIG. 17 in accordance with some embodiments of the invention.

[0040] FIG. 18B illustrates a side view of the cord spool for use in the pulley-gear system of FIG. 17 in accordance with some embodiments of the invention.

[0041] FIGS. 19A-19C illustrates a ball assembly of a 3D-tracking system of FIG. 23 A in accordance with some embodiments of the invention.

[0042] FIGS. 19D-19E illustrate a ball and socket assembly of the 3D-tracking system of FIG. 23 A accordance with some embodiments of the invention. [0043] FIG. 20 illustrates a probe of a 3D tracking system in accordance with some embodiments of the invention.

[0044] FIGS. 20A-20E show views of components of the probe of FIG. 20 in accordance with some embodiments of the invention.

[0045] FIGS. 21A-21B illustrate assemblies of a 3D tracking system including a probe coupled to cord fixation points in accordance with some embodiments of the invention.

[0046] FIG. 22 illustrates an example system enabling 3D tracking of a probe in accordance with some embodiments of the invention.

[0047] FIG. 23A illustrates an example 3D tracking system in accordance with some embodiments of the invention.

[0048] FIG. 23B illustrates 3D tracking system in enclosure in accordance with some embodiments of the invention.

[0049] FIG. 23 C shows an exploded assembly view of the 3D tracking system of FIG. 23B in accordance with some embodiments of the invention.

[0050] FIGS. 24-26 illustrate systems enabling 3D tracking of a probe in accordance with some embodiments of the invention.

[0051] FIGS. 27A-27D includes representations of 3D tracking methods in accordance with some embodiments of the invention.

[0052] FIG. 28A illustrates an example 3D tracking system in accordance with some embodiments of the invention.

[0053] FIG. 28B illustrates a computer system configured for operating and processing components of the system in accordance with some embodiments of the invention.

[0054] FIGS. 29A-29B illustrates a screw-head-registering screwdriver equipped with a tracked dynamic reference frame in accordance with some embodiments of the invention. [0055] FIG. 29C illustrates a close-up perspective view of a screwdriver head and depressible tip of the screwdriver of FIGS. 29A-29B in accordance with some embodiments of the invention.

[0056] FIG. 29D illustrates a cross-sectional view of the screwdriver- screw interface in accordance with some embodiments of the invention.

[0057] FIG. 30A illustrates a 3D-tracking camera system in accordance with some embodiments of the invention.

[0058] FIG. 30B comprises an image of a tracked reference frame accordance with some embodiments of the invention.

[0059] FIG. 31 illustrates a body-mounted 3D-tracking camera in accordance with some embodiments of the invention.

[0060] FIG. 32 displays a method of interpreting the contour of the posterior elements of the spine in accordance with some embodiments of the invention.

[0061] FIG. 33A illustrates pedicle screw in accordance with some embodiments of the invention.

[0062] FIG. 33B illustrates a pedicle screw in accordance with another embodiment of the invention.

[0063] FIG. 33C illustrates pedicle screw mated with a polyaxial tulip head in accordance with some embodiments of the invention.

[0064] FIG. 33D illustrates a tool designed to interface with the pedicle screw of FIG. 33B in accordance with some embodiments of the invention.

[0065] FIG. 33E illustrates a visualization of a couple between the tool of FIG. 33D and the screw of FIG. 33C in accordance with some embodiments of the invention.

[0066] FIG. 33F illustrates a screwdriver coupled to a pedicle screw in accordance with some embodiments of the invention. [0067] FIG. 33G illustrates a top view of the screw of FIG. 33 A in accordance with some embodiments of the invention.

[0068] FIG. 33H illustrates a top view of the screw of FIG. 33B in accordance with some embodiments of the invention.

[0069] FIG. 34 illustrates a tool for interfacing with a pedicle screw accordance with some embodiments of the invention.

[0070] FIGS. 34A-34F illustrate various views of the tool of FIG. 34 in accordance with some embodiments of the invention.

[0071] FIGS. 35A-35E illustrate various views of a tool for interfacing with a pedicle screw in accordance with some embodiments of the invention.

[0072] FIG. 35F illustrates a close-up perspective view of the tool of FIGS. 35A-35E without a coupled pedicle screw or tulip head in accordance with some embodiments of the invention.

[0073] FIGS. 36A-36G illustrate a tool designed to interface directly with tulip heads of pedicle screws in accordance with some embodiments of the invention.

[0074] FIGS. 36H-36I illustrate perspective views of the tool of FIGS. 36A-36G without pedicle screw shaft in accordance with some embodiments of the invention.

[0075] FIGS. 37A-37G illustrate various views of a tool for interfacing directly with two implanted pedicle screws in accordance with some embodiments of the invention.

[0076] FIG. 38 illustrates a pedicle screw shaft with depth stop in accordance with some embodiments of the invention.

[0077] FIG. 38A illustrates a top view of the pedicle screw shaft with depth stop of FIG. 38 in accordance with some embodiments of the invention.

[0078] FIG. 38B illustrates a screw interface region with coupled handle in accordance with some embodiments of the invention. [0079] FIG. 38C illustrates an example assembly view coupling between the screw interface region of FIG. 38B and the pedicle screw shaft with depth stop of FIGS. 38-38A in accordance with some embodiments of the invention.

[0080] FIGS. 38D-38G illustrates view of the screw interface region of FIG. 38B coupled with the pedicle screw shaft with depth stop of FIGS. 38-38 A in accordance with some embodiments of the invention.

[0081] FIG. 39A illustrates a full perspective view of a device used for manipulating bony anatomy and assessing range of motion intraoperatively in accordance with some embodiments of the invention.

[0082] FIG. 39B illustrates another embodiment of the handle of the tool described previously in relation to FIG. 39A in accordance with some embodiments of the invention.

[0083] FIG. 39C illustrates a bottom view of the embodiment described above in relation to FIGS. 39A-B in accordance with some embodiments of the invention.

[0084] FIG. 39D displays a cross-sectional side view of the tool as described previously in relation to FIGS. 39A-C in accordance with some embodiments of the invention.

[0085] FIG. 39E illustrates a bottom view of a width-adjustment mechanism that allows for variation in the distance between screw-interface locations of the tool in accordance with some embodiments of the invention.

[0086] FIG. 39F illustrates a close-up perspective of the width-adjustment mechanism, thread-tightening knobs, and sleeve body of the device as described above in relation to FIGS. 39A-E in accordance with some embodiments of the invention.

[0087] FIG. 40A illustrates a lateral view of a spine model with a straight curve, and two flexibility assessment tools engaged with the model in accordance with some embodiments of the invention.

[0088] FIG. 40B illustrates one embodiment of two flexibility assessment devices interfacing with a spine model with a lordotic curve in accordance with some embodiments of the invention. [0089] FIG. 40C illustrates an embodiment of the invention from a 3D-tracking camera perspective in accordance with some embodiments of the invention.

[0090] FIG. 41 A illustrates a side view of one embodiment of the screw-interface components of the flexibility assessment device described previously in relation to FIGS. 34- 36, 39, 40 in accordance with some embodiments of the invention.

[0091] FIG. 4 IB illustrates a front view of the embodiment described above in relation to FIG. 41 A in accordance with some embodiments of the invention.

[0092] FIG. 41C illustrates the device of FIGS. 41A-41B assembled with a flexibility assessment device previously described in relation to FIGS. 39-40 in accordance with some embodiments of the invention.

[0093] FIG. 41D illustrates a perspective assembly view of a detachable screw-interface component displaying release tabs, center-alignment post, peripheral alignment pins, screw- interface rod, side-tab extensions, and spring-loaded snap arm in accordance with some embodiments of the invention.

[0094] FIG. 42A illustrates the flexibly assessment device of FIGS. 39-40 equipped with detachable screw interface components, previously described in FIG. 41 with adjustable cross-linking devices, described below in reference to FIG. 43 in accordance with some embodiments of the invention.

[0095] FIG. 42B illustrates the flexibility assessment device described previously in relation to FIG. 42A rigidly coupled to the pedicle screws by interfacing with the tulip heads in accordance with some embodiments of the invention.

[0096] FIG. 42C illustrates a second flexibility assessment device interfacing with a spinal level at a user-defined distance from the already mated device described previously in relation to FIGS. 39, 41, and 42A-42B in accordance with some embodiments of the invention.

[0097] FIG. 42D illustrates two mated flexibility assessment devices, as previously described in relation to FIGS. 39, 41 42A-42C in accordance with some embodiments of the invention. [0098] FIG. 42E illustrates two flexibility assessment devices rigidly attached to the spine as described previously in relation to FIGS. 39, 41, and 42A-D in accordance with some embodiments of the invention.

[0099] FIG. 42F illustrates two flexibility assessment devices rigidly attached to the spine as described previously in relation to FIGS. 39, 41, and 42A-42F in accordance with some embodiments of the invention.

[00100] FIG. 42G illustrates an instrumented spine previously described in relation to FIGS. 42A-F in accordance with some embodiments of the invention.

[00101] FIG. 42H displays an instrumented spine previously described in relation to FIGS. 42A-42G in accordance with some embodiments of the invention.

[00102] FIG. 421 illustrates an instrumented spine previously described in relation to FIGS. 42A-42H in accordance with some embodiments of the invention.

[00103] FIG. 42 J illustrates an instrumented spine previously described in relation to FIGS. 42A-42I in accordance with some embodiments of the invention.

[00104] FIG. 42K illustrates an instrumented spine previously described in relation to FIGS. 42A-42J in accordance with some embodiments of the invention.

[00105] FIGS. 43A-43D includes views of an adjustable cross-linking device in accordance with some embodiments of the invention.

[00106] FIGS. 43E-43F illustrate views of an adjustable cross-linking device in accordance with some embodiments of the invention.

[00107] FIG. 44 A illustrates a bone-implanted fiducial equipped with a crossbar and rigidly fixed to the lamina of a vertebra as previously described in relation to FIGS. 3A-3C in accordance with some embodiments of the invention.

[00108] FIG. 44B illustrates a process view of a pre-engagement of a bone-implanted fiducial and bone-fiducial mating screwdriver equipped with a tracked DRF and a TMSM coupled to a depressible sliding shaft at the end of the screwdriver in accordance with some embodiments of the invention. [00109] FIG. 44C illustrates an engagement of a bone-implanted fiducial and bone-fiducial mating screwdriver equipped with a tracked DRF and a TMSM coupled to a depressible sliding shaft at the end of the screwdriver in accordance with some embodiments of the invention.

[00110] FIG. 44D illustrates a bone-implanted fiducia with crossbar and overlying bone- fiducial-mating screwdriver in accordance with some embodiments of the invention.

[00111] FIGS. 45A-45B illustrate a vertebra engagement and rendering process in accordance with some embodiments of the invention.

[00112] FIGS. 46A-46B illustrate a 3D tracking tool in accordance with some embodiments of the invention.

[00113] FIG. 46C illustrates an x-ray imaging and tracking system in accordance with some embodiments of the invention.

[00114] FIG. 46D illustrates a virtual overlay of a tracked surgical tool positioned close to the x-ray detector on top of an x-ray image of the spine in accordance with some embodiments of the invention.

[00115] FIG. 46E illustrates an x-ray imaging and tracking system in accordance with some embodiments of the invention.

[00116] FIG. 46F illustrates a virtual overlay of a tracked surgical tool positioned close to the emitter as shown in FIG. 46E in accordance with some embodiments of the invention.

[00117] FIG. 46G illustrates a virtual overlay of a tracked surgical tool that has been turned 90 degrees from the tool position previously described in FIGS. 46D-46F in accordance with some embodiments of the invention.

[00118] FIG. 47 A illustrates components of a tracked end cap in accordance with some embodiments of the invention.

[00119] FIG. 47B illustrates components of a tracked slider designed to interface with a rod fixed to a tracked end cap, described previously in relation to FIG. 47A in accordance with some embodiments of the invention. [00120] FIG. 48 A illustrates a close-up view of a portion of an end cap in accordance with some embodiments of the invention.

[00121] FIG. 48B illustrates a perspective view of an end cap assembled from components of FIG. 47 A in accordance with some embodiments of the invention.

[00122] FIG. 48C illustrates a side view of the end cap of FIG. 48B in accordance with some embodiments of the invention.

[00123] FIGS. 49A-49C illustrates a single-ring rod assessment device assembly in accordance with some embodiments of the invention.

[00124] FIG. 49D illustrates the assembly of FIGS. 49A-49C coupled with a rod and tracked end cap previously described in relation to FIGS. 47A, and 48A-48B in accordance with some embodiments of the invention.

[00125] FIGS. 50A-50D illustrates a fixed-base, variable-ring, mobile rod assessment device in accordance with some embodiments of the invention.

[00126] FIG. 50E illustrates the fixed-base, variable-ring, mobile rod assessment device of FIGS. 50A-50D engaged with a rod coupled to an end cap in accordance with some embodiments of the invention.

[00127] FIGS. 51A-51G illustrates various views of a handheld, mobile rod contour assessment device in accordance with some embodiments of the invention.

[00128] FIG. 51H-5 II illustrates views of a process or method of registering the contour of a rod prior to implantation with the handheld, mobile rod contour assessment device of FIGS. 51A-51G in accordance with some embodiments of the invention.

[00129] FIG. 52 A illustrates a component of a TMSM-based, implanted rod contour assessment device in accordance with some embodiments of the invention.

[00130] FIG. 52B illustrates a depressible sliding shaft for coupling to the component of FIG. 52A in accordance with some embodiments of the invention.

[00131] FIG. 52C illustrates a top view of the component of FIG. 52 A in accordance with some embodiments of the invention. [00132] FIG. 52D illustrates a close-up perspective view of the depressible sliding shaft of FIG. 52B in accordance with some embodiments of the invention.

[00133] FIG. 53A illustrates an assembly of components of FIGS. 52A and 52B used to assess the contour of a rod after it has been implanted within the surgical site in accordance with some embodiments of the invention.

[00134] FIG. 53B illustrates a close-up back view of a portion of the assembly of FIG. 53 A in accordance with some embodiments of the invention.

[00135] FIG. 53C illustrates a close-up view of the rod-interface region of the assembly of FIGS. 53 A-53B in accordance with some embodiments of the invention.

[00136] FIG. 53D illustrates the assembly of FIGS. 53A-53C interfacing with a rod in accordance with some embodiments of the invention.

[00137] FIGS. 53E-53F illustrates close-up views of a trackable DRF portion of the assembly view of FIGS. 53A-D in accordance with some embodiments of the invention.

[00138] FIG. 54 A illustrates a conductivity -based rod contour assessment device in accordance with some embodiments of the invention.

[00139] FIG. 54B illustrates a rod-centering fork and electrical contact pads of the device of FIG. 54 A in accordance with some embodiments of the invention.

[00140] FIGS. 54C-54D illustrates the rod-centering fork of FIG. 54B interacting with a rod in accordance with some embodiments of the invention.

[00141] FIGS. 55A-55I illustrates various views of a 3D-tracked, manual mobile rod bender in accordance with some embodiments of the invention.

[00142] FIGS. 56A-56F illustrate various views of a tracked DRF-equipped end cap, pre- registered rod, and manual bender equipped with TMSMs accordance with some embodiments of the invention.

[00143] FIG. 57A illustrates a DRF-tracked and trigger-equipped in-situ benders coupled to a rod in accordance with some embodiments of the invention. [00144] FIG. 57B illustrates a DRF-tracked and trigger-equipped in-situ benders coupled to a rod coupled to a spine in accordance with some embodiments of the invention.

[00145] FIG. 57C illustrates a close-up assembly view of the rod of FIG. 57A in accordance with some embodiments of the invention.

[00146] FIG. 57D illustrates a close-up view of a rod interface head of the bender showin in FIG. 57A including a view of a depressible sliding shaft tip in an extended position in accordance with some embodiments of the invention.

[00147] FIG. 58 illustrates a workflow to initialize skin-mounted, or percutaneous, fiducials with two or more x-ray images intraoperatively in accordance with some embodiments of the invention.

[00148] FIG. 59 illustrates a workflow to initialize one or more bone-mounted fiducials placed intraoperatively with 2 or more x-ray images taken before placement of the bone- mounted fiducials in accordance with some embodiments of the invention.

[00149] FIG. 60 shows a workflow to initialize one or more bone-mounted fiducials placed intraoperatively with 2 or more x-ray images taken after placement of the bone- mounted fiducials in accordance with some embodiments of the invention.

[00150] FIG. 61 illustrates methods of registering anatomical reference planes intraoperatively in accordance with some embodiments of the invention.

[00151] FIG. 62 A illustrates an arrangement for acquiring information regarding the contour of the spine via tracing over body surfaces using a tracked probe in accordance with some embodiments of the invention.

[00152] FIG. 62B illustrates a display of the acquired body surface contours via tracing with a 3D-tracked probe in accordance with some embodiments of the invention.

[00153] FIG. 62C illustrates a display of transformed tracing data in accordance with some embodiments of the invention.

[00154] FIG. 62D illustrates a display of the data of FIGS. 62B-62C with depth translation in accordance with some embodiments of the invention. [00155] FIG. 63 shows a workflow for analog triggering detection of one or more tracked mobile stray marker (TMSM) relative to a tracked tool with a dynamic reference frame (DRF) in accordance with some embodiments of the invention.

[00156] FIG. 64A illustrates a tracking probe assembly in accordance with some embodiments of the invention.

[00157] FIG. 64B illustrates an interpretation and calculation of the position of a rotating TMSM relative to the DRF on a probe as described previously in relation to FIG. 64A in accordance with some embodiments of the invention.

[00158] FIG. 65A illustrates displays of a discrete body surface or bony surface annotations on cross-sectional images used for initialization of patient-specific interpretation of body and bony surface tracings with a 3D-tracked probe in accordance with some embodiments of the invention.

[00159] FIG. 65B illustrates 3D perspective of cross-sectional annotations from the CT scan in accordance with some embodiments of the invention.

[00160] FIG. 65C illustrates a plot of coronal projected coordinates in accordance with some embodiments of the invention.

[00161] FIG. 65D illustrates a plot of sagittal projected coordinates in accordance with some embodiments of the invention.

[00162] FIG. 65E illustrates computed cross-sectional distances between corresponding anatomical landmarks and vertebral body centroids in accordance with some embodiments of the invention.

[00163] FIG. 66A illustrates a display of cross-sectional slices of vertebra (a) in their relative anatomical axes in accordance with some embodiments of the invention.

[00164] FIG. 66B illustrates a display of a vertebral body calculated via bilaterally traced coordinates and patient initialization data in accordance with some embodiments of the invention. [00165] FIG. 67 illustrates a workflow to calculate spinal alignment parameters based on intraoperative tracing in accordance with some embodiments of the invention.

[00166] FIG. 68 illustrates a workflow to acquire a spinal alignment curve using probe- based tracing within only the surgical site in accordance with some embodiments of the invention.

[00167] FIG. 69 illustrates a workflow to acquire a spinal alignment curve using probe- based tracing data spanning beyond the surgical site in accordance with some embodiments of the invention.

[00168] FIG. 70 illustrates a workflow to assess flexibility of the spine intraoperatively using flexibility assessment device in accordance with some embodiments of the invention.

[00169] FIG. 71 illustrates a workflow of producing real-time overlays of surgical instruments over intraoperative x-rays in accordance with some embodiments of the invention.

[00170] FIG. 72 shows a workflow to rapidly re-register a surgical navigation system after a navigated/registered screw insertion in accordance with some embodiments of the invention.

[00171] FIG. 73 A illustrates a rod-centering fork on the end of a tool shaft in accordance with some embodiments of the invention.

[00172] FIG. 73B illustrates the fork of FIG. 73 A fully engaged with a rod in accordance with some embodiments of the invention.

[00173] FIG. 74 illustrates a workflow to assess the contour of a rod prior to implantation using two handheld tracked tools in accordance with some embodiments of the invention.

[00174] FIG. 75 illustrates a workflow to assess the contour of a rod prior to implantation using one handheld tracked tool and one rigidly fixed ring in accordance with some embodiments of the invention.

[00175] FIG. 76 illustrates a workflow to assess the contour of a rod after implantation in accordance with some embodiments of the invention. [00176] FIGS. 77A-77C illustrate various displays of interpretation of data generated by assessment of a rod contour after a rod has been implanted to tulip heads within a surgical site in accordance with some embodiments of the invention.

[00177] FIG. 78 illustrates a workflow for interactive user placement of a registered rod as an overlay on patient images on a display monitor in accordance with some embodiments of the invention.

[00178] FIGS. 79A-79G display processes of interpreting and calculating a tracked rod bending device in accordance with some embodiments of the invention.

[00179] FIG. 80 illustrates a workflow for manually bending a rod prior to its implantation with real-time feedback of its dynamic contour in accordance with some embodiments of the invention.

[00180] FIG. 81 shows a workflow for manually bending a rod prior to its implantation with directed software input to overlay a projection of the dynamic rod contour onto an intraoperative x-ray image in accordance with some embodiments of the invention.

[00181] FIGS. 82A-82B illustrates processes or methods of a probe calibration in accordance with some embodiments of the invention.

[00182] FIG. 83 illustrates a workflow to utilize a trigger-equipped probe to serve as a laser pointer analog for a user-interface system with a non-tracked display in accordance with some embodiments of the invention.

[00183] FIGS. 84A-84B illustrates a workflow to utilize a trigger-equipped probe to serve as a laser pointer analog for a user-interface with a 3D-tracked display monitor in accordance with some embodiments of the invention.

[00184] FIG. 85 illustrates a workflow to utilize a trigger-equipped probe to serve as an interface device for a non-tracked display via a user-defined trackpad analog in accordance with some embodiments of the invention.

[00185] FIGS. 86A-86D illustrates output displays of alignment assessments in accordance with some embodiments of the invention. [00186] FIG. 87A illustrates a rod with previously registered contour fixed to a tracked DRF-equipped end cap and interacting with a tracked rod bender in accordance with some embodiments of the invention.

[00187] FIG. 87B illustrates a sagittal projection of the registered rod contour in accordance with some embodiments of the invention.

[00188] FIG. 87C illustrates a coronal projection of the registered rod contour in accordance with some embodiments of the invention.

[00189] FIG. 87D illustrates a display of the location of a rod bender's center rod contouring surface relative to a cross-sectional view of the rod in accordance with some embodiments of the invention.

[00190] FIG. 87E illustrates a display of a sagittal projection of the registered rod contour in accordance with some embodiments of the invention.

[00191] FIG. 87F illustrates a sagittal patient image with an overlay of a registered rod contour as well as an overlay display of the location of a tracked rod bender relative to the previously registered rod in accordance with some embodiments of the invention.

[00192] FIG. 87G illustrates a sagittal patient image adjusted for operative planning with an overlay of a registered rod contour as well as an overlay display of the location of a tracked rod bender relative to the previously registered rod in accordance with some embodiments of the invention.

[00193] FIGS. 87H-87I include displays of a rod and rod bender's location on display monitor in accordance with some embodiments of the invention.

[00194] FIGS. 87J-87M illustrates a display of a bender and rod in accordance with some embodiments of the invention.

[00195] FIG. 88 A illustrates a sagittal projection of a registered rod contour, a display of the current location of the rod bender relative to the registered rod contour, a display of the software-instructed location where the user should place the rod-bender, and anatomical axes labels in accordance with some embodiments of the invention. [00196] FIG. 88B illustrates a display of FIG. 88 A as applied to the coronal plane in accordance with some embodiments of the invention.

[00197] FIG. 88C illustrates a cross-sectional display of the rod, the current location of the rod bender's center contouring surface, the software-instructed location of where the rod bender's center contouring surface should be placed, and anatomical axes labels in accordance with some embodiments of the invention.

[00198] FIG. 88D illustrates a display representation of the current relative position of the bender's handles, directly related to the degree of bending induced on a rod of known diameter in accordance with some embodiments of the invention.

[00199] FIG. 88E illustrates a display representation of the software-instructed relative position of the bender's handles (k), directly related to the degree of bending induced on a rod of known diameter in accordance with some embodiments of the invention.

[00200] FIG. 88F illustrates a bend angle display gauge in accordance with some embodiments of the invention.

[00201] FIG. 89 shows a workflow to match the adjustable benchtop spinal model to mimic alignment parameters from patient-specific imaging in accordance with some embodiments of the invention.

[00202] FIG. 90A illustrates sagittal and coronal patient images with overlaid sagittal and coronal contour tracings of the spine, discrete software-instructed placement of adjustable mounts onto the anatomical model, and instructions for the coordinates of each of those adjustable mounts to be positioned on the adjustable benchtop model in accordance with some embodiments of the invention.

[00203] FIG. 90B illustrates an anatomical model mounting exploded assembly in accordance with some embodiments of the invention.

[00204] FIG. 90C illustrates a fastening interface for anatomical model in accordance with some embodiments of the invention.

[00205] FIG. 90D illustrates a mounted spine anatomical model in accordance with some embodiments of the invention. [00206] FIG. 91 A illustrates an engaged, straight probe extension as the selected modular tool tip and its associated, unique TMSM position relative to the DRF when engaged, in accordance with some embodiments of the invention.

[00207] FIG. 9 IB illustrates a coupling mechanism between the modular tool tip and the TMSM-equipped DRF in accordance with some embodiments of the invention.

[00208] FIG. 91C illustrates an engaged, curved probe extension as the selected modular tool tip and its associated, unique TMSM position relative to the DRF when engaged in accordance with some embodiments of the invention.

DETAILED DESCRIPTION

[00209] Before any embodiments of the invention are explained in detail, it is to be understood that the invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the following drawings. The invention is capable of other embodiments and of being practiced or of being carried out in various ways. Also, it is to be understood that the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. The use of "including," "comprising," or "having" and variations thereof herein is meant to encompass the items listed thereafter and equivalents thereof as well as additional items. Unless specified or limited otherwise, the terms "mounted," "connected," "supported," and "coupled" and variations thereof are used broadly and encompass both direct and indirect mountings, connections, supports, and couplings. Further, "connected" and "coupled" are not restricted to physical or mechanical connections or couplings.

[00210] The following discussion is presented to enable a person skilled in the art to make and use embodiments of the invention. Various modifications to the illustrated embodiments will be readily apparent to those skilled in the art, and the generic principles herein can be applied to other embodiments and applications without departing from embodiments of the invention. Thus, embodiments of the invention are not intended to be limited to embodiments shown, but are to be accorded the widest scope consistent with the principles and features disclosed herein. The following detailed description is to be read with reference to the figures, in which like elements in different figures have like reference numerals. The figures, which are not necessarily to scale, depict selected embodiments and are not intended to limit the scope of embodiments of the invention. Skilled artisans will recognize the examples provided herein have many useful alternatives that fall within the scope of embodiments of the invention.

[00211] As used herein, "tracked" refers to the ability of a particular object to interface with a tracking device (e.g., 3D-tracking optical surgical navigation, electromechanical device in at least FIGS. 16, FIG. 17A-FIG. 17B, FIG. 18A-FIG. 18B, FIGS. 19A-19C, FIGS. 19D-19E, FIGS. 20A-20E, FIGS. 21A-21B, FIG. 22, FIG. 23 A, FIG. 23B, FIG. 23C, FIGS. 24-26, FIGS. 27A-27D, FIG. 28A, etc., that tracks the 3D coordinates of the tracked object relative to the tracking system's coordinate system. One example of an object that is "tracked" is when it possesses a rigidly-attached dynamic reference frame that is tracked in 3D space.

[00212] As used herein, a dynamic reference frame (hereinafter "DRF") refers to three or more points that are positioned in a uniquely identifiable configuration such that discrete points (markers) on its surface are recognized and allow for the calculation of both the location and pose of an object as well as defining a relative coordinate system relative to the DRF. Further, as used herein, stray marker refers to a 3D-tracked object, typically either light-reflective or light-emitting, that is associated with a DRF but is able to be identified as a separate (stray) structure from the nearby DRF.

[00213] As used herein, tracked mobile stray marker (TMSM) refers to a stray marker that is designed to move relative to either other stray markers or to nearby DRFs, and whose position and/or motion relative to those other entities is able to communicate information to a computer acquisition system.

[00214] As used herein, a probe refers and/or defines a device that is tracked in such a way that its location and orientation are known in 3D space, and with that information, the system can extrapolate the location and orientation of other points on the tracked object (e.g., the tip, shaft, unique features, etc.) even if they aren't directly tracked independently.

[00215] As used herein, a fiducial is an object that is used primarily as a reference to another point in space, in that when a fiducial is placed nearby to an object/region of interest, the relative position of the fiducial to the object of interest can be initialized, such that when the location and orientation of the fiducial is referenced in the future, the precise location of the initialized object of interest can then be calculated. Often fiducials have unique surface patterns in the form of either indentations to be tapped or grooves to be traced, such that when interacted with by a 3D-tracked probe, their 3D location and orientation can be calculated by the acquisition system. In addition, a fiducial is most commonly an object with embedded radiopaque markers that enable for its visualization and registration by radiographic imaging. If "fiducial marker" is ever used, that is an equivalent term, unless referring specifically to the embedded "radiopaque markers" within the fiducial structure that can be visualized on x-rays.

[00216] As used here, the term "3D rigid transform" describes the mathematical operation that involves the application of a matrix containing both rotation and translation transformations. The 3D rigid transform is utilized when the system needs to transform the relations of an object from one coordinate axes to another, without deformation of the object. For example, instead of having a 3D-tracked tool's location coordinates and orientation values to be in reference to a 3D-tracking, acquisition system, the 3D-tracked tool can be rigidly transformed to be in reference to the coordinates and orientation of another 3D- tracked tool within the scene.

[00217] As used herein, a pedicle screw is a screw that is inserted into the anatomical structure of a spinal vertebra called a pedicle. Whenever this screw is referenced, it is assumed that the system can also be compatible with any other screw, as well as other surgical implants (e.g., cages, rods, etc.).

[00218] As used herein, a tulip head is an object that attaches to a screw head and is able to be polyaxial or uniaxial in its range of motion. The tulip head typically has internal threads that enable a fastener to engage rigidly with the structure. The tulip head can also have mating features on the external wall/surface that enable a device to rigidly attach to the tulip head. Typically tulip heads are designed to accept the insertion of a rod implant.

[00219] As used herein, a rod can any object with a cross-section similar to a circle, but also other shapes (e.g., keyhole, semi-circle, etc.). A rod can be of any length and curvature. A rod can be coupled to tracked and non-tracked tools. A rod is typically inserted into the cavity of a tulip head and then rigidly fixed in place via a cap screw that is fastened via threads on the interior wall of a tulip head. [00220] As used herein, a register refers to any time a 3D-tracked tool or object signals information to the computer system regarding an object's state, 3D location, 3D orientation, unique identity, relative position to other objects, or other relevant information for the system's algorithms. For example, "a 3D-tracked probe can register the position and identity of a fiducial" means that the 3D-tracked probe is able to communicate to the computer system that a particular fiducial has a specific position in 3D space relative to the 3D- tracking, acquisition system.

[00221] As used herein, a sagittal is an anatomical plane that refers the side view of a patient in which the superior portion of the patient (e.g., the head) is on the right or left side and the inferior portion of the patient (e.g., feet) is on the opposite end, depending on which side of the patient the perspective is from, left or right half.

[00222] As used herein, a coronal is an anatomical plane that refer to the top view of a patient in which the superior portion of the patient (e.g., the head) is on the top or bottom and the inferior portion of the patient (e.g., feet) is on the opposite end, depending on which side of the patient the perspective is from, below or above.

[00223] As used herein, axial is an anatomical plane that refer to the cross-sectional view of a patient in which the posterior portion of the patient is on the top or bottom and the anterior portion of the patient is on the opposite end, depending on which side of the patient the perspective is from, prone or supine.

[00224] As used herein, transverse, "synonymous with axial", and "depressible sliding shaft or plunger" refer to a depressible, sometimes spring-loaded, sliding shaft that actuates via pressing against a surface, a spring-loaded button, or other mechanical means of actuation. A plunger typically has a mechanically linked tracked mobile stray marker that is able to communicate its position along the plunger relative to the position of a nearby DRF or other tracked stray markers. This shaft is typically coaxial with a 3D-tracked tool. The shaft does not necessarily have to be protruding out of an object, as it can also be engaged within an object.

[00225] As used herein, an electromechanical, 3D-tracking system refers to the invention described throughout in which the 3D location and orientation of a probe is tracked in space via mechanical linkage to extensible cords that are independently tracked in 3D space. This system includes rotary encoders for measuring the length of extensible cords as well as sensors for detecting spherical rotation angles of the cord's trajectory traveling through ball- and-socket interfaces.

[00226] As used herein, spinal alignment parameters of an assessment of the segmental and/or full-length spinal alignment is produced with values for each relevant radiographic alignment parameter (e.g., Cobb angle, lumbar lordosis (LL), thoracic kyphosis (TK), C2-C7 sagittal vertical axis (SVA), C7-S1 SVA, C2-S1 SVA, central sacral vertical line (CSVL), Tl pelvic angle (TIPA), pelvic tilt (PT), pelvic incidence (PI), chin-brow to vertical angle (CBVA), Tl slope, sacral slope (SS), Cl-2 lordosis, C2-C7 lordosis, C0-C2 lordosis, C1-C2 lordosis, PI-LL mismatch, C2-pelvic tilt (CPT), C2-T3 angle, spino-pelvic inclination from Tl (TI SPi) and T9 (T9SPi), CO slope, mismatch between T-l slope and cervical lordosis (T1 S-CL), and/or global sagittal angle (GSA). Any time alignment assessments or calculation of alignment parameters are mentioned in this document, it can be assumed that any of the above parameters, and others not mentioned but commonly known, can be calculated in that portion of the description.

[00227] As used herein, a 3D-tracking acquisition system refers broadly to the use of a 3D-tracking system to acquire points in 3D space and register particular commands via 3D- tracked tools. Primary examples of this term are: An optical-tracking system such as that used in surgical navigation (e.g., DI Polaris Spectra stereoscopic camera system, as depicted in FIG. 5A, which tracks tools or objects, as depicted in FIG. 12, FIG. 15A-15C, etc.), and/or an electromechanical tracking system described in at least FIGS. 16, FIG. 17A-FIG. 17B, FIG. 18A-FIG. 18B, FIGS. 19A-19C, FIGS. 19D-19E, FIGS. 20A-20E, FIGS. 21A-21B, FIG. 22, FIG. 23 A, FIG. 23B, FIG. 23C, FIGS. 24-26, FIGS. 27A-27D, FIG. 28A, etc.

[00228] As used herein, 3D-tracked probe is a tool that can be handheld or robot-held, that is tracked in 3D physical space by any 3D-tracking acquisition system, such as optical surgical navigation systems (e.g., NDI Polaris stereoscopic camera in FIG. 5A) or electromechanical, 3D-tracking systems (e.g., novel tracking system described in FIGS. 16, FIG. 17A-FIG. 17B, FIG. 18A-FIG. 18B, FIGS. 19A-19C, FIGS. 19D-19E, FIGS. 20A-20E, FIGS. 21A-21B, FIG. 22, FIG. 23A, FIG. 23B, FIG. 23C, FIGS. 24-26, FIGS. 27A-27D, FIG. 28A). One embodiment, relying on an optical surgical navigation system, includes a probe with a rigidly-attached, 3D-tracked DRF. Some embodiments also involve the inclusion of a mechanically-linked, 3D-tracked mobile stray marker (TMSM) that is mounted on a depressible, spring-loaded, or user-actuated sliding shaft that is able to actuate the motion of the TMSM either linearly or rotationally (e.g., about a hinge pivot on the probe).

[00229] As used herein, an optical, 3D-tracking system refers broadly to any optical system that can provide a 3D mapping of a scene or the location, orientation, and identity of a tracking-compatible object. One example of the optical, 3D-tracking system is a surgical navigation system as depicted in FIG. 5A, which is an DI Polaris Spectra stereoscopic camera system. Note: this example is primarily what we are focusing on across the majority of our inventions, however for broad coverage sakes, we can collect similar information from almost any 3D-tracking, optical-based system.

[00230] As used herein, a skin-mounted fiducial is specifically able to be mounted directly on the skin surface of a patient or within the skin in a percutaneous manner. As used herein, an over-the-drape-mating fiducial is specifically able to mate with another fiducial that is beneath a surgical drape, or any other obstructing material.

[00231] As used herein, a tracked stray marker ("TSM") refers to an optically-3D-tracked stray marker, which is defined as an independent light-reflective or light-emitting marker that is not registered as part of a DRF. This particular stray marker does not exhibit direct movement relative to the dynamic reference marker, however, it can be used as a toggle to signal various, unique commands to the acquisition unit.

[00232] As used herein, a tracked mobile stray marker (TMSM) refers to an optically-3D- tracked stray marker, which is defined as an independent light-reflective or light-emitting marker that is not registered as part of a DRF. This particular stray marker is able to experience movement relative to the dynamic reference marker via a variety of actuating methods (e.g., linear displacement, rotation about a hinge, a combination of the two, etc.) to signal various, unique commands to the acquisition unit and computer system.

[00233] As used herein, a display monitor refers to any display embodiment that is able to visually depict the output of the system, its feedback systems and instructions, its calculations, and other relevant information or settings that are available.

[00234] As used herein, a "tracked end cap" refers to a 3D-tracked object that contains a rigidly-attached, 3D-tracked DRF and is able to rigidly attached to a rod or rod-like object. The end cap provides a reference frame of the rod in a manner of establishing a coordinate system for the implant while its contour is traced, structurally manipulated/contoured, or any other assessment. This term is also being used in the form "tracked DRF-equipped end cap", a synonym.

[00235] As used herein, a tracked slider refers to a 3D-tracked object that contains a rigidly-attached, 3D-tracked DRF and is able to register the contour of a rod via mechanically engaging with its surface and tracing along the length of the rod. The slider tool is typically transformed to output 3D coordinates and orientation values relative to a 3D-tracked end cap tool. This term is also being used in the form "slider tool equipped with a DRF"; typically used for assessing a rod contour.

[00236] As used herein, an cquisition system is synonymous with the 3D-tracking acquisition system term described above. Typically, this system is a 3D-tracking camera (e.g., DI Polaris stereoscopic camera) and the computer system with which it is communicating.

[00237] As used herein, an end effector refers to any component of an object that interfaces with another surface or object in a manner that enables the registration or communication of information including, but not limited to: 3D location, 3D orientation, unique identity, physical or identity -based relations to other objects in a scene, forces applied to an object or forces experienced by an end effector, etc.

[00238] As used herein, a tracing refers to the method of acquiring discrete or continuous points along a surface via a 3D-traced probe or object.

[00239] As used herein, an endplate refers the surface of a spinal vertebra that interfaces with the intervertebral disc and the nearby vertebra coupled on the other side of the intervertebral disc. The endplate is a common anatomical landmark used for measuring the spinal alignment parameters of a patient (e.g., Cobb angles), mainly due to the way that an endplate surface appears on 2D x-rays, since it appears like a line segment that can be easily identified and calculated as a component of a landmark of interest (e.g., L4 vertebra of the lumbar spine).

[00240] As used herein, a pose refers to the orientation of an object with respect to another object or 3D-tracking acquisition system. The pose of an object can be redundant from multiple perspectives or it can be unique and identifiable, outputting 3D orientation values. [00241] As used herein, the term unique in this documents typically refers to the distinct identity of an object, or its identifiable orientation. The phrase "unique pattern" used in the document refers typically to either the 1) embedded pattern surface on the ball component in the electromechanical, 3D-tracking system (depicted in FIGS. 16, FIG. 17A-FIG. 17B, FIG. 18A-FIG. 18B, FIGS. 19A-19C, FIGS. 19D-19E, FIGS. 20A-20E, FIGS. 21A-21B, FIG. 22, FIG. 23 A, FIG. 23B, FIG. 23C, FIGS. 24-26, FIGS. 27A-27D, FIG. 28A; 2) an asymmetric or identifiable arrangement of objects that can be registered in a manner that the group of objects can be identified uniquely compared to another group of tracked/registered objects.

[00242] As used herein, level refers to a specific spinal vertebra within the span of the vertebrae of the spine. A level can refer to any of the vertebrae (e.g., L5, T10, CI, S3, etc.). The abbreviations of that example refer to lumbar, thoracic, cervical, and sacral vertebrae.

[00243] As used herein, "fully engaged" is used to describe two or more objects that are completely linked, mated, or aligned in a manner that enables them to be registered reliably relative to one another in 3D space. Fully engaged typically will trigger a communication to the computer system of a particular command or acquisition to store.

[00244] As used herein, a trigger is used to describe either a button or a moment of communication that signals to the computer or acquisition system to store data, interpret a command, or register an object's identity.

[00245] Some embodiments of the invention include a system that allows a surgeon to make intraoperative assessments and adjustments of the patient's alignment and biomechanical abilities. Embodiments of the disclosed system registers the patient's local and/or full-length spinal curvature and flexibility, and registers the instruments/implants used to manipulate the conformation of the spine, using various calculations and algorithms to produces a quantitative assessment of the patient's spinal biomechanical qualities and the customized implants used to enhance these qualities. These quantitative assessments include, but are not limited to, calculated values for various radiographic parameters related to both global and segmental alignment of the spine (e.g., lumbar lordosis, central sacral vertical line, Tl pelvic angle, thoracic kyphosis, Cobb angle, etc.).

[00246] Some key features of one or more of the embodiments described herein can include anatomical landmark(s) of interest (i.e., C7, SI, etc.) that are initialized relative to the 3D-tracking acquisition system. In some embodiments, a continuous or discrete 3D-tracked acquisition is made along the surface (e.g., posterior, anterior, or lateral) of the spine, both within and beyond the surgical site (e.g., skin surface). In some embodiments, series of algorithms filter continuous or discrete 3D-tracked probe data to identify a relationship between the acquired points and anatomical regions of interest (e.g., centroids of the vertebral bodies). In some embodiments, an assessment of the segmental and/or full-length spinal alignment is produced with values for each relevant radiographic parameter (e.g., Cobb angle, lumbar lordosis, thoracic kyphosis, C2-C7 lordosis, C7-S1 sagittal vertical axis, central sacral vertical line, Tl pelvic angle, pelvic incidence, pelvic-incidence-lumbar-lordosis mismatch, etc.). In some embodiments, an assessment of the contour, position, or alignment of instrumented hardware, such as screws, rods, or cages, can be produced.

[00247] Some embodiments include a visual display and quantitative feedback system for assessing and adjusting implants that are or will be implanted into/onto the anatomy, including 3D, dynamic renderings of registered anatomical landmark(s) of interest. In some embodiments, an assessment of segmental, regional, or full-length flexibility and range of motion can be produced between a selected range of vertebral segments. In some embodiments, the visual display outputs the information about the spine's curvature and alignment, quantitative radiographic alignment parameter values, instrumented hardware analysis, flexibility or range of motion of the spine, and also various ways to acquire or analyze radiographic images. In some embodiments, the visual display enables interactive feedback and interfaces for the user to signal particular commands to the system for computing, beginning operations for, or outputting the quantitative or visual analysis of a system or anatomical region(s) of interest.

[00248] Any of the proposed embodiments can be independent inventions and do not have to be preluded or postluded by other inventions or categorical system workflows (e.g., patient initialization, alignment contour acquisition, etc.), as illustrated in FIG. 1. For example, some embodiments of the invention described herein include devices, assemblies, systems, and methods to assess the intraoperative alignment of the spine, extract information as to the contour or alignment of instrumented hardware, and evaluate some of the biomechanical qualities of the patient's spine. Some embodiments of the overall system are illustrated in FIG. 1, where a central software system can receive inputs from discrete and/or continuous location data (e.g., inside and/or outside of the surgical site), where the data is gathered by non-radiographic or radiographic embodiments, algorithmic calculations, or manual user- based interactions, to generate visual and quantitative outputs relating to the intersegmental or full-length alignment, curvature, position, range-of-motion, and biomechanical flexibility of the patient's spine. Any of the embodiments described herein can be independent embodiments and do not have to be within the categorical series of systematic steps (e.g., 3D trace, local anatomy, landmarks, etc.) shown in FIG. 1, illustrating a system for assessing spinal alignment, local anatomy biomechanics, rod contours, and active contouring of a rod, as well as initialization of fiducials and interactive displays of various outputs in accordance with some embodiments of the invention. The overall system 100 of FIG. 1 can include devices, assemblies, systems, and/or methods described in the following description in reference to one or more of the figures, including processes that utilize one or more software modules 121 of one or more computer-implemented methods. In some embodiments, the system 100 can comprise devices, assemblies, systems, and methods for patient initialization 107, alignment contour aqusition 115, referenced/detected anatomical regions 117, third- party software integration 119, assessment of localized anatomy 105, rod contour assessement 109, assisted rod contouring 111, and output display 113.

[00249] Some embodiments of the invention relate to systems and methods for precise placement of skin surface markers or percutaneous access devices that provide the relative position of underlying bony anatomy to a visible surface grid. In some embodiments, the systems and methods described herein can reduce the number of x-rays needed to be taken to verify location of overlying or percutaneous devices relative to bony anatomy. For example, FIG. 2A shows a representation of a body-surface-mountable fiducial patch in accordance with some embodiments of the invention, where radiopaque grid lines can be visualized on the x-ray image. Other relevant figures and discussions herein can include those related to skin-fiducial marker examples to apply onto patch such as FIGS. 6B, 9A-9B, and FIGS. 11 A- 11B. As shown in FIG. 2A, some embodiments include a body-surface-mountable fiducial patch 200 that can comprise an array of radiopaque markers with visible and/or radiopaque grid lines 201. In some embodiments, the shapes or markers defined by the gridlines 201 can be colored and/or marked with an identifier, including, but not limited to, a red-colored grid surface with radiopaque "R" (label 209), and/or a blue-colored grid surface with radiopaque "B" (label 211), and/or a yellow-colored grid surface with radiopaque "Y" label 205, and/or a green-colored grid surface with radiopaque "G" (label 207). In some embodiments, the grid lines can be further apart or closer than shown. In some embodiments, the markers can be larger, smaller, fewer, or greater in number than shown in this non-limiting embodiment. In some embodiments, the body-surface-mounted fiducial patch 200 can enable precise placement of surface-mounted objects or percutaneous devices that require recognition of underlying bony structures.

[00250] It should be noted that the visible surface of the patch 200 need not be a distribution of colors, but can also consist of any recognizable pattern that is also displayed in a meaningful way on x-ray imaging. In some embodiments, the patch can be adhered to surface anatomy via an adhesive (not shown) or other methods. In some embodiments, the size and density of unique identifiable grid sections on the patch can be varied based on the particular application.

[00251] FIG. 2B displays the radiopaque elements of the fiducial patch of FIG. 2A as would be visible on an x-ray image of a patient with the patch applied in accordance with some embodiments of the invention. For example, x-ray patient image 225 is shown with radiopaque fiducial grid patch 200a displayed on the image 225, and displays the radiopaque elements of the fiducial patch 200 as would be visible on an x-ray image 225 of a patient with the patch 200 applied. In some embodiments, after taking an x-ray of the patch 200 applied to the patient, users can place surface fiducials or direct percutaneous access devices towards the bony anatomy of interest based on the corresponding grid location on the patch that represents the underlying anatomy of interest. In this non-limiting example embodiments, the red-colored grid surface with radiopaque "R" (label 209) is shown as 209a, the blue-colored grid surface with radiopaque "B" (label 211) is shown as 211a. Further, the yellow-colored grid surface with radiopaque "Y" label 205 is shown as 205a, and the green-colored grid surface with radiopaque "G" (label 207) is shown as 207a in the x-ray image 225. In some embodiments, when used in this way, the patch 200 of FIG. 2A and imaging of FIG. 2B can aid with the precise selection of correct surgical site access points, ensuring that incisions overlay the desired bony anatomy on which will be operated. Additionally, in some embodiments, this patch 200 can be used to precisely place secondary skin-mounted fiducials such that they superimpose underlying bony anatomy of interest. Some example embodiments of fiducials that can be applied onto the imaged patch include FIGS. 6B,9A- B, 11A-B. In some embodiments, the patch 200 can be applied to a patient's skin using adhesive or other conventional methods. In some embodiments, the type of identifiable surface marker can be different than the non-limiting embodiment shown. [00252] FIG. 3A-C illustrate a bone-mounted fiducial device that is designed with a crossbar to interface with one or more mating devices that can either help to register the fiducial' s location and pose in 3D space (e.g., tracing, tapping discrete locations, being tracked directly), help initialize the fiducial when taking x-ray images, or directly manipulate the fiducial and attached bony anatomy after they are coupled. In some embodiments, after imaging a fiducial mounted to bony anatomy, the fiducial' s relative location in space to another anatomical segment of the bony anatomy can be registered, such that when the fiducial is positioned in the future, the corresponding bony anatomy elements are also localizable. The vertebra 300 is shown with a bone-mounted fiducial 320 fastened to the bone. In some embodiments, the fiducial 320 can be fastened to the medial border of the right spinal lamina, but because of its small size and profile, it is able to be mounted anywhere on the bony anatomy. In some embodiments, the bone-mounted fiducial 320 can contain a threaded or smooth bone-piercing component (not shown) so that it is able to be rigidly fastened to the bone (e.g., the vertebra 300). In some embodiments, the bone-piercing component can be significantly miniaturized such that it does not pierce through the opposite side of the bony anatomy, or otherwise harm any sensitive anatomical structures.

[00253] In some embodiments, the fiducial 320 can contain one or more rigid crossbars 325 that travel across the fiducial 320. In some embodiments, the crossbars 325 can be positioned such that there is an open space underlying it to allow for a mating interface of a coupled fiducial 350 to directly engage with it. In this instance, the fiducial 320 can be rigidly fixed to the fiducial 350 so as to interpret the fiducial's pose and location in space when accessed by tracked device (see FIG. 3B below).

[00254] In addition, some embodiments involve a patterned perimeter surface (FIG. 3B), including but not limited to groove 327 and other identifiable patterns, that can be traced or discrete registered by a 3D-tracked probe. FIG. 3B shows an assembly view of a vertebra 300 with a bone-mounted fiducial 320 and fiducial 350 for coupling to the bone-mounted fiducial 320, illustrating the mating capability of the bone-mounted fiducial 320 such that it can mechanically couple with an accessory fiducial 350 via a variety of mechanisms. For example, one non-limiting mechanism includes a quarter-turn interlocking mechanism 355 such that the accessory fiducial 350 is tightly pulled into the crossbars 325 of the base bone- fiducial 320 when the accessory fiducial 350 is rotated 90 degrees into the interlocking design of the mechanism 355. In some embodiments, the structure of the accessory fiducial 350 is such that it can contain surface features, including, but not limited to, asymmetric pattern of three or more identifiable indentations 370. In some embodiments, the identifiable indentations 370 can enable a unique position and pose in 3D space to be recognized by interfacing with 3D trackable devices, as further described in more detail below in reference to FIGS. 3C, and FIGS. 44B-44D. In some other embodiments, other conventional mating mechanisms with the fiducial include, but are not limited to, a quarter-turn, half-turn, a rigidly clamping device, and a spring-loaded snap-in device.

[00255] Some embodiments of the uniquely identifiable surface structure of the accessory fiducial 350 that can be used for registration of the fiducial's orientation in 3D space when interacting with a 3D-tracked probe, can include, but not be limited to, 1). three or more uniquely spaced indentations, 2.) a uniquely identifiable groove in which a 3D-tracked probe can trace in order to identify the location and pose of the fiducial, 3.) an insert that contains a set of three or more tracked markers whose location in 3D space are able to be tracked by a 3D-tracking camera, 4.) a tracked DRF, 5.) a larger embodiment with radiopaque features to enable its unique pose and location to be identifiable with x-ray imaging, and 6.) interfacing with a tracked probe that can rigidly couple to the fiducial in such a way that it can interpret the fiducials location and pose in space as described below in reference to FIGS. 44A-44D. For example, FIG. 3C shows a vertebra 300 with a bone-mounted fiducial 320 coupled with a top fiducial (fiducial 350) in accordance with some embodiments of the invention. The bone- mounted fiducial 320 includes an accessory fiducial 350 rigidly attached and demonstrates one embodiment of a uniquely identifiable surface pattern 370 (surface indentations) that can be registered with a 3D-tracked probe. In some embodiments, the three or more discrete indentations that make up the surface pattern 370 can couple with at least a portion of a 3D- tracked probe that can couple into the surface pattern 370. Consequently, one or more computer systems can then be used to compute the fiducial's location and unique pose in 3D space.

[00256] FIG. 4A illustrates an assembly or operation process 450 for a skin-surface- mounted fiducial 400 being applied to a patient 425 in accordance with some embodiments of the invention. The skin-surface-mounted fiducial 400 is applied to the patient's posterior skin as they are positioned prone on an operative table 435. In some embodiments, this fiducial 400 can be adhered to the patient's skin via attached adhesive compound, staples, suture, or overlying adhesive draping. [00257] FIG. 4B illustrates a sample lateral radiograph of skin fiducials markers 444 applied to an anatomical model in accordance with some embodiments of the invention. In some embodiments, the radiopaque elements of the fiducial markers 444 allow it to be clearly visualized and identified on radiograph images. Additionally, the known sizing of the radiopaque markers 444 allow for reference scaling within the x-ray image 441. Furthermore, the nearby anatomical structures that are also within the field of view of the x-ray image 441 can then be initialized such that a displacement vector can be drawn within the plane of the x- ray image 441 as described below in FIG. 4C and FIG. 4F. In some embodiments, the arrangement of the radiopaque fiducial markers 444 can be designed in an asymmetric pattern to enable an x-ray image of the fiducial from any perspective to visualize a unique pose of the pattern that can enable the system to automatically estimate the 3D orientation of the fiducial. For example, FIG. 4C illustrates the sample lateral radiograph 440 of FIG. 4B with annotated vectors in accordance with some embodiments of the invention. FIG. 4C displays one aspect of the initialization process for fiducials located nearby anatomical elements whose position is desired to be known relative to that of the fiducial. In some embodiments, manual or automated software annotation can enable the identification of the radiopaque markers within the fiducial (shown as vectors 465 and 460 extending between markers 444).

[00258] Given their relative sizing to one another as well as their orientation to one another, the pose of the fiducial 442 relative to the plane of the x-ray image 440 is able to be discerned. In some embodiments, the user interfaces with the system to select one or more additional points to which the displacement vector 470 from the fiducial 442 will be calculated. In this example, the central region of a particular vertebral body was selected, indicated by a large circle (e.g., shown as 427), and the software calculated the pixel distance between each radiopaque marker 444 and the annotated region(s) on the display monitor. Based on the known size of the radiopaque markers that are in or on the fiducial, the image is able to be scaled such that length measured in pixels can be converted to length measured in distance units (e.g. mm, cm, etc.). In other embodiments, the software can also calculate displacement vectors from the fiducial to any anatomical landmarks of interest, even across several vertebrae.

[00259] FIG. 4D illustrates a C-arm 480 based mount a type of an x-ray imaging system that can be utilized for image acquisition and subsequent initialization of fiducial markers in accordance with some embodiments of the invention. In some embodiments, following the first x-ray image that was taken, the relative angle between the patient-fiducial complex and the x-ray emitter is rotated by either a known or unknown amount to take a subsequent image. The second image allows for added information outside of the plane of the first x-ray image to construct the 3D displacement vector between the fiducial and the bony anatomy of interest. This x-ray system needs not be a C-arm-based device, but can also consist of other image acquisition systems including but not limited to O-arm, flat-plate x-rays, CT scan, MRI, and wall or bed-mounted acquisition systems.

[00260] FIG. 4E illustrates a sample x-ray image 485 of a spine-fiducial pair from a different imaging angle from that of FIGS. 4 A and 4B in accordance with some embodiments of the invention, and illustrates the fiducial radiopaque markers (shown as 487a, 487b) as one embodiment of an arrangement of radiopaque markers in or on the fiducial distributed to enable image scaling and localization to nearby anatomical areas of interest.

[00261] FIG. 4F illustrates the sample x-ray image 485 of FIG. 4E including annotated vectors in accordance with some embodiments of the invention. FIG. 4F displays the x-ray image initialization process for the fiducial-body pair that was imaged and described above in FIG. 4E. The annotated vectors 488 are used to reference the relative position of each of the radiopaque markers 487a, 487b within the fiducial 442 (FIGS. 4B-4C) as well as calculate the displacement vector to the user-indicated nearby anatomical region of interest (shown as 489), for which the fiducial 442 can serve as a reference point upon future localization of that fiducial. In some embodiments, the arrangement of the radiopaque fiducial markers can be designed in an asymmetric pattern, as seen by the example unique triangular pattern of vectors between the radiopaque markers 487a, 487b, to enable an x-ray image of the fiducial from any perspective to visualize a unique pose of the pattern that can enable the system to automatically estimate the 3D orientation of the fiducial. In this respect, the estimation of the fiducial' s orientation enables the system to calculate the 3D vector with respect to the fiducial axes.

[00262] FIG. 4G displays the axes of a 3D-acquisition system with which the unique location and pose of the fiducial was registered as of FIG. 4H in accordance with some embodiments of the invention. In this non-limiting embodiment, the 3D-tracking acquisition system coordinate axes 492 are shown with transformed 3D-displacement vector 494. For example, FIG. 4G displays the axes 492 of the 3D-tracking acquisition system with which the unique location and pose of the fiducial were registered, as described in FIG. 4H. In some embodiments, based on the known displacement vector from the fiducial origin to the anatomical region of interest, as described in FIGS. 4C, F-G the displacement vector undergoes a rigid body transformation to define the fiducial axes with respect to the 3D- tracking acquisition system's axes. This resulting vector (shown as 494) can enable the annotated anatomical region's location to be known within the 3D-tracking acquisition system's axes, enabling interpretation of this bony anatomy's location in space relative to other locations accessed by the same acquisition system.

[00263] FIG. 4H illustrates a system and method of localizing the fiducial in 3D tracking camera coordinates in accordance with some embodiments of the invention. Shown in the non-limiting embodiment are an identifiable tracing pattern 495, a tracked probe with triggering capability 496, and fiducial coordinate axes 497. FIG. 4H displays one method of localizing the fiducial in 3D tracking camera coordinates as a non-limiting embodiment. As shown, the fiducial is equipped with a unique groove pattern (pattern 495) into which a tracked probe (496) can trace the fiducial 's signature pattern. As described above in relation to FIG. 4A, the recognizable features of the fiducial are not limited to a uniquely traceable pattern, but also discrete points to tap, mount locations for tracked markers, and rigidly coupling with a tracked probe in a way such that the probe's pose can be used to interpret the fiducial' s position and pose. By tracing the unique surface pattern on the fiducial with a tracked probe, the fiducial' s axes (i) and origin are able to then be interpreted with respect to the 3D-tracking acquisition system's coordinate system. In some embodiments, the acquisition system will be able to interpret the location of the initialized nearby anatomical region as described below in FIG. 41.

[00264] FIG. 41 illustrates 3D axes relative to the fiducial origin point onto which displacement vectors drawn over each of the 2D x-rays are able to be added based on input or calculated angle between each x-ray image plane in accordance with some embodiments of the invention. This non-limiting embodiment includes X-ray image coordinate system 498a, and 3D-displacement vector 498b, and displays the 3D axes relative to the fiducial origin point onto which displacement vectors drawn over each of the 2D x-rays are able to be added based on input or calculated angle between each of the x-ray image planes. This resultant vector represents the 3D vector (498b) drawn from the fiducial origin to user-input bony anatomy region(s) of interest (499). In some embodiments, this enables localization of the bony anatomy regions of interest by interpreting the location and pose of the fiducial within other 3D tracking acquisition system axes, as described in FIG. 4H.

[00265] FIGS. 5A-5C display components, systems and methods of initializing a fiducial to serve as a reference point for underlying anatomical regions of interest, as described above in reference to FIGS. 4A-4I. However, instead of utilizing x-ray images, the methods can utlize an ultrasound-based probe equipped with a tracked DRF so that its location and pose are able to be computed when visualized by a tracking camera. For example, FIG. 5A illustrates an optical tracking system 550 in accordance with some embodiments of the invention, and FIG. 5B illustrates an ultrasound probe 575 equipped with a tracked DRF 580 in accordance with some embodiments of the invention. Further, FIG. 5C illustrates an assembly or process view 590 of a patient's skin surface 594 overlying a cross-sectional view of a vertebra 596 as a representation of a particular region of bony anatomy that could be registered to a skin-mounted fiducial 592 in accordance with some embodiments of the invention. In some embodiments of the invention, the optical 3D-tracking system 550 of FIG. 5A can be utilized for the 3D-tracking acquisition system referenced throughout this document. This system utilizes stereoscopic cameras 551 to detect the location of tracked markers that reflect camera-emitted infrared light. This is one example of a tracking system 550 that can be used for acquisition of 3D coordinates throughout this document, but this can also be achieved by other methods including but not limited to light-emitting markers, electronic communication, etc. Further, in some embodiments, the ultrasound probe 575 of FIG. 5B is equipped with a tracked DRF 580 that enables the probe's location and pose to be tracked in 3D space using markers 585. In some embodiments, tracking the precise location of the probe allows for recording the relative angles between each imaging plane that can be used for creating the 3D-displacement vector to the anatomical point of interest.

[00266] FIGS. 6A-D includes depictions of devices, systems and processes of applying a skin mounted fiducial along with its top-mating component that enables mating across surgical drapes so that the fiducial can be both visualized and referenced during procedures during which a drape is obstructing the surface overlying bony anatomy for which the location is desired to be known.

[00267] FIG. 6A portrays a sample scenario for which applying a skin-mounted fiducial (a) and its associated over-the-drape-mating fiducial (b) could be used. With the patient positioned prone on the operative table, skin-mounted fiducials can be applied over regions that will not be surgically exposed but under which contains bony anatomy whose location is desired to be known relative to other anatomical regions. After the surgical drape (f) is applied over the skin-mounted fiducial, the over-the-drape-mating fiducial can then be used to interpret the position of the underlying skin-mounted fiducial, described in more detail below in FIGS. 6B-D. For example, FIG. 6A illustrates an assembly or process view 600 for applying a skin-mounted fiducial 625 and its associated over-the drape fiducial 635 in accordance with some embodiments of the invention, and FIG. 6B illustrates an assembly view 650 of a skin-mounted fiducial 400 and its associated over-the-drape mating fiducial 415 in accordance with some embodiments of the invention. In some embodiments, the fiducial 625 comprise the fiducial 400 and the fiducial 635 can comprise the fiducial 415.

[00268] In reference to FIG. 6B, showing detailed components of one embodiment of a skin-mounted fiducial 400 and its associated over-the-drape-mating fiducial 415, in some embodiments, the skin-mounted fiducial 400 can include a method of adhering to the skin surface (not known) including but not limited to adhesive material, looped regions to be sutured or stapled to the skin, and attached bands to be tightly wrapped around body surfaces. In some embodiments, contained within or on either of the fiducials can be one or more radiopaque markers 408 that are readily visualized on x-ray images of the fiducials. Furthermore, in some embodiments, these radiopaque markers 408 can be positioned relative to one another and the fiducial body itself in such a way that they can be used to identify the pose of the fiducial on 2D x-ray images, as described above in FIG. 4. In some embodiments, the fiducials can contain magnets (e.g., shown as magnet 404 in the fiducial 400, and 419 in the fiducial 415) embedded in or on their surfaces in such a way that it helps to securely fasten the two fiducials when separated by a surgical drape (shown as 605 in FIG. 6A). In some embodiments, the magnets can have varying geometry. For example, some embodiments include spherical magnets can be used to serve both functions of a radiopaque marker as well as feature to help join mating fiducials across drapes. In some embodiments, the skin-mounted fiducial can also be equipped with protrusions to serve as mechanical alignment mates (shown as 402a and 402b). In some embodiments, the mates can protrude from one fiducial (e.g., 400 as shown and/or alternatively from both fiducial 400 and fiducial 415), and have mating cutouts within the opposite fiducial and help to ensure both fiducials are properly aligned relative to one another. The protrusions are conical in shape in the non- limiting embodiment of FIG. 6B, but can also be created with other tapered or non-tapered geometry in other embodiments. [00269] FIG. 6C illustrates one embodiment of a skin-mounted fiducial applied to an anatomical phantom in a region that is outside the surgical site but located over regions of underlying anatomy for which their location within 3D-tracking coordinates is desired to be known in accordance with some embodiments of the invention. Further, FIG. 6D illustrates an embodiment of a skin-mounted fiducial mating with its over-the-drape fiducial across a surgical drape/towel in accordance with some embodiments of the invention. In reference to FIG. 6C, in some embodiments, the skin-mounted fiducial 400 can be applied to an anatomical phantom 677 in a region that is outside the surgical site 681 but located over regions of underlying anatomy for which their location within 3D-tracking coordinates is desired to be known in accordance with some embodiments of the invention. For example, FIG. 6D illustrates an embodiment of a skin-mounted fiducial mating 400 with its over-the- drape fiducial 415 across a surgical drape/towel 679 in accordance with some embodiments of the invention. In some embodiments, because the over-the-drape-mating fiducial 415 is mechanically mated in a predictable fashion with the skin-surface fiducial 400, the location and pose of the over-the-drape-mating fiducial 415 can be used to compute the location and pose of the underlying skin-mounted fiducial 400. Furthermore, if the skin-mounted fiducial 400 had been previously initialized to nearby anatomical structures, the location and pose of the over-the-drape-mating fiducial 415 can then be used as a surrogate reference point for the underlying anatomy of interest.

[00270] FIG. 7 illustrates an assembly view 700 of a fiducial 740 in accordance with some embodiments of the invention, and portrays an embodiment that enables unique identification of one fiducial to another. In some embodiments, this can be applied to scenarios when more than one fiducial is used, and the identity of the fiducial is required. In this embodiment, an interfacing probe 703 is shown designed with electrodes 735 to mate with the fiducial 740. In some embodiments, the electrodes can be coupled to or inserted into the fiducial 740, and based on the circuit characteristics built into the fiducial material (e.g., electrical resistance, capacitance, etc.), the fiducial' s unique identity can be made known by the mating probe. As shown, in some embodiments, the probe 703 can include a probe shaft 705 coupled to a tracked DRF 715 with trackable markers 725. Further, in some embodiments, the fiducial 740 can include two electrodes built-in, and can possess identifying circuit components (e.g., resistors, capacitors, etc.) embedded between electrodes. In this way, a probe 703 equipped with a tracked DRF 715 can be designed such that it has mating electrodes 735 that can interface with the fiducial 740, measuring the unique electrical characteristics of the fiducial 740, while simultaneously identifying its location and pose in 3D space. Thus, the embodiments described above can enable identification of unique fiducials, which can be useful when multiple fiducials are being deployed.

[00271] FIG. 8 illustrates an assembly view 800 of a fiducial in accordance with some embodiments of the invention, and enables unique identification of one fiducial compared to another. This can be applied to scenarios when there are more than one fiducial used, and the unique identity of the fiducial is desired to be known. In this design, a probe equipped with an RFID-reading circuit interfaces with a spring-embedded RFID-tag circuit within the fiducial. In this way, the probe 803 is able to simultaneously trigger that fiducial has been accessed by a depressed the spring-loaded momentary push button, and can also acquire information as to which fiducial has been referenced. As shown, the probe 803 can comprise a tracked DRF 715 with trackable markers 725 configured to be coupled to an embedded RFID reader 850 including a spring-loaded button 855. In some embodiments, the tip 707 of the shaft 705 can couple with the surface 858 of the button 855, compressing the spring 864, and eventually enabling contact of the terminals 862 with the RFID tag 870. In some embodiments, if accessed by a probe 803 equipped with an RFID reader 850 in addition to a tracked DRF 715, a probe 803 that depresses the spring 864 can simultaneously perform three tasks 1.) trigger that it has approximated the fiducial, 2.) interpret the location of the fiducial surface, and 3.) interpret the unique identity of the fiducial based on its embedded RFID tag.

[00272] FIG. 9A displays another embodiment of a skin-surface fiducial described previously in relation to FIGS. 6A-6B. In this instance, the assembled skin-surface fiducial 900 includes a mating top surface fiducial 905 coupled to a skin-mountable fiducial. For example, FIG. 9A displays an assembled skin-surface fiducial 930 with its over-the-drape- mating fiducial 905. The bottom surface fiducial 930 is equipped with a mechanism of adhering to the skin surface. The fiducial pair 905, 930 joins together at an interface 925 designed to accommodate surgical drapes or towels, while maintaining a predictable mating configuration. One embodiment of the top fiducial contains a groove (tracing pattern 910) in a unique geometry (e.g., "z" geometry shown here) such that a tracked probe (e.g., any of the tracked probes described herein) can trace the pattern and from that information interpret the unique identity of the fiducial, as well as interpret its location and pose in space, enabling the identification of a fiducial -based axes as described previously in relation to FIGS. 4A-4I. [00273] The external design of the fiducial 900 is configured to communicate information to the user as embedded instructions. One embodiment of the fiducial possesses an external arrow appearance (i.e., the fiducial 900 as assembled is shaped as an arrow) that can be used to indicate how the user should place the fiducial (e.g., position the fiducial on the skin such that the arrow points away from the surgical site). In some embodiments, a sloped decline 920 of known geometry can be implemented to facilitate a user tracing a probe from the surface 915 of the fiducial 905 down to the body surface 920 of the fiducial 930 onto which the fiducial 905 is placed. In some embodiments, the framed structure of the fiducial 900 can allow for more predictable tracing over the transition from the fiducial groove 910 to the underlying surface. Additionally, in some embodiments, it allows for the ability to calculate the location of the underlying body surface given the known geometry of the fiducial slope design.

[00274] FIG. 9B illustrates an assembly view of the fiducial 900 of FIG. 9A in accordance with some embodiments of the invention. In this non-limiting embodiment, the skin-mounted fiducial 930 contains male alignment-aiding protrusions 940 similar to those described previously in relation to FIG. 6B. Further, the protrusions have a flattened top 922 to accommodate added volume of an overlying material, as in the case of a surgical drape. In this way, the structure allows for close approximation of the two fiducial mates in the presence of a sandwiched drape by avoiding tenting of the drape in between the two. In some embodiments, the fiducial 905, 930 are equipped with cutouts 924 to accommodate both radiopaque markers and magnets which can also be one in the same as described previously in FIG. 6B. One embodiment of the cutouts 924 involves an asymmetric geometric pattern that rigidly embeds the radiopaque markers in a relative configuration that enables for unique pose estimations at any radiographic viewing angle. Instead of magnets used to help approximate the two fiducials, other embodiments can include protrusions with a quarter-turn or twisting mechanism that allows for tight mechanical linking across surgical drapes. In some embodiments, the over-the-drape-mating fiducial 905 is equipped with female alignment-aiding cutouts 908 configured to mate with the location of the protrusions 940, 922 on the skin-mounted fiducial 930. It should be noted that the location, size, and geometry of these protrusions and mating cutouts can vary and that this is just one embodiment. Furthermore, it is not necessary for the protrusions to only be located on the skin-mounted fiducial, and the cutouts on the over-the-drape-mating fiducial can include varying combinations of shapes and size. [00275] In place of magnets, some embodiments can include a "clamp-over-drape" feature (i.e., tabs on the top fiducial to clamp down over the lower fiducial sides, while grabbing the drape in between). Other embodiments of this invention include 2 clamping arms equipped on the over-the-drape fiducial designed to snap onto corresponding regions of the lower fiducial for ensuring proper alignment when separated by a surgical drape.

[00276] In some embodiments, the fiducial can be equipped with other components mentioned throughout the document, (e.g., depth stop-based fiducial and probe combination (FIGS. 10A-10G). Other embodiments of the fiducial that enable it to be uniquely identifiable include detents of discrete depths designed to mate with a probe equipped with depth-sensing technology, as described below in reference to FIGS. 10A-10G, such that the fiducial and unique location of the detent relative to the fiducial can be determined based on the distribution of measured detent depths.

[00277] In some embodiments, the bottom fiducial can have a flexible component to it, to enable it to successfully adhere to the uneven surface contour of patients' skin. Other embodiments of the device include constructing the bottom surface with a flexible material to better enable mating with uneven body surface contours.

[00278] Some embodiments include a tracked probe coupled with an actuating tracked marker that indicates the depth of depression of a spring-loaded sliding shaft as well as an embodiment of mating fiducials that are designed to interface with and deflect the shaft by discrete amounts. The purpose of this design is multifactorial. For example, FIG. 10A illustrates a 3D-trackable probe 1000 equipped with a rigidly attached trackable DRF 1020 in accordance with some embodiments of the invention. In some embodiments, the actuated marker 1030 on the tracked probe 1000 allows for analog communication between the probe 1000 and an acquisition system, as will be described below in reference to at least FIGS. 15A-15C and 63. In some embodiments, the actuated marker 1030 conveys information about the depth of deflection of the shaft at the tip of the probe (shown as 1049). Further, when coupled with mating fiducials that are designed to deflect the shaft tip by set heights when fully-engaged, the probe 1000 can convey the following three things: 1.) when it is fully engaged with a mating fiducial, 2.) the location and pose of the mating fiducial, and 3.) the unique identity of the mating fiducial based on the designed depression depth that the fiducial will cause for the sliding shaft. As shown, the tracked DRF 1020 includes fixed markers 1025a, 1025b, 1025c, 1025d. Some or all of the markers 1025a, 1025b, 1025c, 1025d shown in the frame 1020 can be used in any of the DRFs described herein. In some embodiments, any of the DRFs described herein can use these markers, or may use fewer markers. In some embodiments, any of the DRFs described herein may use more markers similar or identical to any of the markers 1025a, 1025b, 1025c, and/or 1025d. In some embodiments, any of the probes or DRFs described herein can include any of the markers 1025a, 1025b, 1025c, and/or 1025d but with different geometries or shapes (i.e., the markers can be smaller or larger than shown, or can be place at different distances from the probe shaft).

[00279] One embodiment of the invention includes a 3D-tracked probe equipped with a rigidly attached tracked DRF 1020. In addition, a tracked mobile stray marker 1030 is rigidly attached to a spring-loaded shaft 1010 that is coaxial with the probe 1000 and actuates within a through-hole down the length of the probe 1000. In some embodiments, the sliding shaft is able to be actuated via a depressible tip 1049b that translates the shaft along with a mount 1005 for the tracked mobile stray marker 1030. This embodiment of the probe also contains a series of concentrically-oriented, varying diameter, protrusions 1040 near the probe tip 1049b. These varying diameter protrusions 1040 can serve as variable-depth-stop selections (1045, 1047, 1049) when mating with depth-stop fiducials, as described below in reference to FIG. IOC, designed with varying inner diameters for mating with specific depth stops on the probe. For example, FIG. 10B displays a more detailed perspective of the probe 1000 with actuating tip and variable depth stops as described previously in FIG. 10A. The tracked probe shaft 1010 includes coaxial cylindrical extrusions 1040 of various heights that act as a depth stops to actuate the depressible sliding shaft tip 1049b, and its associated TMSM (1030), to different heights, (by 1041, 1045, 1047) for unique trigger signals that are communicated to the computer system.

[00280] FIG. IOC displays one embodiment of depth-stop fiducials designed to mate with the probe previously described above in relation to FIGS. 10A-10B. These depth-stop fiducials (1050, 1052) have variable inner diameters such that they can couple with varying depth stops on the probe. In addition to having variable inner diameters to mate with defined depth stops on the probe (e.g., such as probe 1000), which can lead to identifiable deflections of the tracked mobile stray marker 1030 relative to the DRF 1020. Further, other embodiments of these depth-stop fiducials also contain variable floor depths, such that the sliding probe tip 1049b can be actuating by varying amounts despite mating with depth-stop fiducials with matching inner diameters. In this way, these depth-stop fiducials 1050, 1052 can be distinguished from one another and their mating inner diameters and/or depth stops provide for additional, unique identifiers. These depth-stop fiducials can therefore be coupled as probe-interface components coupled to fiducials previously described in relation to FIGS. 3A-3B, 6A-6D, and FIGS. 9A-9B.

[00281] FIG. 10D displays the probe 1000, previously described in relation to FIGS. 10A- 10B mated with a particular depth-stop fiducial (shown as 1050), previously described in relation to FIG. IOC. With these two components coupled in this way, the tracked mobile stray marker 1030 can be actuated coaxially with the probe shaft 1010 and based on the known geometry of both the probe and its mating depth-stop fiducial, the deflection can be measured relative to the tracked DRF and compared to what deflection amounts are anticipated based on particular mates to the probe's depth-stop heights 1061. In this way, the measured deflection ("M") of the sliding tip and attached tracked mobile stray marker to the sliding shaft is able to serve as a unique identifier of when the probe (e.g., 1000 and/or 1001) is fully engaged with a specific depth-stop fiducial (1060).

[00282] FIG. 10E displays a probe 1002 as previously described in relation to FIG. 10A mated with a depth-stop fiducial 1084 designed to mate with a different depth stop 1082 of the probe 1000 than was shown previously in relation to FIG. 10D. As compared to FIG. 10D, this figure displays the different region of mating on the multi-height selection probe (1082) along with the associated difference in deflection height ("P") of the tracked mobile stray marker (1030), indicating the different depression depth of the sliding probe tip (compare "P" with "M" in FIG. 10D).

[00283] FIG. 10F illustrates an assembly view 1099 of a portion of an embodiments of the probe 1000 in accordance with some embodiments of the invention. In one embodiment, the 3D-tracked probe 1000, as described previously in relation to FIG. 10A, contains an asymmetric, protruding extrusion (1091) that can engage with any of the depth-stop fiducials, as described previously in relation to FIG. IOC, where a corresponding slot (1093) mates with the probe's extrusion, and the probe can only mate in one orientation with the depth-stop fiducial. This asymmetric alignment enables the probe to register the unique orientation of the fiducial 's coordinate axes, and thus detect how the fiducial rotates and translates in 3D space between registrations. FIG. 10G illustrates a perspective view of the depth-stop fiducial partially engaged with the depth-stop-equipped, 3D-tracking probe, both previously depicted in relation to FIG. 10F. [00284] FIGS. 11A-11B displays an embodiment of skin-surface and mating fiducial design as previously described in FIGS. 6A-6B and FIGS. 9A-9B. The primary difference in this design is that there are tracked markers mounted to the top fiducial such that its location, pose, and identity are all able to be identified by a 3D-tracking acquisition unit without the need to interface with a tracked probe. In this way, the fiducial' s information is constantly being registered provided it is in line of site of the 3D-tracking camera system. The assembled fiducial can serve the same purpose as previously described in that once initialized, i.e., as a surface reference point for the 3D location in space of underlying anatomical structures. For example, FIG. 11A displays a top view assembly view 1100 of a skin surface fiducial mated 1155 with an over-the-drape-mating fiducial 1105 that contains three or more tracked markers 1135. These markers are arranged in a predetermined configuration, such that a camera acquisition system can recognize them as a unique entity related to the fiducial. These tracked markers 1135 allow for the constant registration of the fiducial' s location and pose in 3D space provided that they are within line of site of the camera. In the event that these tracked markers 1135 are not within line of site of the camera, the top fiducial component (1105) also contains a surface contour 1110 that can be accessed and traced by a tracked probe. In this way, the fiducial assembly (1105, 1155) is designed with redundancy to ensure it is able to registered in 3D space, regardless of whether the line of site of the tracked markers is obstructed or not.

[00285] In some embodiments, the markers mounted on the fiducial can be placed in a way to enable unique identification of the fiducial. Other embodiments include three or more 3D-tracked markers that are arranged in a unique, identifiable pattern (e.g., asymmetric triangle).

[00286] Some embodiments include embedding the unique pattern, depicted in FIGS. 27A-27B, on a fiducial, example embodiment depicted in FIGS. 6A-6D, 9A-9B, 11A-11B, in order to enable enhanced x-ray imaging fusion with optical systems to provide localization features across two coordinate systems. In some embodiments, a unique pattern (e.g., CALTag / ARtag) can be applied to a fiducial patch or a skin-based fiducial. This design involves a radiopaque, unique-pattern surface (e.g., CalTag) that is able to be easily visualized in both 3D-tracking camera space and 2D or 3D x-ray imaging space. Some embodiments involve using the absolute location of the C-arm relative to the unique-pattern surface to calculate the relative location and pose between separate x-ray images and enable a robust stitching algorithm to understand their spatial relationships and overlaps. This invention could be used with a corresponding optical sensor that is mounted to the x-ray imaging device, and the system knows the relative geometric relationship between the camera and x-ray imaging device's emitter or detector. This system can enable stitching, unique 3D pose detection, absolute location relations, and should be robust with x-ray images that are acquired with a rotated / oblique x-ray imaging system. The unique-pattern surface visualized in the x-ray image could enable automated scaling of the image into physical units (e.g., millimeters), as well as automatically detect the pose of the fiducial relative to anatomical landmark of interest, and relative to the x-ray imaging device.

[00287] FIG. 1 IB displays another view of a fiducial embodiment equipped with tracked markers on the over-the-drape-mating fiducial 1105 coupled with a skin-mounted fiducial 1155 that is mounted to the patient skin via an adhesive backing 1157. This embodiment can also contain insert slots for inserted magnets and electronics 1125, 1160. It should be noted that although not shown in FIGS. 1 1A-11B, this fiducial can also be equipped with protrusions and mating cutouts for alignment as previously described in relation to FIGS. 6A- 6D and FIGS. 9A-9B.

[00288] Some embodiments include a tracked DRF that is equipped with indications of the relative anatomical reference planes. In this instance, the functional aspects reside in the external indication methods to inform the user how to best orient a tracked DRF for it to indicate to the acquisition system, how to interpret camera coordinates relative to anatomical axes coordinates. For example, FIG. 12 displays a representation 1200 of a tracked DRF 1250 with built-in indication for communicating relative referenced anatomical axes. This design includes four tracked markers 1275 that define a DRF, but also an overlying body outline reference 1225 to help instruct the user how to appropriately position the DRF nearby the patient. Attached to this device is an adjustable mounting surface (marked as 1280 as being under the frame 1250) that allows the user to rotate the device until it is aligned with the patient's orientation and then lock it into place. This device allows the acquisition system to register not only DRF, but also define anatomical reference planes relative to the known geometry of the dynamic reference plane. By utilizing this device, it allows for the acquisition system to display data onto anatomical reference planes rather than camera coordinates which often appear skewed and challenging to interpret by a user depending on the camera's orientation to the subject. It should be noted that the methods of indicating anatomical reference axes on this device are not limited to the human body overlay as shown in this figure. Other methods include but are not limited to written text displaying the associated anatomical axes, images of discrete body parts to represent anatomical orientations, and alphanumeric or unique pattern labels for regions that should be aligned with particular anatomical axes so that software interfaces can walk the user through orienting the DRF relative to the patient appropriately. Of note is that the reference frame can be mounted almost anywhere and does not need to have an adjustable mount, and could be rigid / orthogonal. For example, other embodiments involve the reference frame being mounted rigidly in one orientation to the surgical table, or any rigid surface, or rigidly mounted directly to the patient anatomy (e.g., spinous process of the spine).

[00289] Some embodiments include a cross-sectional CT scan view of a spine and highlights a few anatomical regions of interest that maybe used to initialize patient data prior to performing assessments of the contour of the spine via tracing methods that will be described in more detail below in reference to FIGS. 65A-65E, and FIGS. 66A-65B. In some embodiments, this can be used to interpret the cross sectional displacement vectors between certain regions (e.g., the skin surface, lamina, transverse process) and other regions of interest (e.g., centroid of the vertebral body, anterior segment of the vertebral body, etc.). Using a CT scan to initialize a patient prior to intraoperative assessments of spinal alignment enables software to better interpret localization of exposed regions (e.g., lamina) as a surrogate for the location of other regions (e.g., vertebral body centroid). In doing this, intraoperative interpretation of acquired data can be performed with or without the use of fiducial landmarks as described previously in relation to FIGS. 3A-3B, 4A-4I, 6A-6B, 9A-9B, and 11A-11B. For example, FIG. 13 displays a sample cross sectional CT image 1300 of a patient in which particular anatomical regions are visible including posterior skin surface 1335, and cross sectional view of the vertebra 1358 and many of its bony elements. From CT image sets, it is possible to initialize a patient's anatomy by calculating displacement vectors 1325 from particular regions of interest to another (e.g., skin midpoint to vertebral body centroids, and lamina to vertebral body centroids). After initialization in this way, it is possible for software to interpret the location of one region in terms of its relative location to other initialized regions of interest. For example, although the location of the centroid of the vertebral body may be most advantageous for interpreting spinal alignment parameters, if the skin or lamina is all that is exposed during surgery, the coordinates of the exposed elements can be gathered and then translated, based on initialization data, to represent the location of unexposed regions (e.g., vertebral body centroids).

[00290] Some embodiments include an assembly with an arrangement of tracked markers that can be utilized for discrete signaling to an acquisition system. In some embodiments, four tracked markers that make up a dynamic reference frame (DRF), and two tracked stray markers (TSMs) are included in the assembly. In this embodiment, the center of the assembly can include a rotating shield that can be positioned to cover select TSMs, or none at all. With the tools geometry known, the acquisition system software can interpret which TSMs are exposed, and based on pre-programmed combinations, the tool is able to communicate discrete messages with the acquisition system. For example, if a first is covered, this can indicate the system is in a particular state as opposed to if a second TSM is covered, which would indicate another state. Because the tool contains a DRF, its location and pose can be interpreted by a 3D-tracking camera, and the arrangement of covered and uncovered stray markers can then be used for communication.

[00291] FIG. 14A displays a tool equipped with a tracked DRF 1401 with markers 1420, two tracked stray markers labeled identified as 1422a (not visible) and 1422b. The tool is also equipped with a rotating shield 1415 that is currently positioned to cover visibility of 1422a. Because it is equipped with a DRF, a 3D-tracking camera is able to locate its location and pose in space, as well as distinguish between the four markers serving as a DRF and those serving as TSMs. The tool can be programmed to communicate with the acquisition system via having varying combinations of the TSMs visible or invisible. For example, when the 1422a is covered, the system indicates that it is in a certain state, that is different than if 1422b is covered, as is shown in FIG. 14B, which is also different from the state communicated by neither of the TSMs being covered, as is shown in FIG. 14C. It should be noted that there can be any combination of one or more TSMs associated with this tool, and there can also be any permutation of covering or uncovering individual or combinations of TSMs to communicate various states to the acquisition system. The rotating shield shown in this figure is only one embodiment of how to block the 3D-tracking camera's visualization of the TSMs. Other embodiments of blocking visualization include but are not limited to spring- loaded rotational wipers, linear-motion sliders, actuating the TSMs such that they move from covered to uncovered positions, and rotating shields with multiple panels such that varying combinations of TSMs can be covered or uncovered. It should be noted that this technology of signaling through covering and uncovering TSMs can also be combined with actuating TSMs as was previously described in reference to FIGS. 10A-10G and as will be described in more detail below in relation to FIGS. 15A-15C, 63, and 64A-64B.

[00292] FIGS. 14B-14C illustrate the tool of FIG. 14A in different arrangements in accordance with some embodiments of the invention. For example, FIG. 14B displays one embodiment of a tool previously discussed in relation to FIG. 14A, but in this arrangement, the rotating shield 1415 is covering visualization of the TSM 1422b, and the TSM 1422a is uncovered. This combination can be used to communicate its a unique state to the acquisition system software. Further, FIG. 14C displays one embodiment of a tool previously discussed in relation to FIG. 14A, but in this arrangement, the rotating shield 1415 is positioned such that both TSMs 1422a and 1422b are visible, which is used to communicate a unique state to the acquisition system software.

[00293] Some embodiments include a 3D-tracked probe, equipped with a tracked DRF and a tracked mobile stray marker (TMSM) that can be actuated by a user and utilized to indicate analog or binary information to the acquisition system software. For example, FIGS. 15A- 15C shows a probe equipped with a tracked dynamic reference frame (DRF) in various configurations in accordance with some embodiments of the invention. By the user actuating a tracked mobile stray marker that rotates about a pivot point in the probe shaft, the location of the tracked mobile stray marker can be computed relative to the DRF, and when visualized in certain positions, can be used to communicate varying messages to the acquisition system's software. In reference to FIG. 15 A, one embodiment of a probe 1500 can be equipped with a tracked dynamic reference frame (DRF) 1510, a tracked mobile stray marker (TMSM) 1525 couple to arm 1530 that rotates about a pivot hinge 1550 on a hexagonal extruded probe shaft 1505. The arm 1530 is spring-loaded (via spring 1578) via spanning external spring mounts 1580, 1575 that allow for a depressible tab 1570 to be actuated by a user depressing it inward towards the coaxial probe shaft. The embodiment of the probe 1500 shown has a blunt semi-spherical tip 1560 to avoid damaging sensitive anatomical structures, and also has a hexagonal extruded probe shaft 1505 for added grip by the user. This probe 1500 is designed to have the TMSM 1525 rotate about the pivot hinge 1550 when a user depresses or releases the depressible tab 1570. The location and relative angle of the TMSM 1525 to the DRF 1510 is computed by the acquisition software of any of the disclosed systems, and can be used for both binary or analog communication with the system, as will be described in more detail in relation to FIGS. 63 and 64A-64B.

[00294] It should be noted that with regards to the type of motion of components of the TMSM 1525, the TMSM 1525 can move in linearly as described previously in relation to FIGS. 10A-10E, rotationally, or a combination of the two types of motion. With regards to the actuation method, one embodiment is a user-depressible tab as shown here but it can also consist of user sliding buttons, rotating buttons, and depressible sliding shafts as described previously in relation to FIG. 10A-10B. With regards to the spring location, an external compression spring is shown but is only one embodiment which can also include but is not limited to torsion springs, internal compression springs, deformable materials with shape memory. With regards to the probe shaft 1505, the hexagonal extrusion shape as shown is only one embodiment and other embodiments include, but are not limited to, circular, triangular, rectangular, pentagonal extrusions and non-uniform revolved profiles for both user grip and probe placement within limited-access environments. The probe shaft 1505 need not linear or symmetric. With regards to the depressible tab 1570, the location of the tab 1570 can also be positioned anywhere on the body of the tool. With regards to the probe tip 1560, the blunted semi-spherical design is only one embodiment as it can also comprise varying shapes and degrees of sharpness of point at the tip 1560. Other embodiments can include motion type, linear / rotational, and include other actuation methods. Some embodiments include a user button, vs. slider vs. depressible sliding shaft (shown before in FIG. 10A-B). Other embodiments include a different spring location, nternal or external placement, a torsion spring, a compressible spring or a non-compressible spring. Other embodiments include alternative tip shape and size, blunt or sharp. Some further embodiments include a mating tip as shown in other fastening devices such as FIGS. 33D-33F and 44B-44D.

[00295] Referring to FIG. 15B, the tracked probe 1500 with rotating tracked mobile stray marker 1525 can be used for analog communication previously described in relation to FIG. 15 A. This embodiment displays the location of the tracked mobile stray marker 1525 when the depressible tab 1570 is in its undepressed location and the spring 1578 in its most compressed state. The location and angle of the tracked mobile stray marker 1525 relative to the DRF 1510 is able to be calculated as will be described in more detail in relation to FIGS. 63, and FIGS 64A-64B. [00296] FIG. 15C displays one embodiment of a tracked probe 1500 with rotating tracked mobile stray marker 1525 used for analog communication previously described in relation to FIG. 15 A. This embodiment displays the location of the tracked mobile stray marker 1525 (marked as 1525a) when the depressible tab 1570 is in its depressed location, and the spring 1578 in its most extended state. The arc that is traveled by the tracked mobile stray marker (marked as 1509) is able to be visualized by comparing the location of the TMSM 1525 relative to the tracked DRF 1510, with examples depicted in FIGS. 15A-15C. The location and angle of the tracked mobile stray marker 1525 relative to the DRF 1510 is able to be calculated as will be described in more detail in relation to FIGS. 63, and 64A-64B.

[00297] Some embodiments of the invention utilize rotary encoders are used to measure the precise length of an extensible cord that is retracted outside of the electromechanical, 3D- tracking system (e.g., such as the system depicted in FIGS. 23B-23C). This calculation is accomplished by the encoder measuring the amount of rotation a mechanically-linked cord causes due to retraction. The rotary encoder is mechanically linked either directly with the traversing cord or linked with a spool that stores several revolutions of the cord. This component of the electromechanical tracking system provides accurate length measurements of the extensible cord between the acquisition unit and the probe. The rotation measurement system of the electromechanical tracking system consists of a system that is capable of measuring the degree of rotation, and any supporting mechanical systems to enable or enhance the rotation measurement process. The rotation measurement system interfaces mechanically with an extensible cord and/or a retracting spool/tension system to measure the linear distance of extensible cord that has interfaced with the encoder. For example, one embodiment of the rotation measurement system is a rotary encoder 1600 shown in FIG. 16. A rotary encoder is an electromechanical device, which converts the position or motion of a shaft 1630 about the body 1610 to an electrical signal. In some embodiments, the electrical interface 1650 of the rotary encoder is dependent on the type of rotary encoder and the manufacturer. Internal circuitry inside the rotary encoder 1600 can automatically calculate the amount of shaft rotation, the direction of shaft rotation, or communicate the measurement data over a digital or analog interface. The method and interface over which the rotation measurement data is communicated is of no significance to the encoder system. Only the degree and direction of shaft 1630 rotation is of importance to the calculation of linear distance. In other embodiments, potentiometers can also be used to measure rotation, specifically absolute rotation, which can eliminate the need for length calibrations in order to measure the length of the extensible cord that is actively being retracted outside the electromechanical, 3D-tracking system.

[00298] FIG. 17A illustrates a pulley-gear system 1701 for use with the encoder 1600 of FIG. 16 in accordance with some embodiments of the invention, and FIG. 17B illustrates a gear 1710 of the pulley-gear system 1701 of FIG. 17A in accordance with some embodiments of the invention. This component of the electromechanical, 3D-tracking system depicted in FIGS. 23 A-23B enables for the increased accuracy of length measurements of the extensible cord that transverses through the enclosure and extends beyond the system to the probe 2000 illustrated FIG. 20. The pulley-gear embodiment 1701 enables for a gear-based actuation of the encoder shaft 1650, depicted in FIG. 16 (component 1650), in a manner that multiplies the sensitivity of rotational measurements made by the encoder by a factor nearly equal to the gear-ratio between the set of gears that are mechanically arranged between the cord- interfacing pulley and the encoder-shaft gear.

[00299] Some embodiments involve a pulley-gear system that is installed between the encoder shaft, the retracting spool/tension system, and/or the extensible cord to increase the accuracy of the rotation measurement system depicted in FIG. 16. One embodiment of the pulley-gear system is shown in FIG. 17A. Linear movement of the extensible cord 1705 is coupled to the pulley -gear 1710 using surface friction between the extensible cord 1705 and the high-friction O-ring 1748 that surrounds the internal diameter of the pulley. The pulley- gear 1710 (shown in detail in FIG. 17B) mechanically interfaces with a rotary encoder shaft gear 1715, and during linear movement of the extensible cord 1705, any rotation of the pulley-gear 1710 corresponds to a greater degree of rotation of the rotary encoder shaft gear 1715, with the relationship of the corresponding rotations being determined by the gear ratio between 1710 and 1715. The resolution of the rotary encoder 1720 can been increased by a fixed quantity using the described pulley-gear system 1701, and leads to an increase in the measurement accuracy of the extensible cord length. In some embodiments, the described pulley-gear 1710 can be designed with a notch 1745 to allow for the simple removal of the O- ring, and a cutout 1745 placed at the center of the pulley-gear is designed to allow for the insertion of a bearing that enables for the minimally-fictitious rotation of the pulley-gear 1710 about its center axis, which can have a significant effect on the ease-of-use of the system for the user to retract the probe in a responsive manner. [00300] Some embodiments of the surface of the pulley-gear 1710 that interface mechanically with the extensible cord 1705 can involve specific geometric cross-sectional contours that enhance the friction between the extensible cord 1705 and the pulley-gear 1710 surface. One example embodiment includes a v-shaped groove that the pinches on the surface of the cord 1705, and this design forms a tight-tolerance fit between the cord and the pulley- gear 1710 when the overall system is placed under tension. Other embodiments can include the linkage of the pulley-gear system directly with a tensioned spool system, (described in more detail below in reference to FIG. 18A-18B), that stores multiple revolutions of the extensible cord.

[00301] FIG. 18A shows a perspective view of a cord spool for use in the pulley-gear system of FIG. 17 in accordance with some embodiments of the invention, and FIG. 18B shows a side view. This component of the electromechanical, 3D-tracking system, depicted in FIGS. 23A-23B, involves the spiral storage of extensible cord to be exchanged in and out of the spool at pre-defined lengths per revolution. Some embodiments involve the spool directly interfacing mechanically with a rotary encoder, depicted in FIG. 16, to measure the number of revolutions of cord that are extended away from the enclosure at any time.

[00302] One embodiment of the spool system involves a linkage with a tension system that provides an opposing force to the extensible cord 1705 to maximize coupling in the pulley- gear system depicted in FIG. 17A and/or the rotary encoder 1600 depicted in FIG. 16. In some embodiments, the tension system can be pre-loaded with cord and tuned in tension to ensure that there is no slack along the extensible cord. If slack develops on the cord, accurate measurement of the degree of rotation about the encoder system is less optimal. One embodiment of the retracting spool/tensioning system is a spring-based system that provides tension to the extensible cord. One embodiment of the retracting spool/tensioning system can include a sub-system to allow variable degrees of tension of the extensible cord to a user's specification. One embodiment of the retracting spool/tensioning system can include a mechanism that slows and/or stops the motion of the spool to prevent the extensible cord from traveling at dangerously high speeds, in the event that the pre-tensioned extensible cord is suddenly released.

[00303] The retracting spool provides a system by which the extensible cord can be contained within. For example, one embodiment of a cord spool 1800, illustrated in FIGS. 18A-18B, is composed of a cylindrical disc 1805 with a cord entry slot 1840 removed from the side such that the cord 1705 can be rotated about center of the spool in set revolution increments. The embodiment may have the cord entry slot 1840 with a thickness much larger than the diameter of the cord. The embodiment can have the cord entry slot 1840 be the approximate diameter of the cord, such that the cord is forced to spiral outward from the spool's center in a single-revolution-thick spiral stack. The embodiment can have the inner cord spool radius 1820 be a fixed value. The embodiment may have the inner cord spool radius 1820 may be represented by an equation. In one embodiment, the radial distance of the Archimedean spiral is equal to the diameter of the cord such that the extensible cord spools continuously around itself as described by an Archimedes spiral, which simplifies the calculation of the distance between the center of the spool and the center of the cord, in addition to the calculation of the linear cord distance.

[00304] One embodiment involves the cord beginning its fixation to the spool at a known radius set by the designed mount point 1830 of the spool 1805. One embodiment involves the cord wrapping around inner cord spool surface (defined by inner radius 1820) until the cord length is completely contained within the spool or when the cord reaches the outer spool edge (defined by outer radius 1810). The larger the outer spool edge, the more torque that can be applied by the movement of the cord and the less resistance the user will feel when engaging the retraction of the cord tensioning system. However, the large inner radius surface leads to a less accurate measurement by increasing the length of cord contained with a single resolution step of the encoder's rotational sensitivity.

[00305] In the rotational measurement system described herein, the extensible cord 1705 provides a mechanical connection between the retracting spool and the rotation measurement sensor. The extensible cord 1705 provides a mechanical connection between the probe (FIGS. 19A-19E) and the encoder system 1600 (FIG. 16), allowing for the three-dimensional measurement of the probe tip location as the probe moves through space. The generic embodiment of the extensible cord is a thin-diameter low-stretch cord. One embodiment of the extensible cord is a metal cable, with some embodiments containing special coatings, such as a nylon coating. One embodiment of the extensible cord is a Kevlar cable.

[00306] FIGS. 19A-19C illustrates a ball assembly 1900 of a 3D-tracking system of FIG. 23A in accordance with some embodiments of the invention. This component of the electromechanical, 3D-tracking system depicted in FIGS. 23B-23C, involves a ball-and- socket interface that manipulated via the traversing motion of an extensible cord that passes through the center of the ball. In some embodiments, an extensible cord (e.g., such as cord 1705 shown in FIG. 17A, cord 2120 shown in FIG. 21A, or cord 2150 shown in FIG. 21B) can traverse through the ball-and-socket system via entry to the cord insertion point (cord entry passage 1903) through the a central barrel. The entry point for the cord is structured to intersect with the center of the spherical structure, and subsequently aligned with the sphere's center of rotation. This alignment of the cord entry point (barrel 1930) enables the movement of the cord to be mathematically separated into two sections, the straight line between the cord spool and the center of the ball, as well as the straight line between the center of the ball and the probe (FIG. 20). In some embodiments, the barrel is supported by mechanical structures added to minimize undesired forces and torques imposed by the cord, which can deflect the barrel during movement of the cord. In some embodiments, the ball assembly can include barrel support structures of ball (or sphere) 1901. As the barrel exits the front of the ball, the barrel is supported internally by a reinforced wall 1902. To minimize barrel deflection at the cord entry location, support bars 1940 provide mechanical rigidity to the barrel to minimize deflection created during cord movement.

[00307] In some embodiments, the sphere includes a cylindrical groove 1950 extruded out of the top of the spherical surface, which allows for the installation of an image, or any unique pattern, without any spherical distortion of the pattern surface. An imaging sensor can thus be used to measure the ball's rotation in the spherical coordinates, theta and phi, by examining how the pattern on the cylindrical groove 1950 rotates and translates relative to an imaging sensor. In order to maintain the cylindrical groove's alignment with the center of the ball 1901 and imaging sensor, the ball 1901 includes an orthogonal extrusion (roll-prevention rod 1920) relative to the cylindrical window, that prevents the rotation of the ball about the barrel structure.

[00308] In some embodiments, as shown in FIGS. 19B and 19D, the ball 1901 contains a cylindrical barrel 1930, which begins inside the ball 1901 and extends radially to a fixed distance in front of the ball 1901. The cord (e.g., such as cord 1705) can pass through the extrusion in the back of the ball, enters the barrel at the cord insertion point (shown as 1903), passing through and exiting the barrel in front of the ball (through barrel 1930). The barrel 1930 contains a plethora of holes (barrel fenestrations 1922) to reduce the surface contact area between the inside of the barrel 1930 and the outside of the cord, which helps to ensure smooth cord movement through the barrel 1930. The barrel design provides the encoder (e.g., such as encoder 1600) with a fixed exit point that is required to calculate of linear cord distance. As the barrel 1930 exits the front of the ball 1901, the barrel 1930 is supported externally by a reinforced wall by the barrel shaft base fillet (barrel tip fillet 1924). Further, in some embodiments, the cylindrical groove 1950 provides a cross-sectionally-flat surface from which an imaging sensor can calculate the degree of spherical ball rotation without requiring additional transformations caused by distortion of the pattern. In reference to FIG. 19C, a cylindrical groove (groove 1951) is extruded out of the top of the spherical surface, and allows for the installation of an image, or any unique pattern, without any spherical distortion of the pattern surface. In some embodiments, the support structures illustrated to reinforce the rigidity of the barrel are not required in the final manufactured product, and can include components for prototypes created via 3D printing with fragile materials.

[00309] FIGS. 19D-19E illustrate a ball and socket assembly of the 3D-tracking system of FIG. 23 A accordance with some embodiments of the invention. The socket enclosure 1950 for the ball 1901 provides a joint surface to rotate within due to traversing motions and trajectory changes in the extensible cord. The socket embodiment contains a window cutout 1980 that restricts the movement of the barrel 1930 to within a defined range-of-motion (in window 1932). The window's boundaries help maintain the optimal tracking volume for the electromechanical, 3D-tracking system without having multiple ball-and-socket systems allowing for cord to intersect or obstruct each other. The system also contains a complementary roll-prevention channel 1976 that allows for the restricted movement of a rod extrusion from the ball to travel along a path that prevents the rotation of the ball about its barrel. The roll-restriction feature of the system provides assurance that the cylindrical window is in constant view within the preview window 1999, such that any movement of the pattern will always be visible to an imaging sensor. Multiple socket regions 1998 are removed from the top and bottom of the socket structure to minimize surface friction between the outside of the ball and the inside of the socket. As noted multiple times, the need to minimize friction between the socket, ball, and cord is paramount to the functionality of three-dimensional tracking system. The proposed method represents one embodiment of the ball and socket structure. One embodiment may include a layer of ball bearings installed between the ball and the socket surfaces. One embodiment may include some form of lubricant placed in between the ball and the socket surfaces. One embodiment may include some form of lubricant placed in between the barrel and the cord surfaces. A high-strength and high-durability material is required to maintain the structural integrity of the ball and socket. Other embodiments of the ball-and-socket system may be comprised of metals, polymers, or plastics.

[00310] FIG. 20 illustrates a probe 2000 of a 3D tracking system in accordance with some embodiments of the invention, and FIGS. 20A-20E show views of components of the probe 2000 of FIG. 20 in accordance with some embodiments of the invention. This component of the electromechanical, 3D-tracking system, depicted in FIGS. 23B-C, involves a probe that is used to register 3D points in space while the tracking system dynamically registers the probe's 3D location and orientation with respect to the tracking system's coordinate system. The probe 2000 contains two freely-rotating fixation points where extensible cords that are tracked in 3D space mount at a fixed distance apart. In some embodiments, the probe 2000 can comprise a probe shaft 2025. The probe 2000 provides various functions to the electromechanical, 3D-tracking system. First, the probe 2000 enables the user to trace along a three-dimensional surface. Second, the probe provides a fixed mechanical interface to each encoder's extensible cord. The 3D pose of probe 2000 can be derived from the calculated linear cord distances from each encoder, the fixed distance between each cord connection point, and trigonometric identities. With the pose of the probe 2000 and the linear cord distances, the exact location of the probe tip 2024 can be extrapolated in three-dimensional space. Third, the probe 2000 has the ability to identify interactions with multiple materials through electrical, mechanical, or electro-mechanical interfaces. Fourth, the probe 2000 has a grip area that allows the user hold probe 2000 and trace a three-dimensional surface without interfering with the cords or any additional measurement system.

[00311] One embodiment of a probe 2000 is shown in FIG. 20, has mount points for two cords. The cords from an encoder (such as described earlier in FIG. 16) can couple to the cord fixation mounts 2010, each of which is mechanically coupled to individual bearings that are separated by a cord-mount spacer 2001 coupled to the shaft 2025, with each bearing's internal surface linked rigidly to an internal rod structure coaxial with the probe enclosure. The spacer and bearings are coaxial with an internal rod that is fixed to the probe half that the user can grip (e.g., see bearing 2044). In some embodiments, the internal rod structure is maintained within the probe enclosure via a rigid cap 2005. However, it should be noted that several components, including, but not limited to, the probe cap 2005, are optional. The cord mount and bearing system allows the probe 2000 to move freely in any direction without affecting the accuracy of the measurement system of the encoder embodiment. The probe grip area (on shaft 2025) provides spacing for the user to trace in three-dimensions.

[00312] Some embodiments include a component of the electromechanical, 3D-tracking system, depicted in FIGS. 23A-23C, that involves a probe that is mechanically linked to two 3D-tracked cord fixation points that are spaced by adjustable distance via mechanical actuation between the two fixation points. For example, FIGS. 21 A-21B illustrate assemblies of a 3D tracking system including probes 2100a and 2100b coupled to cord fixation points (see extensible cord 2120, 2150 extending from the probes 2100a, 2100b). In some embodiments, the probes comprise probe handle 2130a, 2130b with depressible sliding shaft 2115a, 2115b, and spring-loaded trigger 2140 (of probe 2100b). Each 3D-tracked probe 2100a, 2100b includes an embedded mechanical system such that the distance between the extensible cord fixation mounts is selectively changed when the depressible shaft (spring- loaded, not shown) is pressed against a surface 2115a, 2115b, or manually actuated by the user via a spring-loaded button 2140 on the shaft 2130a, 2130b of the probe 2100a, 2100b. The extensible cords 2120, 2150 are mechanically linked to the electromechanical, 3D- tracking system.

[00313] In some embodiments, a processing algorithm detects the changes in the relative distance between cord mounts and signals to the electromechanical, 3D-tracking system that it should actively register points at the probe tip, or interpret a specific command that designates what type of measurement the probe is performing, or the location identity the probe is interacting with. The distance between the two dynamic cord fixation mounts can be calculated with respect to the axes of the probe by rigidly transforming the 3D cord fixation mount coordinates with respect to the probe tip coordinates and pose. In this way, the 3D distance between the cord fixation mounts can be calculated without variability in calculations caused by the changing relationship between a cord fixation mount and its relative distance to the electromechanical, 3D-tracking system, in comparison with that of the other cord fixation mount.

[00314] FIG. 22 illustrates an example system enabling 3D tracking of a probe in accordance with some embodiments of the invention. This component of the electromechanical, 3D-tracking system depicted in FIGS. 23A-23C, involves a system of active and passive components that communicate to enable the 3D tracking of the probe's location and orientation. A number of embodiments exist for the probe linked to the electromechanical, 3D-tracking system, with FIG. 22 depicting the interface between a system of components that communicate with each other to enable the 3D tracking of a probe. Some embodiments include a probe with no electrical or mechanical feedback systems for which the encoder embodiment and processing software to detect during tracing, as described in the above embodiment. A probe with an embedded electrical subsystems (FIG. 22) can contain a plethora of user controlled toggle switches that allow the user to control the registration of points and active tracking of the probe (FIGS. 21A-21B). Some embodiments include a method of communication to a microcontroller or a computer processing system that can be transmitted through a wireless electromagnetic radiation (RF), light-emitting devices. In some embodiments, cords can be mechanically linked to the docked tracking system. Some embodiments include a method of delivering power to the probe through a voltage applied across two cords that are mechanically linked to the probe for positional tracking. A battery system or equivalent energy source, such as a capacitor, that is capable of being recharged can be included. In some embodiments, an electrical connection that exists between the probe and the enclosure to provide energy during non-use when the probe is located on the enclosure. In some embodiments, a plurality of sensors of a sensing system can be a plurality of inertial measurement unit, accelerometers, and or gyroscopes to measure the motion and/or pose of the probe. This embodiment may negate the necessity for mechanical linkages with an encoder or extensible cord. One embodiment can be a tilt sensor. One embodiment can be a sensor to measure the rotation of the cord mounts on the probe. One embodiment can be a system to measure mechanical force applied to the probe and/or the probe tip. In some embodiments, a radio-frequency identification (RFID) tag and/or reader placed at a fixed location on the probe can include an RFID is an RFID reader placed in the probe that reads an RFID tag to begin or halt the registration of points and active tracking of the probe tip in 3D. One embodiment of RFID is an RFID reader placed in the probe that reads an RFID tag placed at specific locations to identify the locations with specific indentities during use of the probe. For example, see power storage 2212, power interface 2214, communication system 2216, microcontroller 2218, sensors 2220, and RFID 2222 of the probe 2210, cord 2230 couple to encoder 2226, cord 2232 coupled to 2228, digital signals 2234a (from encoder 2226) and digital signals 2234b (from encoder 2228). Further, see data acquisition controller 2224 coupled to a data storage and processing softward in computer system 2238 coupled through interface 2236. [00309] Some embodiments include an enclosure of the electromechanical, 3D-tracking system that houses all of the components of the tracking system in a compact form that can be mounted onto a multitude of various surfaces. For example, FIG. 23A illustrates an example 3D tracking system 2300 in accordance with some embodiments of the invention, including extensible cords 2350 extending from ball structures 2320 (e.g., such as those described earlier in related to FIGS. 19A-19E, a coupled probe 2340 and rigid surface mount 2305 coupled to structures 2310, 2330. 2320. As shown, one embodiment contains an interface for fastening mounting mechanisms enabling it to be utilized in a variety of settings. Fastening mounting mechanisms 2305 may include a suction cup mount, and fastener holes for mating to rigid structures (e.g., such as 2310, 2330, 2320). Some embodiments include hooks and clamps to interface with surgical tables, beds, anesthesia poles, a removable instrument tray on a movable stand that is configured to be positioned over or adjacent to a surgical site of a patient, (e.g., a Mayo stand), the patient's anatomy, or any other rigid structure. Some embodiments involve extensible cords (shown as 2350) retracted out by the user via the use of a probe 2340 to collected discrete and continuous tracing registrations.

[00310] In some embodiments, the components of the electromechanical, 3D-tracking system can be compiled into a compact design and surrounded by an enclosure device. For example, FIG. 23B illustrates 3D tracking system in enclosure in accordance with some embodiments of the invention. In some embodiments, the enclosure 2360 is shown with extensible cord 2370 (which can be cord 2350) extending from barrel 2367, 2372 of spheres 2374, 2365 (with the cord coupling to a probe, such as probe 2340 of FIG. 23 A). In some embodiments, the enclosure 2360 can shield internal components from debris, trauma, bodily fluids, and light exposure. Further, the enclosure 2360 can contains an external probe mounting system to rigidly fix the probe (e.g., such as probe 2340) to the enclosure 2360 for when the extensible probe system is not in use. In some embodiments, the enclosure also houses the spool system which outputs two extensible cords to attach to the probe, and each cord 2370 passes through the barrel structure of each sphere to enable the electro-mechanical triangulation of the probe.

[00311] Some embodiments include internal light sources to prevent variability in lighting for the camera system. Some embodiments include an electrical interface over which power and/or data can be transmitted to and/or received from the probe when in the docked. One embodiment of the electrical interface can be metal contacts extending from the probe mounting system to couple to electrical contacts on the probe.

[00312] FIG. 23C shows an exploded assembly view of the 3D tracking system of FIG. 23B in accordance with some embodiments of the invention. For example, some embodiments include enclosure 2361 housing an rotary encoder 2399, a fixed spring tensioner arm 2390 for spool spring (not shown), a spool 2392, a top half of socket 2395 (reference FIG. 19D-19E), and embedded, unique pattern 2383, ball 2374 (reference FIG. 19A-C), barrel of ball 2365, and enclosure lid 2362 with embedded optical sensors (not shown). FIG. 23 C illustrates the compilation of components from one embodiment of the electromechanical, 3D-tracking system. Each of the two rotary encoders 2399 measure the length of an extensible cord coupled to the probe (not shown). Each extensible cord (not shown) is stored and retracted from the spool 2392 that is being tensioned via a spring (not shown) that is fixed at one end by a spring tensioning arm 2390, which is mounted to the rigid enclosure. Each extensible cord passes through a ball 2374, that can rotate within a socket (2395) with viewing windows (not shown), via a barrel (2365) that originates at the center of the ball 2374to enable controlled movement of the cord during rotation of the ball. The rotation of the ball is measured via an embedded pattern 2383 on the ball surface that is aligned above the center of the ball and able to mirror the phi and theta rotation of the ball in spherical coordinates. The enclosure includes a lid 2362 that couples with the bottom- component of the enclosure (2361) can help to create a protected environment while also housing the optical sensors (not shown), lights (not shown), and microcontrollers (not shown), for recording and analyzing the visual and electrical outputs from the embedded optical sensors and rotary encoders. In other embodiments, wireless communication components (not shown) are also included within the enclosure.

[00313] FIG. 24 illustrates a system enabling 3D tracking of a probe in accordance with some embodiments of the invention. This embodiment depicts a system of components that enable for the electromechanical localization of a 3D point at the tip of a probe (e.g., such as any of the probes described herein). Three extensible cords (2428, 2430, 2432) mechanically link to the probe tip 2421 of probe 2420 via connections extending from three separate rotary encoders 2422, 2424, 2426 that measure the length of each cord, from which the software system calculates the 3D point of the probe tip via triangulation geometric equations. The embodiment of an encoder (such as eny of the encoders 2422, 2424, 2426) is represented by a spool wound with an extensible cord (e.g., such as 2428, 2430, 2432), a spring-loaded retractor system, which can be represented by any system that provides a tensioning force, and a rotary encoder, which can be represented by other sensors used to detect the degree of rotation. The three encoder embodiments are placed at fixed distances relative to each other. The probe 2420 contains a single cord mount connection at the probe tip 2421 , through which all cords 2428, 2430, 2432 interface to the probe 2420. As the probe 2420 is moved in three dimensions, the cord length is measured via rotary encoders 2422, 2424, 2426 (e.g., as illustrated in FIG. 16), however other sensors can be used to detect the length of the extended cord. With the known distance between each encoder 2422, 2424, 2426, the measured cord lengths to the probe tip 2421, the system's triangulation algorithm can process the data through a geometric relationship to calculate the three-dimension location of the probe tip 2421. The three-cord encoder system requires at least three encoder embodiments to calculate the three-dimensional position.

[00314] Another embodiment of the electromechanical, 3D-tracking system, illustrated in FIG. 23B-23C, can contain in the system of components shown in FIG. 25, where the ball- and-socket movement is sensed by mechanically-linked rotary encoders that measure the phi and theta movement of the ball in spherical coordinates (e.g., using two encoders per ball and socket system or assembly). The encoder-based 3D-tracking system embodiment shown in FIG. 25 includes, probe 2510, cords 2520, 2522, encoders 2514, 2526, mechanical linkage and measurement 2518, 2512, 2528, 2530, ball and socket 2516, 2524, data acquisition 2550, 2555, computer 2560. Each ball-and-socket 2516, 2524 is mechanically linked to two encoders 2514, 2526. An extensible cord 2520, 2522 passes radially through the barrel located at the center of the ball and connects to a probe 2510, allowing the barrel to follow the location of the extensible cord. Since the barrel is fixed at the center of the ball and the ball's axis of rotation is fixed by a rod seated in a slot on the socket, the ball is unable to rotate radially about the barrel's axis and the barrel can track the location of the probe. Measurement of the ball's rotation in the socket allows for the calculation of the angular takeoff of the barrel in spherical coordinates as the probe is moved through 3D space. The cord length is measured via rotary encoders as described in relation to FIG. 16, however other sensors can be used to detect the length of the extended cord. The measurement of cord length and angular takeoff provide sufficient data to calculate the 3D location of the probe in the spherical coordinate system. [00315] One embodiment of the measurement system used to calculate the angular takeoff is a mechanical linkage between the surface of the ball and a rotary encoder, however other sensors can be used to detect the degree of rotation. As the ball rotates in the theta and phi directions due to probe translation, a mechanical linkage rotates the shaft of a rotary encoder, and the degree of a ball' s rotation in each spherical coordinate plane can be calculated.

[00316] One possible mechanical linkage is a spherically or cylindrically-shaped coupling object fixed radially to a rotation measurement system as described in FIG. 16. One embodiment of a rotation measurement device could be a rotary encoder. The position of the rotary encoder is fixed such that the cylindrically shaped object makes physical contact with the ball and is mechanically secured to the rotary encoder shaft. Any movement of the probe results in rotation of the ball, rotation of the cylindrically-shaped object, and thus rotation of the rotary encoder shaft. Two embodiments of the described mechanical linkage, oriented orthogonal to each other, are required to calculate the rotation of the ball' s barrel in theta and phi directions.

[00317] In some embodiments, algorithms calculate the degree of ball rotation in theta and phi from the radius of the cylindrically shaped object, the rotation measured by the rotary encoder, and the radius of the ball. After calculating phi and theta of the barrel, the system then uses spherical coordinate formulas to calculate a vector from the center of the ball to the location of the first cord as it mates with the probe. The same process is repeated for the second ball-and-socket pair, also using a mechanical linkage to sense the spherical rotation of the ball. The second ball-and-socket system calculates a three-dimensional vector from the center of the ball to the end location of the second cord as it mates with the probe.

[00318] The pose of the probe is then calculated from the vector subtraction of two calculated cord vectors. The three-dimensional position and orientation of the probe tip can be extrapolated given the known dimensions of the probe and the distance between the cord fixation points on the probe.

[00319] Another embodiment of the electromechanical, 3D-tracking system, illustrated in FIGS. 23A-23C, can contain the system of components shown in FIG. 26, where the ball- and-socket movement is sensed by optical sensors that interpret the rotation and relative location of the ball-mounted pattern with respect to the image sensor. This system measures the phi and theta movement of the ball in spherical coordinates. The combined mechanical, electrical, electro-mechanical, and optical components of the system 2600 shown in FIG. 26 that enable for the 3D-tracking of a probe's location and pose include a probe 2610, coupled cords 2612, 2614, coupled ball and socket 2616, 2620, encoders 2618, 2622, camera 2624, processor or controller 2624, camera 2628, processor or controller 2630, data acquisition 2632, computer 2634, and modem 2636. Two encoders are able to measure length of the cord, and the two ball-and-socket assemblies enable measurements of cord trajectory for cord that is past the center of the ball (see FIGS. 19A-19E). One optical-sensing and unique pattern embodiment per ball-and-socket embodiment for measuring the spherical rotation of the ball (depicted in FIGS. 27A-27D). One probe embodiment to link the 3D-tracked, extensible cords in space and provide the user a medium for acquiring 3D points (as depicted in FIG. 20).

[00320] In one embodiment, an extensible cord passes through the center of rotation of a sphere and exits via a radial barrel that follows the location of the extensible cord end that is mounted to the probe. The location of the center of the sphere is fixed by the sphere being constrained by a socket with a slot to allow for the free movement of the barrel to track the exiting cord. The socket ensures that the sphere cannot rotate about its barrel shaft via a radial slot in the socket that receives a complementary rod tip that is mounted to the sphere and is concentric with the center of the sphere.

[00321] The cord length is measured via rotary encoders, however other sensors can be used to detect the change in length of the cord during use. Since the portion of the extensible cord that has exceeded the center of the sphere is no longer always coaxial with the starting portion of the extensible cord near the encoder, a measurement must be made of the angular takeoff of the sphere's barrel, through which the cord passes, to produce the spherical coordinates needed calculate the 3D location of the cord end that is mounted to the probe.

[00322] One embodiment to calculate the angular takeoff of the sphere's barrel is to embed a pattern on the sphere's cylindrical window such that while the sphere moves due to the translation of the cord in space, the pattern rotates about the center of the sphere in a manner that mimics the phi and theta angles produced by the barrel relative to the coordinate system of the center of the sphere.

[00323] One possible pattern is a checkerboard that has a unique black-and-white tag pattern, similar to that used in augmented reality registration markers, in each square of the board. The unique checkerboard has an established x-y coordinate system, such that one corner of the checkerboard is the origin and each square represents one unit of known size.

[00324] An optical sensor embedded in the socket, with the sensor located concentrically to both the center of the sphere and the preview window of the socket, records the viewable portion of the overall pattern that can be seen through the preview window of the socket. The optical sensor transmits image frames to the processing software to utilize computer vision algorithms to detect all visible corners of checkerboard pattern, identify the signature of each visible square, and reference each square's known location within the overall pattern. The pixels in the image frame are converted into millimeters, or any other physical unit, by calculating the ratio between pixels and millimeters for a known side length of one of the visible squares of the pattern surface. The center of the image frame represents the center of the sphere.

[00325] The algorithms then calculate the absolute location of the center of the image along the unique pattern, identifying the exact location in the units of the physical pattern. The vertical location of the image center is used to calculate the theta of the barrel by identifying the arc length between the current image center in the active image frame and the location on the pattern surface that aligns with the image center when the barrel is concentric with the side window of the socket, producing a theta of zero. This arc length input is combined with the known radius of the pattern surface relative to the center of the sphere, and then theta is calculated using the arc length formula that extrapolates the angle of the arc section. The theta angle of the barrel represents the up and down motion of the barrel.

[00326] In addition, a vector is calculated between the checkerboard corner closest to the image center and a corner nearest that first corner that is vertically in-line with respect to each other in the coordinate system of the pattern. A second vector is calculated along the vertical axis of the image, passing through the image center. The algorithms calculate the relative angle between these two vectors by calculating the inverse cosine of the cross product of the two vectors; this calculation can also be done several different ways using known geometry formulas. The angle between these vectors represents the phi angle of the barrel, which indicates the left and right motion of the barrel. After calculating phi and theta of the barrel via the location of the image center on the unique pattern and the pose of the pattern relative to the optical sensor, the system then uses spherical coordinate formulas to calculate the end location of the cord end that mates with the probe tip, given the input length of the cord that exists past the center of the sphere. Given two cord fixation points with known, calculated 3D locations on the probe shaft, the system can calculate the 3D vector between the two fixation mounts, and then extrapolates the 3D location of the probe tip, given the known dimensions of the probe, and calculating the offset between the probe tip and the 3D line.

[00327] The same process is repeated for the second ball-and-socket pair, which also have an embedded pattern and optical sensor combination, to calculate the 3D location of the second extensible cord end that mounts to the probe. One embodiment of the electromechanical, 3D-tracking system involves using an optical sensor to measure the spherical rotation of a ball in correspondence with the movement of an extensible cord that transverses through the center of the ball's rotation. As the barrel translates left and right in the phi plane of the spherical coordinate system of the ball, the embedded pattern also rotates by the same angle, since the pattern viewable to the camera is aligned to be above the center of the ball. The system thus measures the angle of the pattern with respect to the optical sensor to calculate the phi angle of the barrel in spherical coordinates. Some embodiments of the electromechanical, 3D-tracking system, illustrated in FIGS. 23A-23C, can involve the use of unique patterns embedded on the ball surface, as shown in FIGS. 27A-27D (and discussed earlier with respect to 2383 of FIG. 23C), where the ball-and-socket movement is sensed by optical sensors that interpret the rotation and relative location of the ball-mounted pattern with respect to the image sensor. The unique pattern enables for the computer vision algorithms of the system to calculate the absolute position of the center of the image sensor with respect to coordinate system of the grid-based pattern. This system measures the phi and theta movement of the ball in spherical coordinates. Unlike a typical optical sensor used in a computer mouse, this system does not lose its sense of position with respect to the pattern if image frames are lost or not able to be calculated for any reason, since the pattern provides the system an ability to calculate absolute position on its surface. As shown, barrel phi rotation 2710, ball 2705, and pattern 2701.

[00328] In reference to FIG. 27B, and barrel theta rotation 2715, one embodiment of the electromechanical, 3D-tracking system involves using an optical sensor to measure the spherical rotation of a ball in correspondence with the movement of an extensible cord that transverses through the center of the ball's rotation. As the barrel translates up and down vertically in the theta plane of the spherical coordinate system of the ball, the embedded pattern translates away from the center of the image sensor as the ball rotates about the y- axis. Subsequently, the system measures the location of the image center with respect to the grid coordinate system to calculate the translation along the vertical portion of the grid, and then using the known radius between the ball center and pattern surface, the system calculates the theta angle 2715 of the barrel in spherical coordinates.

[00329] In reference to FIGS. 27C-27D, a vector is calculated between the checkerboard corner closest to the image center and a corner nearest that first corner that is vertically inline with respect to each other in the coordinate system of the pattern. A second vector is calculated along the vertical axis of the image, passing through the image center. The algorithms calculate the relative angle between these two vectors, by calculating the inverse cosine of the cross product of the two vectors; this calculation can also be done several different ways using known geometry formulas. The angle is calculated using one vector from each of the grid axes 2721a and camera axes 2719a, selecting the two vectors with the closest angles to the zero phi angle. The angle between these vectors represents the phi angle of the barrel, which indicates the left and right motion of the barrel. After calculating phi and theta of the barrel via the location of the image center on the unique pattern and the pose of the pattern relative to the optical sensor, the system then uses spherical coordinate formulas to calculate the end location of the cord end that mates with the probe tip, given the input length of the cord that exists past the center of the sphere. The theta angle of the barrel represents the up and down motion of the barrel. The system algorithms calculate the absolute location of the center of the image along the unique pattern, identifying the exact location in the units of the physical pattern. First, the grid axes 2721b rotation is identified and then the image center 2722 relative to the camera axes 2719b. Next, the projected length of the vector between the grid axes origin and the image sensor is calculated. This arc length input is combined with the known radius of the pattern surface relative to the center of the sphere, and then theta is calculated using the arc length formula that extrapolates the angle of the arc section.

[00330] Another embodiment of the electromechanical, 3D-tracking system, illustrated in FIGS. 23A-23C, can contain the system of components shown in FIG. 28A, where the ball- and-socket movement is sensed by optical sensors that interpret the relative translation of the ball surface with respect to the image sensor as the ball rotates due movement of the barrel. This system measures the phi and theta movement of the ball in spherical coordinates. The system 2800 can include encoder embodiments to measure length of the cord, two ball-and- socket assemblies to enable measurements of cord trajectory for cord that is past the center of the ball, two optical sensors per ball-and-socket assembly for measuring the translation of the ball surface with respect to the image sensor to calculate the spherical rotation of the ball, and one probe assembly to link the 3D-tracked, extensible cords in space and provide the user a medium for acquiring 3D points. For example, the system 2800 can include couple components comprising probe 2802 with probe tip 2803, cords 2804, 2805, ball and sockets 2809, 2815, opticall coupled sensor and processing boards 2807, 2813, 2819, and 2821, coupled encoders 2811, 2817, data acquisition microcontrollers 2823, 2825, and computer system 2827 with data storage and processing software.

[00331] For each ball-and-socket embodiment there is one encoder embodiment and two optical sensor embodiments. An extensible cord passes radially through the barrel located at the center of the ball and connects to a probe, allowing the barrel to follow the location of the extensible cord. Since the barrel is fixed at the center of the ball and the ball's axis of rotation is fixed by a rod seated in a slot on the socket, the ball is unable to rotate radially about the barrel's axis and the barrel can track the location of the probe. Measurement of the ball's rotation in the socket allows for the calculation of the angular takeoff of the barrel as the probe is moved through three-dimensional space. The cord length is measured via rotary encoders as described in FIG. 16, however other sensors can be used to detect the length of the extended cord. The measurement of cord length and angular takeoff provide sufficient data to calculate the three dimensional location of the probe in the spherical coordinate system.

[00332] One embodiment of the measurement system used to calculate the angular takeoff is a pair of optical sensors oriented normal to the ball and socket and orthogonal to each other, each one aligned with the theta and phi spherical coordinate planes of the ball system.

[00333] In one embodiment, a light-emitting device emits light in a finite spectrum that is reflected off the surface of the ball and is converted to electrical signals via a photodetector array. The converted data is then processed using an algorithm to transform the photodetector array data into translational changes of the ball surface with respect to the camera. A data acquisition and computing system converts the translational data from cartesian to spherical coordinates, and subsequently calculates the theta and phi rotation of the sphere, based on the known radius of the ball that is being sensed. One embodiment of the system may include a laser diode and photodiode array, light-emitting diode and photodiode array, and/or an imaging sensor. A pattern or image installed on the cylindrical window of the ball to increase the contrast, reflectivity, or sensitivity of the optical signal, as well as to produce higher signal-to-noise ratios, and increase the accuracy of theta and phi spherical coordinate calculations. The pattern or image may contain repeating variations of patterned and/or colors, and may be manufactured with a reflective surface, which maximizes the optical coupling between the light-emitting device and the photodetector array.

[00334] Another embodiment involves a surface pattern that is etched on the ball surface during the manufacturing process, and the surface pattern enhances the sensitivity of optical signals to change at the slightest of translational changes of the ball surface with respect to the image sensor.

[00335] Some embodiments can involve additional lighting sources that provide lighting on the ball surface at any possible finite spectrum of light, from which certain light source frequencies provide an optimal sensitivity for the system to have a high-resolution sensing of rotational changes, but not erroneously estimating movement that is not actually occurring, but rather just artifacts of optical noise.

[00336] FIG. 28B illustrates a computer system 2829 configured for operating and processing components of the any of the systems disclosed herein. For example, in some embodiments, the computer system 2829 can operate and/or process computer-executable code of one or more software modules of any of the systems shown in one or more of the figures herein, including, but not limited to FIGS. 24-26, and 28 A. In some embodiments, the system 2829 can comprise at least one computing device including at least one processor 2832. In some embodiments, the at least one processor 2832 can include a processor residing in, or coupled to, one or more server platforms. In some embodiments, the system 2829 can include a network interface 2850a and an application interface 2850b coupled to the least one processor 2832 capable of processing at least one operating system 2840. Further, in some embodiments, the interfaces 2850a, 2850b coupled to at least one processor 2832 can be configured to process one or more of the software modules 2828 (e.g., such as enterprise applications). In some embodiments, the software modules 2838 can include server-based software and/or can can operate to host at least one user account and/or at least one client account, and operating to transfer data between one or more of these accounts using the at least one processor 2832. [00337] With the above embodiments in mind, it should be understood that the invention can employ various computer-implemented operations involving data stored in computer systems. Moreover, the above-described databases and models throughout the system 2829 can store analytical models and other data on computer-readable storage media within the system 2829 and on computer-readable storage media coupled to the system 2829. In addition, the above-described applications of the 2829 system can be stored on computer- readable storage media within the system 2829 and on computer-readable storage media coupled to the system 2829. These operations are those requiring physical manipulation of physical quantities. Usually, though not necessarily, these quantities take the form of electrical, electromagnetic, or magnetic signals, optical or magneto-optical form capable of being stored, transferred, combined, compared and otherwise manipulated. In some embodiments of the invention, the system 2829 can comprise at least one computer readable medium 2836 coupled to at least one data source 2837a, and/or at least one data storage device 2837b, and/or at least one input/output device 2837c. In some embodiments, the invention can be embodied as computer readable code on a computer readable medium 2836. In some embodiments, the computer readable medium 2836 can be any data storage device that can store data, which can thereafter be read by a computer system (such as the system 2829). In some embodiments, the computer readable medium 2836 can be any physical or material medium that can be used to tangibly store the desired information or data or instructions and which can be accessed by a computer or processor 2832. In some embodiments, the computer readable medium 2836 can include hard drives, network attached storage (NAS), read-only memory, random-access memory, FLASH based memory, CD- ROMs, CD-Rs, CD-RWs, DVDs, magnetic tapes, other optical and non-optical data storage devices. In some embodiments, various other forms of computer-readable media 2836 can transmit or carry instructions to a computer 2840 and/or at least one user 2831, including a router, private or public network, or other transmission device or channel, both wired and wireless. In some embodiments, the software modules 2838 can be configured to send and receive data from a database (e.g., from a computer readable medium 2836 including data sources 2837a and data storage 2837b that can comprise a database), and data can be received by the software modules 2838 from at least one other source. In some embodiments, at least one of the software modules 2838 can be configured within the system to output data to at least one user 2831 via at least one graphical user interface rendered on at least one digital display. [00338] In some embodiments of the invention, the computer readable medium 2836 can be distributed over a conventional computer network via the network interface 2850a where the 2829 system embodied by the computer readable code can be stored and executed in a distributed fashion. For example, in some embodiments, one or more components of the system 2829 can be coupled to send and/or receive data through a local area network ("LAN") 2839a and/or an internet coupled network 2839b (e.g., such as a wireless internet). In some further embodiments, the networks 2839a, 2839b can include wide area networks ("WAN"), direct connections (e.g., through a universal serial bus port), or other forms of computer-readable media 2836, or any combination thereof.

[00339] In some embodiments, components of the networks 2839a, 2839b can include any number of user devices such as personal computers including for example desktop computers, and/or laptop computers, or any fixed, generally non-mobile internet appliances coupled through the LAN 2839a. For example, some embodiments include personal computers 2840a coupled through the LAN 2839a that can be configured for any type of user including an administrator. Other embodiments can include personal computers coupled through network 2839b. In some further embodiments, one or more components of the system 2829 can be coupled to send or receive data through an internet network (e.g., such as network 2839b). For example, some embodiments include at least one user 2831 coupled wirelessly and accessing one or more software modules of the system including at least one enterprise application 2838 via an input and output ("I/O") device 2837c. In some other embodiments, the system 2829 can enable at least one user 2831 to be coupled to access enterprise applications 2838 via an I/O device 2837c through LAN 2839a. In some embodiments, the user 2831 can comprise a user 2831a coupled to the system 2829 using a desktop computer, and/or laptop computers, or any fixed, generally non-mobile internet appliances coupled through the internet 2839b. In some further embodiments, the user 2831 can comprise a mobile user 2831b coupled to the system 2829. In some embodiments, the user 2831b can use any mobile computing device 2831c to wireless coupled to the system 2829, including, but not limited to, personal digital assistants, and/or cellular phones, mobile phones, or smart phones, and/or pagers, and/or digital tablets, and/or fixed or mobile internet appliances.

[00340] In some embodiments of the invention, the system 2829 can enable one or more users 2831 coupled to receive, analyze, input, modify, create and send data to and from the system 2829, including to and from one or more enterprise applications 2838 running on the system 2829. In some embodiments, at least one software application 2838 running on one or more processors 2832 can be configured to be coupled for communication over networks 2839a, 2839b through the internet 2839b. In some embodiments, one or more wired or wirelessly coupled components of the network 2839a, 2839b can include one or more resources for data storage. For example, in some embodiments, this can include any other form of computer readable media in addition to the computer readable media 2836 for storing information, and can include any form of computer readable media for communicating information from one electronic device to another electronic device.

[00341] FIGS. 29A-29B illustrates a screw-head-registering screwdriver equipped with a tracked dynamic reference frame in accordance with some embodiments of the invention. FIG. 29C illustrates a close-up perspective view of a screwdriver head and depressible tip 2957 of the screwdriver of FIGS. 29A-29B in accordance with some embodiments of the invention. Further, FIG. 29D illustrates a cross-sectional view of the screwdriver-screw interface in accordance with some embodiments of the invention. FIG. 29A-29B displays a tool that serves three functions: 1.) it indicates the position and pose of screw by 2.) fully engaging in the screwdriver interface and 3.) signals when it is fully engaged by a depressable sliding shaft that extends from the 2957 of the tool and is coupled to a tracked mobile stray marker that is actuated when the tool is fully engaged with the mating screw. The overall purpose of this invention is to identify the location and pose of a screw via this tracked tool, and have a triggering system via the tracked mobile stray marker to indicate to the acquisition system when the tool is fully engaged with the screw. This tool and other embodiments can be applied when there is not a rod seated in the screw obstructing the tool's interface with the screw head. As shown, the tool can comprise tracked DRF 2929 (with 2930 markers), a screw-head-registering screwdriver 2910, tracked mobile stray marker (undepressed) 2945, handle 2940, screwdriver head 2950, depressible sliding shaft (undepressed) 2957, pedicle screw 2960, and 2935 coupler.

[00342] This tool (screwdriver) 2900 is designed to interface with pedicle screws 2960 in such a way that it can engage with the head of the screw to both tighten and loosen the screw, but furthermore, that when it is fully engaged in the screw head, its shaft is fixed in one orientation relative to the screw 2960 shaft. In this way, this tool 2900 can be used to quickly register both the location and pose of the screw 2960 shaft by only accessing the screw head 2950. As shown, the tracked mobile stray marker 2945 is in the position corresponding with an undepressed, and therefore unengaged, screwdriver depressible shaft 2957. This embodiment possesses a similar design of actuating a tracked mobile marker 2945 via a depressible tip 2957 as described previously in relation to FIG. 10A-10G. It should be noted that the depressible tip 2957 and the screw head interface component of the tool can have many different embodiments.

[00343] In some embodiments, the sliding shaft (tip 2957) can be structured such that it always remains within the shaft of the tool or screwdriver, and the screw 2960 head is designed with a center protrusion to deflect the inner sliding shaft of the screwdriver. In this way, the tip 2957 of the sliding shaft is unable to be actuated by any object that cannot fit inside the shaft. When the tracked mobile stray marker 2945 is actuated, the acquisition system's software detects its motion and is able to distinguish when it is fully or partially engaged with a screw head by the known geometry of the tool and interfacing screw as described in more detail below in reference to FIG. 63. It should be noted that the motion of the tracked mobile stray marker 2945 can be linear, rotational, or any combination thereof. Further, the mechanism of detecting the motion of the tracked mobile stray markers can also consist of covering and uncovering a particular stray marker with actuation of the sliding shaft as described previously in relation to FIG. 14. Additionally, the design of the screwdriver head can be such that it also has components that allow for ensuring it will mechanically couple with the screw 2960 such that it can only achieve one orientation when fully engaged. In some embodiments, structures to help with engaging in that way include but are not limited to expanding screwdriver heads, a depth stop flange to help the screwdriver head align with the screw head, and screws designed with screw heads of increased depth to ensure the screwdriver shaft firmly engages in one orientation when fully seated into the head. In addition, since the displayed location of the tracked DRF 2929 is not the only manner to rigidly attached the DRF, it must must be noted that the DRF can be placed anywhere on the surgical tool screwdriver as long as it can be rigidly attached, even on adjustable joints.

[00344] FIG. 29B displays another embodiment of the tool shown previously in reference to FIG. 29A, except in this image, the tool 2900 is fully engaged with the screw head 2950, highlighting the new position of the tracked mobile stray marker 2945 to indicate to the acquisition software system that it is fully seated and the location and pose of the screw 2960 shaft can be calculated from that position.

[00345] FIG. 29C illustrates a close-up perspective view of a screwdriver head 2909 and depressible tip 2950 of the screwdriver 2900 of FIGS. 29A-29B in accordance with some embodiments of the invention, and shows the aforementioned depressible sliding shaft 2957(undepressed). FIG. 29C shows a more detailed perspective of the screwdriver head 2950 and the depressible tip 2957 of the screwdriver tool 2900 previously described in relation to FIG. 29A-29B, and its interface with a pedicle screw head 2960. In this view it is possible to see the interface of the screwdriver and the screw head, as well as the depressible tip 2957, shown undepressed. Other embodiments involve a depressible sliding shaft that is contained within the screwdriver head. This spring-loaded, depressible shaft can only be engaged when a male protrusion in the screw head engages the screwhead coaxially, and then the shaft is pushed up and actuating the TMSM attached to the shaft, to signal that the 3D- tracked tool and the screw are engaged and coaxial, and thus ready to be registered in 3D space.

[00346] FIG. 29D illustrates a cross-sectional view of the screwdriver- screw interface in accordance with some embodiments of the invention, and shows depressible sliding shaft tip (partially depressed) 2965. As shown in this figure, the screwdriver would not signal to the acquisition system that it is fully engaged, as the tracked mobile stray marker 2945 would not be fully-actuated relative to the tracked DRF.

[00347] In some embodiments, the tracked DRF does not have to be rigidly attached to the tool's shaft, but can be allowed to rotate about the tool shaft (e.g., linked with a bearing). As it shown in the drawing simply, it makes it very challenging for users to use the tool as a screwdriver because the DRF gets in the way. It should be noted that in other embodiments of the design, the tracked DRF is both located and attached to the screwdriver in different ways. For instance, in some embodiments, the tracked DRF is coupled to the screwdriver shaft via a bearing, such that it is allowed to rotate about the long-axis of the screw driver shaft. In other embodiments it is positioned above the handle with or without bearings to enable it to rotate about the screwdriver shaft axis.

[00348] In some embodiments, a pedicle screw insert cap can attach a series of tracked 3D markers to the head of the tulip head on the screw. In this way, the tulip head can be tracked in 3D space whenever the markers are within line of site of the camera and do not require a probe to interface with them to register their position in space. FIG. 30A displays an optical, 3D-tracking system 3000 that can be used as the acquisition device for this and any tracked markers throughout this document. FIG. 30B displays a tracked DRF 3070 equipped with a mating mechanism 3060 to rigidly mount to the tulip head 2955 of a pedicel screw 2960. With this tracked reference frame 3070 attached to the screw 2960, the location of the pedicle screw 2960 can be tracked in space, provided it is in line of sight of the 3D-tracking camera. The interface between the DRF 3070 and the tulip head 2955 can consist of an array of mechanisms, described in more detail below in reference to FIGS. 34-37.

[00349] FIG. 31 illustrates a body-mounted 3D-tracking camera in accordance with some embodiments of the invention, and operates in a way to avoid line of sight obstruction between a 3D-tracking camera and a surgical site. This design involves a user equipped with a body-mounted tracked DRF rigidly fixed to a body-mounted 3D-tracking camera such that information can be fused between the user's field of view and the external 3D-tracking camera, because the location and pose of the body-mounted camera will always be visible and known to the larger field of view 3D-tracking camera. FIG. 31 displays the body- mounted 3D-tracking sensor 3135 equipped with a tracked DRF 3110. In this embodiment, surgical areas that are typically obstructed from the line of sight of a large field-of-view camera can be visualized via the body-mounted, 3D-tracking optical sensor. Since the body- mounted, optical sensor is equipped with a rigidly-mounted tracked DRF, the larger-field-of- view camera can register the body-mounted, optical sensor's location and pose in 3D space, and with that information, interpret the scene visualized by the headset-mounted, 3D-tracking optical sensor to create a dynamic, 3D stitched mapping of the global coordinate system relative to the large field-of-view camera coordinate system.

[00350] FIG. 32 displays a method of interpreting the contour of the posterior elements of the spine by placing a malleable object over the surgically-exposed bony elements such that it matches the contour of the exposed spine, and then the malleable object is removed and its contour registered with optical systems, including stereoscopic cameras, and from that information about the surface contour of the malleable object which now serves as a surrogate for the contour of the posterior elements of the spine, the spinal alignment parameters can be calculated. Other relevant other figures (relating to the 3D contour of a malleable material processed by software algorithms) include FIGS. 65A-65E, 66A-66B, and 68. FIG. 32 displays the method 3200 where a malleable rod 3215 that is placed over the surgically exposed elements of the spine 3230 with a adjustable clip 3210 to register particular spinal level for software interpretation. After the rod 3215 is inserted into the surgical site, the malleable material is conformed to match the contour 3225 of the exposed spinal elements. This malleable rod is then optically registered 3241 to interpret the 3D contour of the rod. The 3D contour of the malleable material is then processed by software algorithms described in detail below in reference to FIGS. 65A-E, 66A-B, and 68. The optical registration system (not shown) can be any optical system to register 3D surface contours including but not limited to a depth sensor array with a rotating base for the rod, stereoscopic vision cameras, and structured light systems. Based on some embodiments for registering the 3D contour of the malleable rod using optical methods, and the associated clip (a) that indicate spinal levels, the system can calculate the spinal alignment parameters 3250 of each anatomical plane of the rod.

[00351] Some embodiments include a screw and screwdriver combination that allows for the ability to mechanically couple both devices such that the screwdriver becomes coaxial with the screw shaft, and also has the ability to then rigidly manipulate the shaft, which if fixed in bone, has the ability to then manipulate the bony structures. For example, FIG. 33A illustrates pedicle screw in accordance with some embodiments of the invention, and FIG. 33B illustrates a pedicle screw in accordance with another embodiment of the invention. Further, FIG. 33C illustrates pedicle screw mated with a polyaxial tulip head in accordance with some embodiments of the invention, and FIG. 33D illustrates a tool designed to interface with the pedicle screw of FIG. 33B in accordance with some embodiments of the invention. FIG. 33E illustrates a visualization of a couple between the tool of FIG. 33D, and the screw of FIG. 33C in accordance with some embodiments of the invention. Further, FIG. 33F illustrates a screwdriver coupled to a pedicle screw in accordance with some embodiments of the invention, FIG. 33G illustrates a top view of the screw of FIG. 33A in accordance with some embodiments of the invention, and FIG. 33H illustrates a top view of the screw of FIG. 33B in accordance with some embodiments of the invention. As shown, some embodiments include Allen key inset 3325, rigid single crossbar 3320, coupled threaded shaft 3305, and curved screw head 3315, where FIG. 33 A displays one embodiment of a screw that consists of an alien key inset 3325, a rigid crossbar 3320 that spans across the sidewalls of the screw head but allows for a gap above the inset, a threaded shaft 3305 and a curved screw head 3315 to accommodate mating with a tulip head. FIG. 33B displays another embodiment of the screw described in detail above in relation to FIG. 33A. The embodiment displays the screw head with two intersecting crossbars 3350, to enable interfacing with a different tool. It should be noted that the examples of screws portrayed in these figures only represent some embodiments of the invention. The crossbars can be of varying contour, number, and relative arrangement for each screw head. FIG. 33C displays an embodiment of the screw described previously in relation to FIG. 33B mated with a polyaxial tulip head 3365 with a cutout to interface with a rod 3375, and a thread 3370to receive a tightening cap.

[00352] FIG. 33D displays one embodiment of a tool designed to interface with the screw previously described in detail in relation to FIG. 33B. This tool consists of four mechanically- coupling extensions 3390 designed to engage with the screw head cross-bars via a quarter- turn. After performing a quarter-turn, the tool becomes rigidly fixed to the screw head and shaft. The end of the center shaft of the screw has a depressible sliding shaft 3393 that can be coupled to a tracked mobile stray marker (not shown) to indicate full engagement of the tool and screw, in a communication method previously described in detail in relation to FIG. 10A- 10E and FIG. 29A-29C. It should be noted that the center of the tip of this tool can also consist of a threaded shaft that is tightened down at the top of the tool (not shown) to push a sliding rod against the rigid cross bars of the screw head. In this way, the tool has increased fixation strength at the screw head interface. This threaded middle shaft can also be attached to a tracked mobile stray marker to indicate its position relative to a tracked DRF (not shown) mounted to the screwdriver. Further, FIG. 33E displays a transparency view the interface between the screw and screwdriver combination previously discussed in relation to FIG. 33C and FIG. 33D. From this view, the threaded screw shaft 3391, curved screw head walls 3318, and the mechanically-coupling extensions 3390 of the tool are visible as the two parts engage with one another. Further, FIG. 33F displays a different perspective of the screwdriver (3392 and crossbar equipped screw 3395interfacing with one another than that which was shown in FIG. 33E. From this perspective, the coaxial alignment of the screwdriver shaft with the screw shaft is appreciable. FIG. 33G displays an underside view of the cross-bar-equipped sere previously described in relation to FIG. 33B and this view highlights the circular cutout 3380 of the tulip head interfacing with the curved walls of the screw head.

[00353] Some embodiments include a tool or assembly to interface directly with the tulip heads of pedicle screws, in such a way that it rigidly fixes the rotating tulip head relative to the pedicle screw shaft, to then enable measurement and manipulation devices to act on the spinal elements to aid with alignment measurements and fixation as will be described in more detail below in reference to FIGS. 39A-39F, and 42A-42K.

[00354] FIG. 34 illustrates a tool for interfacing with a pedicle screw accordance with some embodiments of the invention. FIG. 34A displays a cross-sectional view interfacing directly with the threaded inserts of the tulip heads of pedicle screws. This figure displays a pedicle screw shaft 3410 (threading not shown), its associated tulip head 3420, the interfacing device's thread-tightening knob 3440, its sleeve body 3425, device body connection 3430, protruding tip 3423 to rigidly push towards the screw head, and inner shaft threading 3422 of the device. Tightening of the device through the thread-tightening knob 3440 leads the inner shaft threading 3422 to interface directly with the tulip head threads to cause the protruding tip 3423 to push against the screw head. Tightening in this way provides a rigid connection between the device, tulip head, and pedicle screw, such that the motion of the polyaxial tulip head has been restricted and all three parts coupled to one another. The device body connection 3430 displayed in this figure is designed to interface with a larger tool that will be described in more detail below in reference to FIGS. 39A-39D, 40A-40C, 41C, 42A42-F. It should be noted that the protruding tip displayed in this figure is only one embodiment of the device and other embodiments include but are not limited to cylindrical extrusion, spherical tip, and a non-rigid cylindrical extrusion coaxial or perpendicular to the inner shaft and coupled via rivet or other mechanism that enables its rotation about the axis of the inner shaft.

[00355] FIGS. 34B-34C display a non-cross-sectional, side view of the device described in relation to FIG. 34 interfacing with a pedicle screw. Visible are side-tab extensions 3421 that extend over the tulip head cutouts for interfacing with a rod. These side tabs extensions provide additional rigid interfacing between the device and the tulip head of the screw, further helping to rigidly fix the device, tulip head, and screw to one another.

[00356] FIG. 34D displays a cross-sectional view of the device described in relation to FIG. 34A interfacing with a pedicle screw. FIG. 34E displays a non-cross-sectional, rendered side view of the device described in relation to FIG. 34A interfacing with a pedicle screw. FIG. 34F displays a non-cross-sectional, rendered front view of the device described in relation to FIG. 34A interfacing with a pedicle screw.

[00357] FIGS. 35A-35F display an assembly or tool 3500 designed to interface directly with the tulip heads of pedicle screws, in such a way that it rigidly fixes the rotating tulip head relative to the pedicle screw shaft, to then enable measurement and manipulation devices to act on the spinal elements to aid with alignment measurements and fixation as will be described in more detail below in reference to FIGS. 39A-39F, and 42A-42K. This is an alternative embodiment from that previously described in detail in relation to FIG. 34A-34F. As shown, the tool 3500 comprises pedicle screw shaft 3510, tulip head 3503, drafted shaft advancement knob 3540, sleeve body 3525, device body connection 3530, protruding tip 3504, outer shaft threading 3535, protruding-tip advancement knob 3545, drafted pin 3546, retaining ring 3502, and expanding teeth 3527. In operations, after interfacing directly with the tulip head 3503, the drafted pin advancement knob 3540 leads the outer shaft threading 3535 to drive the expansion of the expanding teeth 3527 to interface directly with the tulip head threads. The retaining ring 3502 limits expansion of the device to prevent over stress, and the protruding tip advancement knob 3545 can then be tightened to increase the tension on the expanded teeth with the tulip head threads and thereby rigidly fix the device, tulip head, and screw shaft together. The device body connection 3530 displayed in this figure is designed to interface with a larger tool that will be described in more detail below in reference to FIGS. 39A-39F, and 42A-42K.

[00358] FIG. 35B displays a non-cross-sectional, front view of the device described in relation to FIG. 35 A interfacing with a pedicle screw. Visible in this figure are side-tab extensions 3529 that extend over the tulip head cutouts for interfacing with a rod. These side tabs provide additional rigid interfacing between the device and the tulip head of the screw, further helping to rigidly fix the device, tulip head, and screw to one another. FIG. 35C displays a non-cross-sectional, perspective view of the device described in relation to FIG. 35 A interfacing with a pedicle screw. FIG. 35D displays a cross-sectional, rendered view of the device described in relation to FIG. 35 A interfacing with a pedicle screw. FIG. 35E displays a non-cross-sectional, rendered front view of the device described in relation to FIG. 35 A interfacing with a pedicle screw. FIG. 35F illustrates a close-up perspective view of the tool of FIGS. 35A-35E without a coupled pedicle screw or tulip head in accordance with some embodiments of the invention. FIG. 35F displays a non-cross-sectional, rendered front view of the device described in relation to FIG. 35 A without the interfacing pedicle screw and tulip head. In this view, the expanding teeth and side tab extensions are more clearly visual. [00359] Some further embodiments include a tool or assembly able to interface directly with the tulip heads of pedicle screws via a quarter turn, in such a way that it rigidly fixes the rotating tulip head relative to the pedicle screw shaft, to then enable measurement and manipulation devices to act on the spinal elements to aid with alignment measurements and fixation as will be described in more detail below in reference to FIGS. 39A-39F, and 42 A- 42K. This is an alternative embodiment from that previously described in detail in relation to FIGS. 34-34F, and 35A-35F. For example, FIG. 36A displays a cross-sectional view of one embodiment of an invention for interfacing directly with the threaded inserts of the tulip heads of pedicle screws via a quarter-turn mechanism. This figure displays a pedicle screw shaft 3610 (threading not shown), its associated tulip head 3620, the quarter-turn knob 3635, its sleeve body 3640, device body connection 3645, protruding tip 3650 to rigidly push towards the screw head, protruding tip advancement knob 3637, side-tab extensions 3695, and quarter-turn retainer 3699. After inserting the device into the tulip head such that the threads are not engaged, the quarter-turn knob is rotated 90 degrees to engage the quarter-turn threads with the threads of the tulip head. After rotating 90 degrees, the quarter-turn retainer prevents excess rotation, to ensure the threading is engaged prior to increasing tension on the threads via tightening the protruding tip advancement knob. By tightening the protruding tip advancement knob, the protruding tip is driven directly against the head of the screw and increasing tension on the quarter-turn threads, thereby removing tolerance from thy polyaxial tulip head. In this way, this device rigidly fixes the tulip head and screw shaft together. The device body connection (e) displayed in this figure is designed to interface with a larger tool that will be described in more detail below in reference to FIGS. 39A-39F, and 42A-42K.

[00360] FIG. 36B displays a non cross-sectional, front view of the device described in relation to FIG. 36A interfacing with a pedicle screw. More clearly visible in this figure are side-tab extensions 3695, previously described in detail in relation to FIG. 35B. Also more clearly visualized in this figure is the quarter-turn retainer 3699, previously described in detail in relation to FIG. 36A. Further, FIG. 36C displays a non cross-sectional, side view of the device described in relation to FIG. 36A interfacing with a pedicle screw, and FIG. 36D displays a non-cross-sectional, perspective view of the device described in relation to FIG. 36A interfacing with a pedicle screw. FIG. 36E displays a non-cross-sectional, perspective view of the device described in relation to FIG. 36A interfacing with a pedicle screw, and FIG. 36F displays a cross-sectional, rendered view of the device described in relation to FIG. 36A interfacing with a pedicle screw. This figure displays the quarter-turn threads engaged with the tulip head threads. FIG. 36G displays a cross-sectional, rendered view of the device described in relation to FIG. 36A interfacing with a pedicle screw. This figure displays the quarter-turn threads disengaged from the tulip head threads. FIG. 36H displays a non- cross-sectional, rendered side view of the device described in relation to FIG. 36A interfacing with a tulip head (pedicle screw shaft not shown). FIG. 361 displays a non-cross-sectional, rendered front view of the device described in relation to FIG. 36A interfacing with a tulip head (pedicle screw shaft not shown).

[00361] Some embodiments include a device for interfacing directly with two implanted pedicle screws in such a way that it rigidly connects to the tulip head and removes tolerance between a polyaxial tulip head and pedicle screw such that the device is mechanically linked to a vertebra or other bony anatomy in which the screw(s) is/are inserted. For clarity, FIGS. 37A-37G do not include a tracked DRF and triggering mechanism, which can be attached to this device to allow it to provide quantitative data to the user while manipulating or holding the spinal elements, as will be described in more detail in reference to FIGS. 39A-39F, and 42A-42K. Embodiments of the invention comprising the assemblies of FIGS. 37A-37G may include various coupled components including a tightening knob 3740, handle 3705, width- adjustment mechanism 3707, guide rail (x2) 3723, tulip head side rests 3727, footplate 3710, and/or clamp release lever 3750. For example, FIG. 37A displays a back view of one embodiment of the invention designed to rigidly interface two screws already implanted into the spine or other bony elements. This embodiment is equipped with a tightening knob 3740, handle 3705, width-adjustment mechanism 3707, two guide rails 3723, tulip head rests 3727 to approximate the sidewall of the tulip heads, footplates 3710 to slide under the tulip head, and a clamp release lever 3750. Not shown (for clarity purposes) are tracked DRF, and tracked stray markers that can be applied to the device to make assessments of the tool's position and motion during use, as described in detail below in reference to FIGS. 39A-39F, and 42A-42K. Further, FIG. 37B displays a front view of one embodiment of the invention previously described in FIG. 37A. Visible from this perspective is the width-adjustment knob 3709, used to adjust the distance between the handle and the tulip head side rests. This viewpoint also provides the front perspective of the width-adjustment mechanism that enables the tulip head side rests to be drawn closer to or farther away from one another. Further, some embodiments include a screw-head interface protrusion 3760, and clamp 3749. For example, FIG. 37C displays a perspective view of one embodiment of the invention previously described in FIG. 37A in the closed position. Visible from this perspective is the screw-head interface protrusions 3760, the clamp 3749 used to securely fasten the device to the pedicle screws, and footplate 3710 to slide underneath the tulip head. This viewpoint displays a better view point of the guide rails 3723, which connects the handle and screw- interfacing arms. Further, FIG. 37E displays a rendered oblique side view of one embodiment of the invention previously described in FIG. 37A in the open position, and FIG. 37D displays a side perspective view of one embodiment of the invention previously described in FIG. 37A in the closed position. Visible from this perspective is the spring 3728 and over center spring structure 3732 in its collapsed position.

[00362] FIG. 37F displays a rendered oblique side view of one embodiment of the invention previously described in FIG. 37A in the closed position with detailed view of the device interfacing on one side with a tulip head 3770 attached to a pedicle screw shaft 3790 (threads not shown). From this perspective, the screw-head interface protrusion is seen engaging with the screw, and by tightly driving the screw head down while the footplate is pulling the tulip head upwards, the tolerance between a polyaxial tulip head and pedicle screw shaft is reduced, resulting in rigid fixation between the three structures. It should be noted that the design and geometry of the screw-head interface protrusion can have a number of embodiments including but not limited to a cylindrical extrusion, spherical head, and a pivoting lever arm.

[00363] FIG. 37G displays a rendered bottom view of one embodiment of the invention previously described in FIG. 37A. This perspective does not include the width-adjustment mechanism, to aid in visibility of the guide rails, and their cutout groove to enable applying a torque between the tulip head side rests and the screw-head interface protrusion. It should be noted that because the width-adjustment mechanism is not shown in this figure, the handle is not centered between the two screw head interfacing components of the device. In other embodiments of this device previously described, the width- selector mechanism ensures that the handle remains centered between the screw head interfacing components.

[00364] In reference to FIGS. 38, and 38A-38G, some embodiments include FIG. 38 include a pedicle screw shaft (represented without threads) with depth stop in accordance with some embodiments of the invention. Some embodiments enable assessment of the screw shaft location and pose when equipped with a polyaxial tulip head and with or without the presence of an already-implanted rod seated into the tulip head. The first aspect of the embodiment is a screw designed with a depth stop ring rigidly attached to the screw shaft at a location beneath the tulip head that still enables full mobility of the attached polyaxial tulip head. In some embodiments, the depth stop possesses a particular pattern that will interface with the second aspect of the embodiment, a tracked depth-stop assessment tool, in such a way that it allows for the interpretation of the screw shaft location and pose in 3D space, as well as indicate when the assessment tool is fully seated in the depth stop, to ensure assessment of the screw shaft location is only made when the tool is properly engaged. The indication method shown is via actuation of a tracked mobile stray marker, as previously described in detail in relation to FIGS. 10A-10G, 14A-14C, and 29A-29C, but can also be achieved by other methods including, but not limited to, hand actuation of a tracked mobile stray marker, covering or uncovering of a tracked stray marker, and electronic communication.

[00365] FIG. 38A illustrates a top view of the pedicle screw shaft with depth stop of FIG. 38 in accordance with some embodiments of the invention. For example, some embodiments include a pedicle screw with a shaft 3810 (threads not shown), a depth stop 3815 rigidly attached to the screw shaft and designed with a depth-stop mating pattern 3818, depth-stop mating holes 3817, as well as an interface for a polyaxial tulip head. In some embodiments, the depth-stop distance from the tulip head interface 3820 is designed to stop the screw against bony anatomy such that the polyaxial head maintains full mobility about its ball joint on the screw. In some embodiments, the depth stop as shown can be circular but can be designed to be of many shapes including interrupted and partial shapes to allow for better fitting within tight anatomical areas. In some embodiments, the mating pattern and mating holes on the depth stop are designed such that an assessment tool, described in detail below in relation to FIG. 38B-38G, is able to interface with the device and interpret the screw shaft location and pose, irrespective of the position of the tulip head relative to the screw.

[00366] FIG. 38B illustrates a screw interface region with coupled handle, with a partial view of an assessment tool designed to mate with the screw previously described in detail in relation to FIG. 38 A. The tool consists of a handle 3825, partial-cylinder screw interface region 3827, mating protrusions 3828, and spring-loaded (not shown) mating pins 3829. Further, FIG. 38C illustrates an example assembly view coupling between the screw interface region of FIG. 38B and the pedicle screw shaft with depth stop of FIGS. 38-38 A in accordance with some embodiments of the invention, and FIG. 38C displays the closer perspective of the screw, described previously in relation to FIG. 38A with the assessment tool, described previously in relation to FIG. 38B, aligned and ready to engage with the mating depth stop. In this image, the tulip head 3804 is visible attached to the top of the screw and an implanted rod 3803 is displayed engaged within the tulip head. In the position displayed, the assessment tool is not engaged with the rigid depth stop and therefore the mating pins are not depressed. It is not until the assessment device fully is seated into the depth stop that the spring-loaded mating pins are depressed and an associated tracked mobile stray marker (not shown) can be actuated to communication to the acquisition system.

[00367] Some further embodiments involve a combination of staggered heights and shapes of the depth-stop protrusions providing several unique permutations of height changes of TMSM linked to the probe. This could involve two TMSMs on the probe. The depth-stop design can be comprised of a radially-repeating pattern of two unique depth heights. This unique combination of heights, which is also sensitive to direction/order of height changes will interact with two mating pins of the probe and those will interact with one or two TMSMs that are subsequently actuated to specific heights along the probe shaft, each height signaling a unique screw identity or anatomical identity. In another embodiment, instead of two TMSMs, the two mating pins that get engaged at different depth stops can add up their depth differences mechanically against one lever that subsequently actuates a single TMSM to unique, identifiable height along the probe shaft.

[00368] FIG. 38D displays a front view of the screw, described previously in relation to FIG. 38A with the assessment tool, described previously in relation to FIG. 38B, aligned and fully engaged with the mating pattern on the depth stop. From this view it is apparent that the partial-cylinder screw-interface region allows for engagement of the assessment device with the screw, regardless of the position of the polyaxial tulip head and/or rod attached. FIG. 38E displays a back view of the screw, described previously in relation to FIG. 38A with the assessment tool, described previously in relation to FIG. 38B, aligned and fully engaged with the mating pattern on the depth stop. FIG. 38F displays a side view of the screw, described previously in relation to FIG. 38A with the assessment tool, described previously in relation to FIG. 38B, aligned and fully engaged with the mating pattern on the depth stop.

[00369] FIG. 38G displays a perspective view of the screw, described previously in relation to FIG. 38A with the full assessment tool, described previously in relation to FIG. 38B, aligned but unengaged with the depth stop of the screw. Visible in this figure is the tracked DRF 3870 attached to the tool handle for a 3D-tracking camera to acquire the location and pose of the assessment tool, a tracked mobile stray marker 3875 and a groove 3880 for the mating pins to slide up and down to actuate the stray marker. One example embodiment for the linear actuation mechanism for the mating pin depressible shaft coupled to the TMSM is a slot 3885 for the TMSM above or near the handle. It should be noted that the location of the tracked mobile stray marker can be positioned anywhere on body of the tool and actuation related to the mating pins can be achieved via linear motion (as shown), rotational motion, or a combination thereof. It should also be noted that other embodiments of the device can contain more than one tracked mobile stray marker, paired to individual spring-loaded mating pins to indicate tool engagement with the screw or to communicate other states to the acquisition system. Once the assessment tool is firmly engaged with the screw depth-stop mating pattern, the acquisition system calculates the location and pose of the screw based on the screw's known geometry and known mating geometry of the tool- screw combination.

[00370] Some embodiments include a device that can be used to assess the intraoperative flexibility of the spine with two mountings to rigidly interface with implanted pedicle screws, (as previously described in relation to FIG. 33A-33H, FIG. 34, FIG. 35A-35F, and FIG. 36A- 361). After rigidly fixing two tools, each to individual spinal levels, the spine can be manipulated via directly pushing on body surfaces or indirectly by interacting with the tool's handles to establish a range of motion between the spinal levels onto which the tool's are engaged. The range of motion can be displayed to the user on a display monitor via 3D mobility or 2D projection onto relevant anatomical planes, as described in more detail below in reference to FIG. 70. Furthermore, after adjusting two or more spinal levels to a desired relative orientation using this tool, another embodiment will be described in which the tools can lock together to temporarily hold the anatomy in that configuration prior to the insertion of a rod, as will be described in more detail in reference to FIG. 42A-42K.

[00371] FIG. 39A displays a full perspective view of a device 3900 used for manipulating bony anatomy and assessing range of motion intraoperatively. In some embodiments, two devices can be used at once, such that each securely fasten onto a level of the spine and move each level relative to one another while being tracked in 3D space to assess the achievable ranges of alignment between the two or more segments with coupled devices. One embodiment of the device consists of a tracked DRF 3905 (with markers 3907) for a 3D- tracking camera to interpret its location and pose in 3D space, an adjustable handle 3910, width-adjustment knob 3911 equipped with a tracked stray marker 3913 to enable the acquisition system software to interpret the angle of the handle relative to the tool end- effectors based on distance between the tracked DRF and this marker, width-adjustment mechanism 3920, a retractable spring plunger 3915 to allow for the handle to lock into discrete preset angles, sleeve bodies 3930 for housing the screw-interface component of the tool, thread-tightening knobs 3909 for tightly interfacing with tulip heads as described in detail previously in relation to FIGS. 34, 34A-34F, 35A-35E, and 36A-36G, and tracked stray markers 3908 for labeling the location of the screw interface component of the device. It should be noted that this is one embodiment of the device and that in other embodiments the angle of the sleeve bodies relative to the width-adjustment mechanism can either be adjustable or fixed at varying angles to accommodate the pedicle screws with which the tool will interface. It should also be noted that the handle of the tool can be outfitted with a spring-loaded trigger to actuate the motion of the tracked mobile stray marker, used to indicate its active state to the acquisition system, as will be described in more detail in reference to FIG. 39B. It should also be noted that other embodiments of the tool can possess varying numbers of tracked stray markers over the width-adjustment knob or screw-interface component of the tool.

[00372] FIG. 39B displays another embodiment of the handle of the tool described previously in relation to FIG. 39A in which it is equipped with a TMSM 3956 coupled to a spring-loaded trigger 3950 via a sliding shaft 3959. With this embodiment, the user is able to communicate to the acquisition system that the probe is in an active state, during which its coordinates can be recorded, by actuating the TMSM relative to the tracked DRF on the tool, as described previously in detail in relation to FIGS. 10A-10G and 29A-29D. Additionally, other embodiments of this tool are designed for it to be used with one or more additional flexibility assessment device, each equipped with uniquely identifiable tracked DRFs, so that their relative motion is able to be recorded while adjusting patient positioning, as described below in reference to FIGS. 40A-40C, and 42A-42K.

[00373] FIG. 39C displays a bottom view of the embodiment described above in relation to FIGS. 39A-B. From this view, the width-adjustment mechanism 3920 is visualized (with linear gears 3922, 3924, which allows for adjustment of the distance between the screw- interface components of the device to accommodate varying locations of screw with which it will interface. FIG. 39D displays a cross-sectional side view of the tool describe previously in relation to FIGS. 39A-C. From this perspective, the retractable spring plunger 3993 is visualized, engaged within one of the detents at discrete angles 3934 for adjusting the angle of the tool's handle. In this way, the tool handle can be adjusted such that it does not interfere with additional tools placed within the surgical site, as described below in relation to FIGS. 40A-40C, and 42A-42K. It should be noted that this is only one embodiment of the handle, in which it is joined at the middle of the width adjustment mechanism. In other embodiments, the tool's handle is joined at an off-center location on the width-selection mechanism, and in other embodiments, the tool's handle projects at non-orthogonal angles to the width- adjustment mechanism to allow for enhanced tracking-camera visibility of the tracked markers on each tool.

[00374] FIG. 39E displays a bottom view of the width-adjustment mechanism 3920 that allows for variation in the distance between screw-interface locations of the tool. Further, FIG. 39F illustrates a close-up perspective of the width-adjustment mechanism 3920, thread- tightening knobs 3909, and sleeve body 3930 of the device as described above in relation to FIGS. 39A-E in accordance with some embodiments of the invention.

[00375] Some embodiments can be equipped with the quarter-turn tip as described in relation to FIGS. 33A-33H to mate with the screws described. Other embodiments of the device include variations in the screw interface components such that they are able to mate with crossbar-equipped screws, as previously described. For embodiments interfacing with screws of this design, the screw-interface components are designed with the quarter-turn mechanism previously described in relation to FIGS. 3B, 33D-33F, and 44D.

[00376] FIGS. 40A-40C display the application of the flexibility assessment device previously described in detail in relation to FIGS. 39A-39E, as a applied to an anatomical model of the spine. The figures show the application of the device as applied across spinal levels Ll-Sl . Because the assessment device tools both contain tracked DRFs, their pose is tracked during motion such that the maximum and minimum angles as well as positions can be recorded and displayed to the user. Furthermore, other embodiments of this device allow for the relative position of two or more of these devices to lock to one another and allow for the insertion of hardware to fix the spine into that conformation, as described below in reference to FIGS. 41 A-41C, and 42A-42K. [00377] FIG. 40 A illustrates a lateral view of a spine model with a straight curve, and two flexibility assessment tools engaged with the model in accordance with some embodiments of the invention. FIG. 40A displays a straight curve 4010a, and two flexibility assessment tools engaged with the model (4075a, 4075b) and screw-interface component 4015. In this non- limiting embodiments, the user's hand 4008 interfaces with each tools' handle 4077a, 4077b and each tool is equipped with a unique tracked DRF (4076a, 4076b) to enable tracking of their location and pose in 3D space by a 3D-tracking camera (not shown). In this embodiment, the width and height between the screw-interface components are fixed. Within this configuration, when the assessment devices are activated, their relative 3D angles can be calculated, and projected onto anatomical reference planes. In FIG. 40 A, the angle between handles shown is 10 degrees, which can be displayed to a user as the maximum limit of spine flexion.

[00378] FIG. 40B displays one embodiment of two flexibility assessment devices (4076a, 4076b) interfacing with a spine model with a lordotic curve 4010b. 3D-tracking acquisition systems can display relative angles and positions to a user, as described above in relation to FIG. 40A, and as applied to this embodiment, can display the maximum limit of spine extension to be 45 degrees. Further, FIG. 40C displays an embodiment of the invention from a 3D-tracking camera (not shown) perspective. Both tool's unique tracked DRFs 4076a, 4076b are shown, as well as the mirrored angles of the handles relative to the screw-interface components of the device. Different embodiments of the device position the handles at varying angles to the width adjustment mechanism, and also possess spring-loaded triggers (not shown), to communicate the probe's active state to the acquisition system, as described above in relation to FIG. 39B.

[00379] FIGS. 41A-41D displays an embodiment of the flexibility assessment device, described previously in detail in relation to FIGS. 37A-37G, and 40A-40C, equipped with detachable components to allow for the removal of the tool handle and body without detaching the screw-interface components. The removal of the handle allows for retaining rigid fixation on the screws while regaining workable space within the surgical site. It also enables utilization with locking the alignment into a certain configuration on one side, removing the handle and body of the device, and then placing a rod to secure the spine in that configuration, as will be described in detail below in FIG. 42A-42K. [00380] Referring to FIG. 41 A, illustrating a side view of one embodiment of the screw- interface components of the flexibility assessment device described previously, where a detachable component of the screw-interface devices mates with the bottom component via spring-loaded snap arms 4105 that can be released by pressing the release tabs 4110. The top component contains a post 4115 for the thread-tightening knob (not shown) previously described in relation to FIGS. 34, 34A-34F, 35A-35F, and 36A-36I. The mating interface of the two components contains a center-alignment post 4120 and peripheral alignment pins 4125 to facilitate alignment and enable rigid mating of the components.

[00381] FIG. 4 IB displays a front view of the embodiment described above in relation to FIG. 41A. This view of the embodiment displays (partially) the screw-interface rod 4130 intended to interface with the top surface of the pedicle screw thread to interface the tulip head 4135, side-tab extensions 4140, snap-arm mating detent 4145, and spring-loaded snap arm 4105. Further, FIG. 41C illustrates the device of FIGS. 41A-41B assembled with a flexibility assessment device previously described in relation to FIGS. 39A-39F, and 40A- 40C in accordance with some embodiments of the invention. For example, FIG. 41C displays an embodiment of the device in which the detachable screw-interface components previously described in relation to FIGS. 41A-B are assembled with a flexibility assessment device previously described. In this embodiment, one side of the flexibility assessment device is equipped with a detachable screw-interface component, and the other is equipped with a non-detachable component, as described in FIGS. 34, 34A-34F, 35A-35E, and 36A- 361. For example, the screw-interface rod 4130 is visible on the non-detachable screw interface component, as is the thread to interface tulip heads 4135. The side-tab extension 4140, snap-arm mating detent 4145, and spring-loaded snap arm 4105 are visualized on the detachable screw-interface component. Further, on the flexibility assessment device, previously described in relation to FIGS. 39A-39B, and 40A-40C, the tracked DRF 4150, handle 4160, retractable spring plunger 4165, width-adjustment knob 4170, TSM 4175 for width-adjustment knob, thread-tightening knob 4178, TSM 4182 for thread tightening knob, width-adjustment mechanism 4184, and sleeve body 4186 are all displayed. Additionally, the detachable screw interface component is shown interfacing with a tulip head 4192 attached to a pedicle screw (threads not shown) shaft 4188.

[00382] FIG. 4 ID displays a perspective assembly view of one embodiment of the detachable screw-interface component displaying the release tabs 4110, center-alignment post 4120, peripheral alignment pins 4125, screw-interface rod 4130, side-tab extensions 4140, and spring-loaded snap arm 4150.

[00383] Some embodiments include an assessment device equipped with detachable screw interface components and adjustable cross-linking devices. For example, in reference to FIGS. 42A-42C, some embodiments include a spinal flexibility assessment device as described above in relation to FIGS. 39A-39F, 40A-40C, and 41A-41D, equipped with a fixation mechanism, described below in reference to FIGS. 43A-43F, that allows for the flexibility assessment devices to be locked in a particular position, and removed from one side to accommodate the placement of a fixation rod on the contralateral side. In this way, the user can position the spine into a desired conformation with feedback from the 3D tracking acquisition system tracking the location of each flexibility assessment device. It should be noted that the feedback displayed to the user can either be relative positioning of the tools, or relative positioning of initialized vertebra, as described in detail below in reference to FIG. 70.

[00384] One non-limiting embodiment is shown in FIG. 42A, and shows the flexibly assessment device 4201, as described previously equipped with detachable screw interface components with adjustable cross-linking devices. This embodiment of the device includes a width-adjustment mechanism 4205 (e.g., 4170 of FIG. 41C) to match the distance between screw-interface components with the distance between implanted pedicle screws and their associated tulip heads 4225. As shown, this embodiment is intended to be used after the pedicle screws have been placed into the spine 4210 during surgery. In other embodiments (not shown), this device can be equipped with a bone-clamping mechanism that enables it to rigidly fix to the spine in the absence of pedicle screw and tulip heads with which to interface.

[00385] Further, FIG. 42B illustrates the flexibility assessment device described previously in relation to FIG. 42A rigidly coupled to the pedicle screws by interfacing with the tulip heads in accordance with some embodiments of the invention, and shows thread- tightening knob 4209. Illustrated is the flexibility assessment device, where the screw interface components can rigidly couple to the tulip heads via the thread-tightening-knobs 4209. When they are tightly coupled to the tulip heads, the tolerance between the pedicle screw shaft and polyaxial tulip head is removed, thus resulting in a rigidly fixed system between the screw shaft, tulip head, and flexibility assessment device. [00386] Further, fIG. 42C displays a second flexibility assessment device (4202) interfacing with a spinal level at a user-defined distance from the already mated device (4201) described previously. Because both assessment devices possess unique tracked DRFs, the 3D-tracking acquisition system is able to distinguish them from one another. Further FIG. 42D displays the two mated flexibility assessment devices 4201, 4202. After the devices are rigidly attached to the spine, their handles can be adjusted relative to their screw- interface components by releasing and subsequently re-engaging the retractable spring plunger 4165 to enable greater degrees of freedom without the devices obstructing one another. The 3D acquisition system interprets the position of the handle by comparing the individual tool's tracked DRF to the location of the TSMs located over the corresponding tools' width-adjustment mechanism or screw-interface components. Furthermore, in this embodiment, after the assessment devices are rigidly fixed to the spine through mating with screws, they can be placed in an active state by user-triggering, and then manipulate the contour of the spine until the user is satisfied with the software-displayed measurements. The relative contour of the spine between devices can then be held in place by utilization of adjustable cross-linking devices, described below in reference to FIGS. 42E-42I, and 43A- 43D.

[00387] FIG. 42E displays two flexibility assessment devices rigidly attached to the spine as described previously in relation to FIGS. 39A-39F, 41A-41D, and 42A-42D. When the devices are positioned in a way such that the spine 4210 is held in a desirable contour, they can be locked together utilizing adjustable cross-linking devices 4250 attached to the width- adjustment devices 4201, 4202. Further, FIG. 42F illustrates two flexibility assessment devices 4201, 4202 rigidly attached to the spine 4210, further inclujding an adjustable cross- linking device for screw-interface device 4255. For example, in addition to rigidly connecting the devices between the width-adjustment mechanisms, the screw-interface components can also be rigidly fixed to one another via the adjustable cross-linking devices 4255. FIG. 42G illustrates an instrumented spine previously described in relation to FIGS. 42A-F in accordance with some embodiments of the invention, and shows adjustable cross- linking device for screw-interface device 4255 coupled to the spine 4210. In this instance, the detachable screw-interface components, as described enable the body and one screw- interface component of the assessment device can be removed to leave behind two screw- interface components, held in place by the connecting adjustable cross-linking device 4255. [00388] FIG. 42H displays an instrumented spine 4210 previously described in relation to FIGS. 42A-42G. With the spine 4210 held in a fixed contour, the removed components of the flexibility assessment devices allow for the placement of a rod 4269 within the exposed set of screws. Further, FIG. 421 illustrates an instrumented spine previously described in relation to FIGS. 42A-42H in accordance with some embodiments of the invention. The rod placed within the exposed set of pedicle screws is secured in place with cap screws 4271. With the rod holding the spine 4210 in the desired contour, the remaining screw-interface components are now able to be removed. Further, FIG. 42J displays an instrumented spine 4210 previously described in relation to FIGS. 42A-42I. With the contour of the spine held in place with the already-secured rod 4269b, the remaining components of the flexibility assessment device is removed, enabling placement of a second rod 4269a within the screws. Further, FIG. 42K displays an instrumented spine previously described in relation to FIGS. 42A-42J. This figure displays the final step of securing the pre-set alignment of the spine achieved with flexibility assessment devices. During this step, the second rod is secured with cap screws 4271.

[00389] FIG. 43A displays a top view of one embodiment of the device 4300 which is an adjustable cross-linking device, a described above in relation to FIG. 42A-42K, mates with components of the flexibility assessment device, as described previously in relation to FIGS. 39A-39F, 40A-40C, 41A-41D, and 42A-42K. This embodiment consists of an outer-slider ball socket 4301 designed to mate with protruding balls on components of the flexibility assessment device including the width-adjustment mechanism, as described previously in relation to FIGS. 39A-39F, 40A-40C, 41A-41D, and 42A-42K, and the screw-interface components of the device, as described previously in relation to FIGS. 34-36, 41A-41D. This embodiment also contains a retractable spring plunger with teeth 4303 that engages with an internal rack with teeth 4304. Additionally, there is an inner-slider ball socket 4306 designed to mate with a secondary flexibility assessment device component, as described previously in FIG. 42A-42K.

[00390] FIG. 43B displays a bottom view of one embodiment of the device 4300, shown previously in FIG. 43A, which is an adjustable cross-linking device, a described above in relation to FIG. 42A-42K. From this perspective, the outer-slider ball socket 4301, internal rack with teeth 4304 and inner-slider ball socket 4306 are all visible. In order to adjust the length of the adjustable cross-linking device, a user depresses the retractable spring plunger with teeth such that it disengages from the internal rack with teeth. When the length is as desired, the user releases the retractable spring plunger with teeth such that it re-engages with the internal rack with teeth 4304. FIG. 43D illustrates a retractable spring plunger 4303 with teeth 4304, outer-slider set screw 4320, and inner-slider set screw 4322.

[00391] FIGS. 43E and 43F shows an adjustable cross-linking device 4333, described previously in relation to FIGS. 42A-43K, 43A-43D, engaged with detachable screw-interface components (shown here as 4335a, 4335b, and adjustably coupled through coupler 4380, with rotation balls or joints 4381) of the flexibility device previously described in relation to FIG. 41A-41C. As shown, coupled components can include fixation ball 4330a, 4330b, snap- arm mating location 4345a, 4345b (e.g., shown previously in relation to FIG. 4 IB as snap- arm mating detent 4145), peripheral alignment pin(s) 4350a, 4350b, pedicle screw shaft 4355a, 4355b, and tulip heads 4360a, 4360b. In this embodiment, the detachable screw- interface devices 4335a, 4335b possess a fixation ball 4330a, 4330b to interface with the inner and outer-slider ball sockets, a snap-arm mating location 4345, and peripheral alignment pins 4350a, 4350b. Further, screw-interface components are engaged with the tulip heads 4360a, 4360b of pedicle screw (threads not shown) shafts 4355a, 4355b.

[00392] Some embodiments include a bone-implanted fiducial equipped with a rigid crossbar that rigidly mates with a tracked probe equipped with a TMSM to indicate to the acquisition system when it is fully engaged. Because the probe is only able to mate with the fiducial in one conformation, when the tracked probe fully engages with the fiducial, the location and pose of the fiducial can be interpreted. If the fiducial has been previously initialized to the vertebra, reassessing the location and pose of the fiducial enables re- registration of the location and pose of the vertebra. Furthermore, if the fiducial is placed under surgical navigation, interfacing the probe with the fiducial enables rapid re-registration of bony anatomy for surgical navigation cases, providing value when anatomy moves relative to a reference DRF or when the anatomy changes conformation from when its imaging was last registered for surgical navigation. In this way, the bone fiducial serves as another method of rapid re-registration of anatomy, as described in FIGS. 38, and 38A-38G. For example, FIG. 44A illustrates a bone-implanted fiducial equipped with a crossbar and rigidly fixed to the lamina of a vertebra as previously described in relation to FIGS. 3A-3C in accordance with some embodiments of the invention. The bone-implanted fiducial 4410 is equipped with a rigid crossbar 4412 and rigidly fixed to the lamina 4401 of a vertebra 4400 as previously described. Further, FIG. 44B illustrates a process view 4401 of a pre- engagement of a bone-implanted fiducial 4410 and bone-fiducial mating screwdriver 4450 equipped with a tracked DRF 4420 and a TMSM 4415 coupled to a depressible sliding shaft at the end of the screwdriver in accordance with some embodiments of the invention. This embodiment is an alternative to other embodiments used to interpret the location and pose of a vertebra in space, as previously described in FIGS. 3A-3C, 29A-29C, 33A-33H, and 38, 38A-38G. In this embodiment, the probe tip (4450a) is equipped with a quarter-turn mechanism to tightly engage with the bone-implanted fiducial. By fully engaging with the crossbar on the fiducial, the depressible sliding shaft is actuated to move the attached TMSM and thereby signal to the 3D-tracking acquisition system to record the coordinates of the screwdriver, and calculate the location and pose of the implanted-bone fiducial, and associated vertebra if it has been initialized. For example, FIG. 44C illustrates an engagement of a bone-implanted fiducial and bone-fiducial mating screwdriver equipped with a tracked DRF and a TMSM coupled to a depressible sliding shaft at the end of the screwdriver, and FIG. 44C displays the bone-fiducial mating screwdriver 4450 engaged with the bone-implanted fiducial 4410. When fully engaged, as shown, the bone-fiducial mating screwdriver 4450 is aligned coaxially with the bone-implanted fiducial 4410, and the TMSM 4415 is actuated, indicating to the acquisition system that the screwdriver tip 4450a is fully engaged with the bone-implanted fiducial. Further, FIG. 44D illustrates a bone-implanted fiducia with crossbar and overlying bone-fiducial-mating screwdriver in accordance with some embodiments of the invention. In some embodiments, a quarter-turn mating tip 4455 and depressible sliding shaft 4450b. In some embodiments, the quarter-turn mating tip 4455 is shown as is the depressible sliding shaft 4450b which is depressed upon complete engagement between the screwdriver 4450 and fiducial 4410 (engaging around cross-bar 4412). It should be noted that in other embodiments, the acquisition system can be triggered to calculate the location of the fiducial, based on user-input to the software and hand- triggering a TMSM or electronic communication system, and can be used for rapid re- registration of a vertebra's location within camera coordinates prior to rod implantation, as described below in FIGS. 45A-45B, and 72.

[00393] Some embodiments include rapid re-registration with depth stop screws and depth stop engaging screw-assessment tool. For example, some embodiments include a system and method to enable rapid re-registration and 3D-rendering of vertebra's relative location in space by utilizing a depth-stop equipped pedicle screw and depth-stop engaging assessment tool, as previously described in relation to FIGS. 38, and 38A-38G. In this embodiment, the depth stop attached to the screw can be accessed by the depth-stop engaging assessment tool, with or without an implanted rod present, to accurately calculate the location and pose of the screw in 3D-tracking camera coordinates. If screws were initially placed under image guidance, the acquisition system has already stored and recorded the relative position of each screw to the vertebra in which they are implanted. With this information, after re-registering the new location of both screws in space, the acquisition software is able to reconstruct the location of the vertebra in which they are inserted. In this way, if a surgical navigation system becomes decoupled from the patient's anatomy, either through movement of the tracked DRF serving as a patient reference or through change in contour of the spine from the time the image was acquired, the system can be rapidly re-registered to the patient's current position in space.

[00394] FIG. 45A displays one embodiment of the invention in which two vertebra 4525a, 4525b are instrumented with depth-stop-equipped pedicle screws 4540, described previously in relation to FIGS. 38, 38A-38G, which can be registered in 3D space by having the depth- stop-engaging tracked tool 4505 interface with each screw on each vertebra. If the screws were initially placed under surgical navigation, and the position of the screw shafts relative to the vertebrae are known, then assessment of screw shafts' location and pose for each vertebra, is able to yield a 3D rendering of each vertebra (shown as representations 4561, 4562) in space relative to one another. It should be noted that utilizing depth-stop-equipped pedicle screws and their associated assessment tool, is only one embodiment of obtaining the information needed for the software to make this assessment. Other embodiments include mating directly with screw heads to interpret their location and pose, as previously described in FIG. 29A-29C, and FIGS. 33A-33H. In cases when an assessment of the screw, and thereby vertebrae locations are desired after implantation of a rod, the depth-stop-equipped pedicle screws preserve access to the screw shaft with the assessment tool. Further, FIG. 45B shows one embodiment of the invention previously described in FIG. 45A, in which case the position of vertebra #1 4525c has changed relative to that of vertebra #2 4525b. By engaging the depth-stop-equipped tracked assessment tool, into both depth stop-equipped pedicle screws 4540 in vertebra 4525c and vertebra 4525b, the acquisition system's software can then reconstruct a rendering 4563 on the display monitor of each vertebra in their relative position to one another. [00395] In some embodiments, the probe depicted in FIG. 38, used to update 3D renderings of a vertebra via re-registration of screws can also be updated via mating with a bone fiducial, depicted in FIGS. 3A-3C and 44A-44D. Other embodiments include mating directly with bone-mounted, percutaneous, or skin-mounted fiducials that are initialized to anatomical landmark(s) of interest for 3D renderings

[00396] Some embodiments can enable significantly reduced x-ray and radiation exposure during minimally invasive surgeries and procedures. In some embodiments, tracked surgical tools are able to be placed in the field of view of previously-acquired x-ray images, such that their projected contour can be displayed over anatomy visualized in a previously-acquired x- ray image. The acquisition software interprets the location of the tool surface relative to the x-ray emitter/detector and using that information is able to accurately display a real-time overlay of the tools' position on the previously acquired x-ray image, accounting for the appropriate size scaling of the tool's outline, as described below in reference to FIG. 71.

[00397] FIGS. 46A-46B illustrate a 3D tracking tool in accordance with some embodiments of the invention. In this embodiments, a 3D-tracked tool 4600 includes a handle 4610, tracked DRF 4605 (with marker 4607) and tool tip 4620. It should be noted that in other embodiments of this invention, each mobile component of the surgical tool that is used, requires 3D-tracking relative to each of the other components within said tool. FIG. 46C displays one embodiment of the invention in which an x-ray emitter 4684 is equipped with a tracked DRF 4686 positioned in a known location relative to the emitter, and the x-ray detector 4682 can also be equipped with a tracked DRF 4699 positioned in a known location relative to the detector. With the x-ray system imaging a spine 4691 resting on an operative table 4683, the x-ray emitter produces a conical volume of its x-ray beam 4695. All objects within this conical volume are then projected onto the x-ray detector 4682. With known geometry of the x-ray system 4680, the location and pose of this conical volume (4695) is known relative to either of the tracked DRFs mounted to the x-ray system. With a 3D- tracking camera having recorded the location of the emitter, and thereby the conical imaging volume, when an x-ray is taken, the acquisition system can determine when any component of the tracked surgical tool enters within the volume. When the surgical tool 4689 is positioned within the volume, its virtual projection can be overlaid on the previously- acquired x-ray image, as shown in FIG. 46D. The proximity of the tracked tool's surface to the emitter, enables the acquisition software to determine its relative size scaling in the overlay image, as described below in reference to FIG. 71.

[00398] FIG. 46D illustrates a virtual overlay of a tracked surgical tool positioned close to the x-ray detector on top of an x-ray image of the spine in accordance with some embodiments of the invention. As shown, the X-ray image of spine 4601 includes an overlay image of surgical tool close to detector 4615a. This virtual overlay is updated in real-time as the tool moves relative to the previously acquired x-ray's conical volume as described below in reference to FIG. 71. FIG. 46E displays an embodiment of the invention previously described in FIG. 46C, with the tracked surgical tool 4689 positioned closer to the x-ray emitter. Further, FIG. 46F displays a virtual overlay of a tracked surgical tool (x-ray 4602), 4620a positioned close to the emitter, as shown in FIG. 46E. Because the tool's surface is located closer to the x-ray emitter, its virtual projection is scaled to be larger to match the case of if a real x-ray image was acquired of the tool in that position. The software interpretation of the tool's relative scaling size is described below in reference to FIG. 71. Further, FIG. 46G displays a virtual overlay of a tracked surgical tool (overlay image of surgical tool close to emitter, turned 90 degrees, (x-ray 4603) 4620b, from the tool position previously described in FIGS. 46E-46F. In this way, the tool's real-time location in space relative to the previously acquired x-ray volume, can be displayed via an overlay onto the previously acquired x-ray image.

[00399] Some embodiments include components that make up the two-part system for a handheld mechanism of assessing the contour of the rod prior to implantation. For example, FIG. 47A displays components of an embodiment of a tracked end cap, used to rigidly hold the rod, define anatomical reference planes relative to the 3D-tracking camera, and establish the coordinate system within which all coordinates of the rod's location will be recorded. Further, FIG. 47B displays components of an embodiment of a tracked slider, used in combination with the tracked end cap, to slide along the surface of a rod and interpret its coordinates within the coordinate system established by the tracked end cap, as described in detail below in reference to FIG. 74. As shown, some embodiments include an end cap handle 4720, mount 4722 for interfacing with the mount-mate 4714 containing anatomical axes reference arrow labels consisting of, but not limited to inferior 4718 and posterior 4719. This embodiment also consists of a rod mount hole 4712 to insert a rod and a threaded hole 4716 for a set screw to secure the rod in place relative to the end cap, a mounting platform 4710 for a tracked DRF, a tracked DRF 4730, and fasteners 4740. Some embodiments utilize a separate, tracked DRF, but in other embodiments, the DRF-based markers mount directly into the tool surface itself, as described below in reference to FIGS. 52A-52B, and 53A-53F. Furthermore, other assembled embodiments of this invention are shown below in reference to FIGS. 48A-48B, 49D, 50E, 51A-51C, 51H-51I, and 56A-56F.

[00400] FIG. 47B displays the components of one embodiment of a tracked slider, designed to interface with a rod fixed to a tracked end cap, described previously in relation to FIG. 47A. This embodiment of the slider consists of a handle 4770, mount 4772 for joining with the mount-mate 4797, a rod-centering fork 4798 designed to straddle and center the rod during acquisition of the rod's contour, a through hole 4784 for receiving a depressible sliding shaft 4786 that mates with a TMSM mount 4754 via a fastener 4790 and is spring- loaded 4795. This embodiment also consists of a DRF mount 4760 to receive a tracked DRF 4780and a TMSM 4753 attached to its corresponding mount. Other embodiments of this device are described below in reference to FIGS. 51D-51I. It should be noted that other embodiments of the rod-centering fork component, meant to interface with the rod, are ring- shaped designs meant to accommodate specific rod diameters, adjustable diameter rings, U- shaped designs, and polygonal-shaped designs including but not limited to triangular, rectangular, pentagonal etc.

[00401] FIGS. 48A-48C relate to the tracked end cap previously described in relation to FIG. 47A. This embodiment is equipped with a spring-loaded tracked mobile stray marker actuated by a trigger on the handle used to communicate with the 3D-tracking acquisition system. Additionally, it contains an alternative method of fixing the rod than a set screw which was previously described in FIG. 47A. In this embodiment, the rod mount hole is split and tightened by the combination of a cam lever and threaded fastener for more rapid exchange and fixation of rods with the end cap. For example, FIG. 48A illustrates a close-up view of a portion of an end cap in accordance with some embodiments of the invention, showing an assembly comprising rod mount hole 4824, rod 4805, end cap handle 4830, cam lever 4823, hinge pin 4821, and threaded fastener 4825. The rod 4805 is inserted into the rod mount hole 4824 and secured in place by a cam lever 4823 rotating about a hinge pin 4821 to tighten against a threaded fastener 4825.

[00402] FIG. 48B illustrates a perspective view of an end cap 4800 assembled from components of FIG. 47A in accordance with some embodiments of the invention, and shows a rod 4805, trigger 4833, spring-loaded hinge 4831, trigger arm 4841, TMSM 4819, and end cap tracked DRF 4815, 4817. The perspective shows the end cap previously shown in FIG. 47A, in which a rod 4805 is fixed. This embodiment also contains a hand-actuated trigger 4833 that rotates about a spring-loaded hinge 4831 inside the handle 4830, to actuate a trigger arm 4841 with a coupled TMSM 4819. This embodiment also contains a tracked DRF 4815 used to interpret the location of the end cap and its attached rod via a 3D-tracking camera (not shown). The location of the TMSM actuated by the trigger on this embodiment is compared to the location of the tracked DRF by the acquisition software, to determine if the user is triggering the device, as described in more detail below in reference to FIGS. 64A- 64B, and 65A-65E. It should be noted that in other embodiments of this device, the trigger can be actuated via other mechanisms such as covering or uncovering a tracked marker, as described previously in relation to FIG. 14, using linear motion rather than rotational, as described previously in relation to FIGS. 10A-10G, 29A-29D, 38, 38A-38G, 39A-39F, 42A- 42K, 44A-44D, and 45A-45B, using electronic communication, or via direct user-input to a display monitor interface. Further, FIG. 48C illustrates a side view of the end cap 4800 of FIG. 48B in accordance with some embodiments of the invention. This perspective shows a rod 4805 fixed inside the end cap handle 4830, equipped with a trigger 4833 rotating on a spring-loaded hinge 4831 and mounting a TMSM 4819 on the trigger arm 4841. This figure also displays the tracked DRF 4815 used for interpreting the end caps location and pose in 3D space, and two relative anatomical axes indicators with inferior 4849 and posterior 4843 shown. This embodiment can be applied to any application mentioned below with regards to a tracked DRF-equipped end cap, in reference to FIGS. 49D, 50E, 51H-51I, 56, and 87A.

[00403] Some embodiments of the invention can be used to assess the contour of a rod prior to implantation via coupling an embodiment of a tracked end cap, previously described in FIGS. 47 A and 48A-48C, with a fixed-base, single-ring assessment device. Rather than utilizing two handheld tools to assess the rod contour, as previously described, this device enables rod contour assessments via mounting the rod to one handheld end cap and passing the rod through a rigidly fixed ring device. Because the diameter of the ring is designed or adjusted to be closely matching the diameter of the rod, this embodiment forces the portion of the rod engaged with the ring to be nearly concentric with the ring. To compute the contour of the rod from this embodiment, the acquisition system interprets the path traveled by the end cap, rather than the path traveled by the slider relative to the end cap, as previously described. The software interpretation of this invention is described in detail below in reference to FIG. 75.

[00404] FIG. 49A displays assembly 4900 used to assess the contour of the rod prior to implantation, applied to when a rod is attached to a tracked end cap. This embodiment consists of a fixed base 4905 with a coupled post 4915 holding a rod-receiving ring 4910 designed for a rod of set diameter to pass through. Attached to the ring is a TSM 4903 as well as a hinge 4907 about which a hinged flap 4909, shown in the closed position, rotates. A TMSM 4920 is attached to the hinged flap and used to signal to the acquisition system when a rod is engaged with the ring via the TMSM attached to the hinged flap moving relative to the TSM attached to the ring. The software interpretation of this motion is completed by simply comparing the distances between the TSM and the TMSM when the hinge is closed vs. opened. In this embodiment, the hinged flap stays closed in the absence of a rod through the force of gravity acting on the TMSM attached to the hinged flap. In other embodiments, the hinged flap can also be spring loaded. It should be noted that in other embodiments of this design, the fixed base can be resting on a surface, or mounted to a rigid surface including a component of a robot.

[00405] FIG. 49B displays an embodiment of the invention described previously in FIG. 49A, except with the hinged flap 4909 and its attached TMSM 4920 in the open position, analogous to its position when a rod is inserted into the ring and pushing up on the hinged flap 4909. FIG. 49C displays a different view of the embodiment of the invention described previously in FIGS. 49A-B, with the hinged flap 4909 and its attached TMSM 4920 in the open position, and direct visualization of the rod-receiving ring 4910. FIG. 49D illustrates the assembly of FIGS. 49A-49C coupled with a rod and tracked end cap previously described in relation to FIGS. 47 A, and 48A-48B in accordance with some embodiments of the invention.

[00406] FIG. 49D displays an embodiment of the fixed-base, single-ring rod assessment device as previously described in FIGS. 49A-C, coupled with a rod 4960 and tracked end cap 4990, previously described in FIGS. 47A, and 48. This embodiment shows the rod pushing the hinged flap 4909 out of the way and by doing so, actuating the TMSM 4920 attached to the hinged flap 4909. When the software acquisition system detects the distance between the TSM 4903 and the TMSM 4920 closer than that when the hinged flap is closed, it is triggered to record the coordinates of the end cap. The recorded coordinates of the end cap's path can then be used to calculate the contour of the rod, as described in detail in FIG. 75. It should be noted that in other embodiments, the user can trigger the acquisition via other triggering methods described previously in relation to FIG. 48B. Following registration of the contour of a rod attached to a tracked end cap, the tracked end cap can be used for the user to directly interface with the display monitor portraying the rod contour, as described in detail below in reference to FIG. 78.

[00407] FIG. 50A-50D illustrates embodiments of a fixed-base, variable-ring, mobile rod assessment device in accordance with some embodiments of the invention. In some embodiments, the device assembly is described in FIGS. 49A-49D, in which it is able to accommodate the contour assessment of a series of rod diameters via a variable-ring-size selector component. After the user rotates the appropriate diameter ring in front of the hinged flap by using the retractable spring plunger, a rod of corresponding diameter attached to a tracked end cap can then be passed through the ring and have its contour interpreted in the same method previously described in relation to FIGS. 49A-49D.

[00408] Referring initially, FIG. 50A, illustrating a front view of an embodiment 5000, fixed base 5001 coupled to post 5005 is shown to which a revolving rod-width selector 5007 containing multiple rod-receiving rings 5009 of varying diameter is coupled via a fastener 5011 and can be rotated into preset angles via a retractable spring plunger 5013, and a TSM 5017 fixed to the post. The rod-width selector containing rings of varying diameter is designed to enable this embodiment of the device to accommodate varying diameter rods rather than necessitating multiple devices.

[00409] FIG. 50B displays an oblique view of an embodiment 5001 of the device shown in FIG. 50A with the rotating rod-width selector, retractable spring plunger, and fastener removed. Discrete-angle detents 5015 receive the retractable spring plunger at set angles. A hinge 5019 interfaces with a hinged flap 5021, shown in the closed position, and with an attached TMSM 5023, as previously described in relation to FIG. 49A-49D. FIG. 50C displays a back view an embodiment 5002 of the invention shown in FIG. 50B. FIG. 50D displays an embodiment 5003 of the invention as described previously in relation to FIGS. 50A-C, interfacing with a rod 4960 passing through one of the fixed rings and pushing the hinged flap 5021 and its attached TMSM 5023 to the open position.

[00410] FIG. 50E illustrates the fixed-base, variable-ring, mobile rod assessment device of FIGS. 50A-50D engaged with a rod 4960 coupled to an end cap 5095 in accordance with some embodiments of the invention. As described previously in FIG. 49D, the end cap 5095 is used to track the path of the end of the rod 4960 as its length is passed through the fixed ring. The software to calculate the rod's contour from this interaction is described below in reference to FIG. 75. It should be noted that the hinged flap shown in this figure is only one embodiment of the invention. Other embodiments include a linearly actuated TMSM that is moved when the rod is passed through the fixed ring. Following registration of the contour of a rod attached to a tracked end cap, the tracked end cap can be used for the user to directly interface with the display monitor portraying the rod contour, as described in detail below in reference to FIG. 78.

[00411] Some embodiments include a handheld, mobile rod contour assessment device. In reference to FIGS. 51A-51I, some embodiments include a method of using two handheld tracked devices to assess the contour of a rod prior to implantation. To utilize these embodiments to register the contour of a rod, the rod is rigidly fixed within the tracked end cap, as previously described in FIGS. 48A-C, 49D and 50E, and then the tracked slider, previously described in FIG. 47B, is slid over the surface of the rod one or more times. For example, FIG. 51 A displays a side view of one embodiment 5100 of the invention which is a tracked end cap, previously described in FIGS. 47A, 48, 49D, and 50E. It consists of a handle 5101, rod mount hole 5103, anatomical axes reference labels (5105, 5107), a tracked DRF 5189, and a set screw 5109 for rigidly fixing the rod in place. When inserted and fixed within this device, the rod is interpreted by the acquisition software relative to the anatomical labels contained on the device. FIG. 5 IB displays a front view of one embodiment of the invention, a tracked end cap, shown previously in FIG. 51 A. FIG. 51C displays a back view of one embodiment of the invention, a tracked end cap, shown previously in FIGS. 51A-B.

[00412] FIG. 5 ID displays an assembled view of one embodiment of the invention, a tracked slider, described previously in relation to FIG. 47B, consisting of a handle 5129, rod- centering fork 5130, tracked DRF 5135, spring-loaded depressible shaft 5140, and shaft- mounted TMSM 5145. When used with a rod fixed to the tracked end cap previously described in relation to FIGS. 51A-C, this embodiment is able to register the coordinates of the rod by sliding along its surface. When it is fully engaged with the surface of the rod, the sliding shaft and attached TMSM are actuated, and the acquisition system is triggered to record the coordinates corresponding to the center of the rod. The software to calculate the coordinates of the rod is described below in reference to FIGS. 73 A-73B, and 74. It should be noted that the rod-centering fork attached to the slider is only one embodiment of the device. Other embodiments include a coupled ring as previously described in reference to FIGS. 49A-49D, and 50A-50E. Additionally, linearly actuating a TMSM is only one method of triggering to the acquisition system that the slider is fully engaged with the rod. Other embodiments include, but are not limited to, rotational motion of a TMSM, handheld triggering on the tracked slider or tracked end cap, electronic communication from embedded electronics on the tracked end cap or tracked slider, or direct user input via software interface.

[00413] FIG. 5 IE displays a back view of the embodiment shown previously in FIG. 5 ID displaying the depressible shaft 5140, rod-centering fork 5130, and tracked DRF 5135. FIG. 5 IF displays a closeup view of the embodiment shown previously in FIGS. 51D-51E in which the tracked DRF 5135, spring 5130 and spring-loaded depressible shaft tip 5140, and its attached TMSM 5145 are visible. In this configuration of the embodiment, the sliding shaft 5140 and its mounted TMSM are in the extended position, indicating that the tracked slider is not engaged with a rod.

[00414] FIG. 51G displays a closeup view of the embodiment shown previously in FIGS. 51D-F in which the depressible shaft 5155 and its mounted TMSM 5160 are in the depressed location, which if at a preset height corresponding to the rod diameter being used, would indicate to the acquisition software that the tracked slider is firmly engaged with a rod and its coordinates should be recorded. Further, FIG. 51H displays one embodiment of the invention which is a mechanism of registering the contour of a rod prior to implantation by rigidly fixing a rod 5170 in a tracked end cap and sliding the tracked slider over the rod one or more times. Following registration of the contour of a rod attached to a tracked end cap, the tracked end cap can be used for the user to directly interface with the display monitor portraying the rod contour, as described in detail below in reference to FIG. 78. FIG. 511 displays another view of an embodiment of the invention previously shown in FIG. 51H.

[00415] Some embodiments include a TMSM-based, implanted rod contour assessment device. Some embodiments areused to assess the contour of a rod after it has been implanted into a patient. This embodiment utilizes the rod-centering fork design with a sliding shaft and spring-loaded TMSM, previously described in FIGS. 47A and 51D-51I on the end of a tracked probe, such that it can fit into the surgical site and trace over the implanted rod. The probe is able to skip over any obstructing hardware without its coordinates being recorded because the acquisition system is only triggered to record when the TMSM is in the position corresponding to the sliding shaft being depressed by a rod of a preset diameter. The software for calculating and interpreting the rod contour is described below in relation to FIGS. 76, and 77A-77C.

[00416] FIG. 52 A illustrates a component of a TMSM-based, implanted rod contour assessment device 5200 in accordance with some embodiments of the invention. In some embodiments, the device 5200 comprises a probe shaft 5210, rod-centering fork 5230, 5235 for interfacing with a rod, mounts 5215 for tracked DRF markers to be inserted, mounts 5225 for spring(s), a depth-stop for a sliding shaft 5225 and sliding shaft guides 5205 to prevent the inserted shaft (not shown) from rotating. This embodiment is intended to be coupled with the embodiment described below in reference to FIG. 52B.

[00417] FIG. 52B illustrates a depressible sliding shaft for coupling to the component of FIG. 52A comprising a depressible sliding shaft 5250 with rounded tip 5264, mounts 5260 for springs, threaded hole 5268 for adjustable depth stop, mount 5209 for a TMSM, and a guide-fitting profile 5252 to prevent rotation when inserted within its complementary probe described above in relation to FIG. 52 A. some embodiments of the invention.

[00418] FIG. 52C illustrates a top view of the component of FIG. 52 A in accordance with some embodiments of the invention, and shows spring mount 5225, and sliding shaft through hole 5229, able to accommodate the sliding shaft 5250 in relation to FIG. 52B. FIG. 52D displays another view of the embodiment shown previously in FIG. 52B, enabling closer visualization of the depressible sliding shaft 5250, spring mounts 5260, threaded hole 5268 for an adjustable depth stop, mount 5209 for a TMSM, and a guide-fitting profile 5252.

[00419] FIG. 53A displays one embodiment of a device 5300 configured to assess the contour of a rod after it has been implanted within the surgical site. The embodiment described in this figure comprises an assembly of the components described previously in relation to FIG. 52A-52D. In some embodiments, the device 5300 comprises a tracked probe 5310 with a rod-centering fork 5315, through hole (not shown) to accommodate a depressible sliding shaft 5335, with a coupled TMSM 5325, and tracked DRF 5320. This embodiment is used to engage with an implanted rod such that the rod depresses the depressible sliding shaft, thereby moving the attached TMSM relative to the attached tracked DRF. When the TMSM moves relative to the tracked DRF by a preset amount based on the rod diameter, the acquisition system is triggered to record the coordinates corresponding to the center of the rod, as described below in reference to FIGS. 76-77. Further, FIG. 53B illustrates a close-up back view of a portion 5301 of the assembly of FIG. 53A in accordance with some embodiments of the invention. Further, FIG. 53B displays a back view of the embodiment of the invention shown previously in 53A, visualizing the depressible sliding shaft 5325, its attached TMSM 5225, the tracked DRF 5320, springs 5354, depth stop 5356 for sliding shaft, and depth-stop set screw 5352 used to adjust the maximum protrusion length of the sliding shaft tip beyond the bifurcation of the fork. It should be noted that the adjustable depth-stop design is just one embodiment of this invention. Other embodiments do not possess a mechanism of adjusting the maximum protrusion length of the sliding shaft. Additionally, the external springs referenced in this embodiment can consist of internal compressible springs, torsion springs, and memory-embedded materials within other embodiments. This figure displays how the sliding shaft guides prevent rotation of the sliding shaft, restricting the TMSM to linear motion relative to the tracked DRF.

[00420] FIG. 53C displays a closer view of the rod-interface region of the embodiment shown previously in FIGS. 53A-53B. In this embodiment, the spring-loaded depressible sliding shaft 5335 is in its extended position. In this position the acquisition system is not triggered to record the coordinates of the probe, as it is not indicating that it is interfacing with a rod to be measured. Further, FIG. 53D displays a view of the embodiment described previously in FIGS. 53A-C interfacing with a rod 5367 within the rod-centering fork 5315 and depressing the sliding shaft 5335 into the depressed position causing the attached TMSM (not shown) to move relative to the probe's attached DRF, indicating for the acquisition system to record coordinates corresponding to the center of the rod's cross-section.

[00421] FIG. 53E displays a closer view of the tracked DRF portion of the device embodiment described previously in relation to FIGS. 53A-D. The location of the TMSM 5325 relative to the tracked DRF 5320 as shown, corresponds to the depressible shaft being in the extended position, as shown in FIG. 53C. In this configuration, the acquisition software is not triggered to record the probe's coordinates. FIG. 53F displays a closer view of the tracked DRF portion of the device embodiment described previously in relation to FIGS. 53A-E showing sliding shaft guide 5329. The location of the TMSM 5325 relative to the tracked DRF 5320 as shown, corresponds to the depressible shaft 5335 being in the depressed position, as shown in FIG. 53D. In this configuration, the acquisition software is triggered to record the location of the probe, from which the rod's coordinates can be calculated as described below in reference to FIGS. 76-77.

[00422] Some embodiments include a conductivity-based, implanted rod contour assessment device. Some embodiments are intended to assess the contour of a rod after it has been implanted within the surgical site. This embodiment differs from those previously described in relation to FIGS. 52A-52D, and 53A-53F, in that it possesses electrical contact terminals on the inside walls of the rod-centering fork. These electrically-isolated terminals are used then to sense conductivity between them. In the absence of a rod touching both terminals, no current flows between them. When a rod is fully engaged within the fork however, current flows from one contact to another, indicating that the device is fully engaged with the rod, and the contour assessment device electrically communicates, either wirelessly or through a wire, with the 3D-tracking acquisition system that it should record the coordinates of the device. Therefore, embedded in the probe is a small power supply via battery or capacitor, and circuit components to communicate with the acquisition system. For example, FIG. 54A displays one embodiment of the invention (assembly 5400) which includes a probe shaft 5410 equipped with a rod-centering fork 5425 on one end and a tracked DRF 5415 on the other. This embodiment of the invention can be applied to an already-implanted spinal rod and used to assess its 3D contour by sliding it along the exposed surfaces of the rod. This device possesses electrical contact terminals, described below in reference to FIG. 54B, on the inside surfaces of the rod-centering fork, and internal electronics within the rod (not shown) that detect when current flows between them. When current flows between the terminals, the contour assessment tool signals for the acquisition system to record its location in space. Other embodiments of the probe's communication method with the acquisition system include but are not limited to wireless radiofrequency transmission, optical signaling via infrared or visible light illumination of elements on the probe that are detected by the system, and wired signal transmission. The process of interpreting the rod's location and contour relative to the probe is described below in reference to FIGS. 76, and 77A-77C.

[00423] FIG. 54B illustrates a rod-centering fork and electrical contact pads of the device of FIG. 54A in accordance with some embodiments of the invention. FIG. 54B provides better visualization of the rod-centering fork 5425 and electrical contact pads 5427a, 5427b located on the inner surface of each arm of the fork. With this embodiment, the probe is unable to signal that it is active, unless an electrical conductor connects both contact terminals. It should be noted that the shape of the contact terminals can be different in other embodiments, including but not limited to cylindrical, semi-cylindrical, flat, and curved surfaces with variation in their distance of protrusion from the inside surface of the fork.

[00424] FIG. 54C displays the embodiment previously described in relation to FIGS. 54A- B interacting with a rod 5440 that is not fully seated within the fork. In this configuration, the rod 5440 is not approximating both electrical contact plates, and therefore the assessment device is in the inactive, non-tracking state. Further, FIG. 54D displays the embodiment previously described in relation to FIGS. 54A-C interacting with a rod 5440 that is fully engaged within the fork. In this configuration, the metal rod is approximating both electrical contact pads (5427a, 5427b of FIG. 54B) of the fork and therefore conducting a current across it. When current is being conducted, the probe then signals to the 3D-tracking acquisition system that it is in the active state and its coordinates are recorded to be used for computing the rod contour as described below in reference to FIGS. 76, and 77A-7C.

[00425] Some embodiments include a 3D-tracked, manual mobile rod bender. Some embodiments can be utilized with an already -registered rod attached to a tracked end cap, to both bend and re-register the updated contour of the rod during bending. This embodiment also allows for visualization of the precise position of the tracked handheld rod bender relative to a previously registered rod on a display monitor. Additionally, this system also allows for software-assisted and software-directed bending, instructing the user where to place and how to maneuver a tracked, handheld rod bender, to contour the rod to a predetermined shape. The capabilities of this embodiment and its variations are described in more detail below in reference to FIGS. 56A-56F, 79A-79G, and 81.

[00426] FIG. 55A displays one embodiment of the invention, which is a handheld rod bender 5501 consisting of two handles with handle #1 5507a, containing the center rod contouring surface 5503, and left outer roller 5505 and handle #2 5507b containing the right outer roller 5506. The embodiment shown is interfacing with a straight rod 5511a approximating both rollers and center bend surface, as the bender handles (5507a, 5507b) are positioned at an open angle to one another. Further, FIG. 55B displays the embodiment of the invention described in relation to FIG. 55 A, with the rod bender's handles approximated, resulting in a bent rod 5511b contour. FIG. 55C displays a closer view of the rod-interface points of the bender 5501, shown previously in FIG. 55B interfacing with a bent rod 551 lb. [00427] FIG. 55D displays one embodiment of the invention which consists of a handheld rod bender coupled to rod 5511a, previously described in relation to FIGS. 55A-C, equipped with a tracked DRF 5550 fixed to handle #1 5507a, a roller mount 5508 on outer roller 5506 and a TMSM 5540 fixed to the roller mount 5508. As displayed, the rod bender 5501 is interfacing with a straight rod 5511a, necessitating that the bender's handles 5507a, 5507b are positioned at a wide angle from one another to accommodate the straight rod. With the tracked DRF 5550 mounted to handle #1 5507a, the 3D-tracking acquisition system can register the location and pose of both the center rod contouring surface and the left outer roller. With the TMSM 5540 attached to the right outer-roller 5506, it enables the acquisition system to then register the location of the right outer roller relative to the two other rod- interface points of the bender. With the ability to locate all three rod-interface points on the bender in 3D space, the acquisition system can interpret the relative angle between the bend handles, and with known rod diameter, the degree of bending induced into a rod. When this embodiment of the invention is coupled to a previously registered rod, fixed to a tracked end cap, as described previously in relation to FIGS. 49D, 50E, 51H-I, the acquisition system is able to interpret when the three rod-interface points on the tracked bender are engaged with the previously registered rod. When that is the case, the software system is able to provide live tracking of the bender relative to the rod, real-time updates of the rod contour during bending, and software-assisted bending instructions, as described below in reference to FIGS. 56, 79-81, 87-88. Further, FIG. 55E displays one embodiment of the device 5501 as previously described in FIG. 55D, except with the rod bender handles 5507a, 5507b coupled, resulting in a bent rod 5511b. Further, FIG. 55F displays another view of the embodiment shown in FIG. 55E and described previously in relation to FIG. 55D. This perspective enables visualization of the mounting post 5551 for the tracked DRF 5550 attached to handle #1 5507a. It should be noted that in other embodiments, the tracked DRF 5550 is coupled to varying locations on handle #1 5507a and at varying angles and offset heights from the handle. This figure displays only one embodiment of the relative positioning of the tracked DRF 5550 to the rod bender handle. The same variation applies for the relative positioning of the TMSM 5508 (as marked in FIG. 55D) to handle #2 5507b. Although in the embodiment shown, it is located directly over the right outer roller 5506, it can be positioned anywhere on handle #2 5507bto provide the input information the software needs to calculate the aforementioned embodiments of the invention. [00428] Some embodiments include a spring-loaded tracked mobile stray marker attached to the center rod contouring surface of the rod bender such that it moves the stray marker only when the rod is fully pressed up against the surface of the center rod contouring surface, and thereby serving as an indicator of when the rod is fully engaged with the bender (i.e., only when the rod is "being bent"). For example, other embodiments include a spring-loaded (not shown) tracked mobile stray marker (not shown), connected to the center rod-contouring surface in such a way that it is fully deflected only when the rod is fully approximated against the center rod-contouring surface of the rod bender. In this way, the acquisition system has an additional method of indicating when the contour of the rod is actively being bent.

[00429] In reference to FIGS. 55A-55I, and 56A-56F, in some embodiments, the tracked bender can be protected such that it can be applied to other user-operating rod benders, especially table-top benders that are used in the operating room. Further, it is also essential to note that rod cutters can also be equipped with tracking in the same way to see where the digital overlay of the rod will be cut. It should be noted that these embodiments can also be applied to other user-operating rod benders that involve two or more contact points with a rod to induce curvature. In other embodiments, these principles are applied to instruments used for rod cutting, such that the location of the cutter relative to a previously registered rod can be visualized.

[00430] FIG. 55G displays an alternative bender embodiment of the invention from that described previously in relation to FIGS. 55D-55F, in which the rod bender is equipped with two TMSMs, TMSM handle #1 5507a (shown as 5571, 5572), and one TMSM 5573 on handle #2 5507b. The three TMSMs 5571, 5572, 5573 are utilized to localize the position of each rod-interface point on the bender. Because the three TMSM mounting points shown are directly over the three rod-interface points of the rod bender, the acquisition software can localize the plane of the rod bender defined by the three markers 5571, 5572, 5573, and then offset it by a known amount based on the known offset between the TMSMs and the rod- interface points on the bender. The acquisition system is able to reliably interpret the direction of offset from the plane defined by the three TMSMs, based on the viewing angle restrictions of a single optical 3D-tracking system, which defines the normal vector the TMSM plane as that which is less than 90 degrees from the vector drawn from the center of the three markers to the 3D-tracking camera. In this configuration, the tracked bender is able to achieve the same functionality as described previously in relation to FIG. 55D. It should be noted that three TMSMs attached to the rod bender is only one embodiment of the invention, and other embodiments include attaching more than three TMSMs to the bender, as well as placing the TMSMs in alternative locations than directly over the rod-interface components of the rod bender. As shown in this figure, the tracked bender is interfacing with a straight rod 551 1a, necessitating that the angle between the bender handles be positioned at a wide angle relative to one another. In this configuration, because the distance from the center bend surface to each of the outer rollers is the same, the angle between bender handles, and thereby the degree of bending, can be calculated based on the angle between the two equally spaced TMSMs 5572, 5573 from the center TMSM 5571.

[00431] FIG. 55H displays one embodiment of the invention as previously described in FIG. 55G, except with the rod bender handles approximated, resulting in a bent rod 5511b. FIG. 551 displays another view of the embodiment shown in FIG. 55H and described previously in relation to FIG. 55G

[00432] FIGS. 56A-56F further describe an embodiment of the invention previously described in relation to FIGS. 55A-55I. Depicted are the necessary components of the invention to track bending in real-time, as well as utilize software-assisted instructed bending are all displayed. Furthermore, an additional embodiment of the device is introduced within this figure, that enables the ability to account for shape memory that rod material may during and after bending when computing the real-time tracking of bending and computing the reregistered rod. For example, FIG. 56A displays one embodiment of the device 5600 previously described in relation to FIGS. 55G-55I, in which a pre-registered rod 5610 is fixed within a tracked DRF-equipped end cap 5605, and a tracked rod bender 5501g is equipped with three TMSMs interfaces with the rod. In this configuration, the acquisition software can interpret the location of the tracked rod bender relative to the previously-registered rod within the tracked end cap's relative coordinate system. With this configuration, the acquisition system can provide live tracking of the bender relative to the rod, real-time updates of the rod contour during bending, and software-assisted bending instructions, as described below in reference to FIGS. 79A-79G, 81, 87A-87G, and 88A-88F.

[00433] FIG. 56B shows another configuration of the embodiment previously described in relation to FIG. 56A, in which the tracked rod bender 5600 is engaged with an alternative location of the rod that is bent, displaying how the angle between the handles and associated TMSMs changes from when the bender is interfacing with a straight portion of the rod, as shown in FIG. 56 A.

[00434] FIG. 56C displays one embodiment of the device (assembly 5601) previously described in relation to FIGS. 55D-55F, in which a pre-registered rod is fixed within a tracked-DRF-equipped end cap and a tracked rod bender (assembly 5601 with end cap 5605 and rod bender 5501) is equipped with a tracked DRF 5550 on one handle and a TMSM on the other. With this configuration, the acquisition system is able to provide live tracking of the bender relative to the rod, real-time updates of the rod contour during bending, and software-assisted bending instructions, as described below in reference to FIGS. 79A-79G, 81, 87A-K, and 88A-88F.

[00435] FIG. 56D shows another configuration of the embodiment 5601 previously described in relation to FIG. 56C, in which the tracked rod bender 5501 is engaged with an alternative location of the rod that is bent (5610), displaying how the angle between the handles and associated TMSM relative to the tracked DRF changes from when the bender is interfacing with a straight portion of the rod, as shown in FIG. 56C.

[00436] FIG. 56E displays a further embodiment of the invention 5600, which consists of a tracked DRF-equipped end cap 5605, fixed to a pre-registered rod 5610, non-tracked manual bender 5501c, and rod cap 5690 with TMSM 5695 mounted to it. This embodiment represents an alternative mechanism and method of updating the previously-registered contour of a rod while it is being bent with a handheld bender. In this embodiment, because the bender is not tracked, the location of the TMSM is detected relative to the tracked end cap to which the rod is fixed. Whenever the system detects relative motion between the TMSM and the tracked DRF on the end cap, the acquisition system records the path traveled by the TMSM relative to the end cap. With known geometry of the rod bender's center bend surface, the path of the TMSM is used to calculate the location and curvature of each bend, as described below in reference to FIG. 80.

[00437] FIG. 56F displays an embodiment of 5601 comprising a tracked DRF-equipped end cap 5605, fixed to a pre-registered rod 5610, tracked manual bender 5501 equipped with a tracked DRF 5550and one TMSM, and rod cap 5690 with a TMSM 5695 mounted to it. In this embodiment, the contour of the previously-registered rod is updated during bending by the combination of tracking both the rod bender's conformation at interfacing regions of the rod, as described previously in relation to FIGS. 55D-F, as well as the motion of the TMSM- equipped rod cap relative to the tracked end cap to which the rod is fixed. In this configuration, the acquisition system is able to account for shape memory within the rod material, that previously described embodiments without the TMSM-mounted rod cap were not. Because the end of the rod opposite to the DRF-equipped end cap is tracked in this embodiment, after the rod bender achieves its minimum angle between handles when interfacing with a particular region of the rod, if the rod material retains some of its shape memory and recoils, the TMSM-equipped rod cap will move relative to the DRF-equipped end cap, and the acquisition system software can now account for this memory when recomputing the rod's contour as described in more detail in relation to FIG. 80. As with other embodiments described in FIGS. 56A-E, this configuration also enables software- assisted bending and interfacing with display monitor, as described below in reference to FIGS. 79A-79G, 80-81, 87A-87G, and 88A-88F.

[00438] Some embodiments include a 3D-tracked, manual implanted rod bending system which enables the ability to track the bending of a rod that has already been implanted within the surgical site. In this embodiment, the user interfaces with an implanted rod using DRF- tracked and trigger-equipped in-situ benders after already registering the contour of the implanted rod via mechanisms described previously in relation to FIGS. 52A-52D, 53A-53F, and 54A-54B. For example, some embodiments include DRF -tracked and trigger-equipped in-situ benders coupled to a rod in accordance with some embodiments of the invention. In some embodiments, two tracked in-situ benders, each equipped with unique tracked DRFs, can interface with a pre-registered rod to alter its contour after implantation. Because the tracked in-situ benders interface with an already-registered rod, their position relative to the registered rod can be displayed via display monitor. Additionally, because they are equipped with depressible sliding shafts to serve as triggers indicating when they are fully engaged with the rod, their movement will not result in alteration in the software-recorded-contour of the registered rod unless two or more in-situ benders are triggered simultaneously and moved relative to one another while triggered. For example, FIG. 57A displays one embodiment 5700 of the invention consisting of a tracked in-situ bender with handle 5710a, 5710b, rod interface head 5725a, 5725b equipped with depressible sliding shaft tip (not shown) coupled to pre-registed rod 5711, TMSM 5707a, 5707b mounted to depressible sliding shaft, and tracked DRF 5705a, 5705b. Further, in reference to FIG. 57B, showing embodiments 5701 with spine 5713 with pedicle screw shafts 5718, tulip head 5739, on implanted pre-registered rod 5750, and cap screw 5738, in some embodiments, both triggers on the benders can be depressed, actuating the TMSMs relative to the associated DRFs, indicating to the acquisition system that they are fully engaged with the rods.

[00439] FIG. 57C illustrates a close-up view of the rod (marked as 5711) of FIG. 57A in accordance with some embodiments of the invention, and FIG. 57C displays another view of the embodiment shown in FIG. 57A engaging with a pre-registered rod 5711. FIG. 57D illustrates a close-up view of a rod interface head 5725 of the bender showin in FIG. 57A including a view of a depressible sliding shaft tip 5735 in an extended position towards surface 5730 that can accept the rod 5711 in this assembly view.

[00440] Some embodiments of the invention enable the use of skin-mounted fiducial markers to serve as surrogate markers from which the location of the underlying anatomical landmarks can be calculated. For example, FIG. 58 illustrates a workflow 5800 to initialize skin-mounted, or percutaneous, fiducials with two or more x-ray images intraoperatively in accordance with some embodiments of the invention. This figure describes the process of the user and acquisition system interfacing to initialize and calculate the 3D-displacement vector between a fiducial marker and the anatomical region of interest. Some figures relevant to the process include X-ray initialization of 3D-displacement vector w/ multi-planar x-rays (FIGS. 4A-4G, FIG. 13), feedback on fiducial placement on or in a patient's skin surface (FIGS. 2A- 2B), a trans-drape / two-halves fiducial design (FIGS. 6A-6D, and FIGS. 9A-9B), registration of a fiducial in camera coordinates + determining its unique identity (FIGS. 4H-4I, FIG. 5, and FIGS. 7-8, FIGS, 10A-10D, and FIGS. 11A-11B).

[00441] In some embodiments, one or more steps of the workflow 5800 can be utilized for the registration of a 3D-displacement vector between a skin-mounted or percutaneous fiducial marker and the anatomical landmark of interest. Following a step 5802 of positioning a patient on an operative table, step 5804 can include the placement of a fiducial on or inside the soft tissue within the anatomical region of interest. For example, one embodiment involves the user placing the fiducial on or inside the general region of interest. Another embodiment of the invention can involve the user receiving feedback on the placement of a fiducial marker via a radiopaque patch that identifies the optimal location on the surface to place or insert the fiducial device; this was previously depicted and discussed in related to FIGS. 2A and 2B. [00442] Some embodiments involve the mating of a second-half fiducial to the original fiducial marker placed on or inside soft tissue to maintain access to the fiducial after the introduction of surgical drapes and other obstructing materials outside of the surgical site. Example embodiments to accomplish one or more embodiments of this invention are depicted in FIGS. 6A-6D, and FIGS. 9A-9B. In some embodiments, step 5806 can include obtaining a first x-ray image containing fiducial and desired bone anatomy to be identified with the fiducial. Further, step 5808 can include rotation of the x-ray emitter, and step 5810 can include obtaining a second x-ray image containing fiducial and desired bone anatomy to be identified with the fiducial.

[00443] Some embodiments further include the process of annotating 2D vectors between the fiducial marker and the anatomical landmark of interest for each image acquired from a unique perspective relative to the fiducial. This displacement vector initialization process is depicted and discussed in reference to FIGS. 4A-4F. The overall goal of the initialization process can be visualized in the cross-sectional view depicted previously in FIG. 13. Further some embodiments include the process of using the relative rotational and translational offset information between two or more x-ray images of the fiducial to calculate the 3D- displacement vector between the fiducial marker and the anatomical landmark of interest using the 2D-displacement vectors for each image as inputs into the calculation. This process of calculating the 3D-displacement vector based on a rigid transformation between multiple 2D-displacement vectors is previously depicted in FIG. 4G. For example, step 5812 can include annotation of x-ray images with desired bony anatomy locations, and step 5814 can include calibration of x-ray image distances by known size of the radiopaque markers on the fiducials. Further, step 5816 can include draw a scaled displacement vector on x-ray images from fiducial origin to indicated bony anatomy of interest, and step 5818 can include input or compute displacement angle between x-ray images. Further, step 5820 can include add displacement vectors to produce 3D displacement vector from fiducial origin to annotated regions.

[00444] Steps 5822-5830 describe the process of using 3D-tracked devices to register the location and orientation of the fiducial marker relative to the coordinate system of the 3D- tracking acquisition unit, and then applying the acquired positional information as a rigid transformation to the x-ray-based 3D-displacement vector to convert the vector from imaging units into units of the 3D-tracked acquisition unit. This process can be depicted in FIGS. 4H, 41, 5, 7-8, 10A-10D, and 11A-11B. In addition, these previous figures depict some of the embodiments for determining the unique identity of a fiducial marker in order for the system to be able to utilize several fiducial markers at once and understanding which fiducial is associated with a specific mathematical relationships to a unique anatomical landmark of interest. For example, step 5822 can include interpretation of fiducial origin into camera coordinate, and step 5824 can include tracing or tapping the fiducial with tracked probe in discrete points to indicate fiducial pose. Further, step 5826 can include mechanical mating or coupling of tracked probe with fiducial to obtain fiducial pose, and step 5828 can include directly tracking markers mounted on fiducial, and with step 5830 including access to fiducial which then serves as a reference point to initialized nearby bony points of interest.

[00445] In some embodiments, any of the above processes, methods, or procedures related to the workflow 5800 can include or be accomplished with one or more of steps or processes 5802, 5804, 5806, 5808, 5810, 5812, 5814, 5816, 5818, 5820, 5822, 5824, 5826, 5828, and 5830. In some embodiments, the steps of workflow 5800 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 5800 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 5800 can be skipped.

[00446] Some embodiments of the invention enable the registration of bone-mounted fiducial markers to represent anatomical landmarks that are located within or nearby the bony anatomy that the marker is rigidly attached to. For example, FIG. 59 illustrates a workflow 5900 to initialize one or more bone-mounted fiducial placed intraoperatively with two or more x-ray images taken before placement of one or more bone-mounted fiducials in accordance with some embodiments of the invention. This figure describes the process of the back-end system to use prior x-ray initialization of a skin-based fiducial and its 3D- displacement vector to the anatomical landmark of interest and transform the bone-mounted fiducial location and pose relative to the camera-based registration coordinates of the prior 3D-displacement vector to describe the relationship between the bone-mounted fiducial marker and the anatomical region of interest. Other relevant figures can include embodiments for bone-mounted fiducial design and coupling to additional fiducial (see FIGS. 3A-3C), and registration of fiducial in camera coordinates + determining its unique identity (FIGS. 10A-10D, and FIGS. 44A-44D). [00447] In some embodiments, the steps 5910, 5912 of this process can involve the steps described in the workflow of FIG. 58, which outline the process for registering the 3D- displacement vector for a skin-based or percutaneous fiducial in imaging coordinates as well as units of the 3D-tracking acquisition unit. If the registered fiducial marker has to be removed due to the location of the surgical site requiring access to the that location of the anatomy, then the user can utilize the process to reinstate access to the 3D-displacement vector that provides information about other anatomical landmarks of interest. Step 5914 can include removal of the skin fiducial, and step 5916 can include skin incision and exposure of the surgical site.

[00448] In some embodiments, step 5918 and 5920 can involve the user implanting the miniature fiducial marker into the bony anatomy and then registering its location and orientation relative to a 3D-tracking acquisition unit via a 3D-tracked probe. One embodiment of this process is depicted in FIGS. 3A-3B, and FIGS. 4A-4D.

[00449] Some embodiments, described in steps 5922, and/or 5924, and/or 5926, and/or 5928 can involve the 3D-tracked probe tracing the fiducial surface or tapping discrete points on the fiducial to register the fiducial' s 3D location and orientation with respect to the coordinates of the 3D-tracking acquisition unit. Some of the other embodiments are depicted in FIGS. 10A-10D.

[00450] In some embodiments, step 5930 can include comparing the location and orientation of the registered bone-mounted fiducial to that of the registered landmarks initialized via the prior 3D-displacement vector converted into coordinates of the 3D-tracking acquisition system via initialization of the skin-based fiducial before the incision of the surgical site. Further, in some embodiments, steps 5932 and 5934 can include utilizing the relationship calculated in step 5930 as in input for the rigid transformation applied to the registered anatomical landmarks with coordinates from the 3D-tracking acquisition system.

[00451] In some embodiments, any of the above processes, methods, or procedures related to the workflow 5900 can include or be accomplished with one or more of steps or processes 5910, 5912, 5914, 5916, 5918, 5920, 5922, 5924, 5926, 5928, 5930, 5932, and 5934. In some embodiments, the steps of workflow 5900 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 5900 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 5900 can be skipped. [00452] Similar to embodiments depicted in FIGS. 58 and 59, FIG. 60 shows a workflow to initialize bone-mounted fiducials placed intraoperatively with 2 or more x-ray images taken after placement of bone-mounted fiducials in accordance with some embodiments of the invention. In some embodiments, once the user has created a surgical site and exposed the bony anatomy, the user can implant the miniature fiducial marker into the bony anatomy surface until it is rigidly fixed to the anatomy. Examples of this embodiment are depicted in FIG. 3 A and 3B. Some embodiments involve the use of a larger fiducial marker that mates to the surface of the bone-mounted fiducial marker to enhance its visualization in x-ray images for the purpose of annotating the 3D-displacement vector to the anatomical landmark of interest. An example of this embodiment is depicted in FIG. 3C.

[00453] In step 6002, incise skin and expose the surgical site, and step 6004, fasten bone- mounted fiducial to spinal level of interest at accessible location, and further, in step 6006, attach mating device (optional) to bone-mounted fiducial to aid with x-ray initialization. In some embodiments, steps 6012, 6010, 6008, 6014, 6016, 6018, 6020, 6022, and 6024 can include the x-ray -based registration of the fiducial marker as described in FIG. 58 to produce a 3D-displacement vector in imaging coordinates between the bone-mounted fiducial marker and the anatomical landmark of interest. Some embodiments then register the bone-mounted fiducial' s 3D-displacement vector to the anatomical landmark of interest in the coordinates of the 3D-tracking acquisition system via acquiring the location and orientation of the fiducial marker with respect to the coordinates of 3D-tracking acquisition system. Examples of this process are depicted in FIG. 4H-4I, FIG. 10A-10D, and further in FIGS. 44A-44D.

[00454] In some embodiments, once the bone-mounted fiducial is registered in both the x- ray imaging system and the 3D-tracking acquisition system, every time the user returns to register the updated location and orientation, the relative relationship between its current position and that of the prior registration are calculated and applied via a rigid transformation to calculate the most accurate location of the anatomical landmark of interest as they currently exist in relation to the fiducial marker in 3D space. For example, in step 6026, the process can include assess location and pose of initialized fiducial, including, but not limited to step 6028 including trace a unique pattern imprinted over fiducial with tracked probe, step 6030 rigidly couple tracked mating probe to fiducial, step 6032, rigidly coupled tracked markers to fiducial, and step 6034, tap discrete points on fiducial or on fiducial mating attachment with tracked probe. [00455] In some embodiments, any of the above processes, methods, or procedures related to the workflow 6000 can include or be accomplished with one or more of steps or processes 6002, 6004, 6006, 6012, 6010, 6008, 6014, 6016, 6018, 6020, 6022, 6024, 6026, 6028, 6030, 6032, 6034, and 6036. In some embodiments, any of the steps of the workflow 6000 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 6000 can be skipped.

[00456] Some embodiments of this invention pertain to the initialization of the patient's anatomical planes in relation to the coordinates of the 3D-tracking acquisition system to enable the measurements made during a procedure to be accurately referenced to the dimensions of the anatomy being assessed. For example, FIG. 61 illustrates methods of registering anatomical reference planes intraoperatively in accordance with some embodiments of the invention. In some embodiments, if a user has already established the coordinates of the measurement system via the initialization process of surgical navigation technologies, then coordinates of the data outputted by the 3D-tracking acquisition system are already referenced in relation to the anatomical planes of the patient. In some embodiments, if the user has not already established the coordinates of the measurement system via the initialization process of surgical navigation technologies, then the user will utilize a few of the embodiments described in FIG. 61 to initialize the 3D-tracking data outputs with respect to the patient's anatomical planes.

[00457] Some embodiments include utilizing a tracked DRF (e.g., FIG. 12) and its associated 3D orientation and location in relation to the 3D-tracking acquisition system as inputs to a 3D rigid transformation of the measurements that are outputted by the 3D-tracked devices to reference the anatomical planes of the patient. One example of this process of transforming measurements outputted by 3D-tracked devices to be relative to the patient anatomical planes, via a tracked dynamic reference aligned with the patient anatomical planes, is depicted in FIGS. 62A-62C.

[00458] Some of the other embodiments for initializing the patient anatomical planes can involve acquiring two or more data points in space with a 3D-tracked probe to define the direction, location, and orientation of the anatomical planes of the patient relative to the 3D- tracking acquisition system. Some further embodiments can involve holding the probe in particular orientation and location in space and registering that position relative to the 3D- tracking acquisition system as the new coordinates system of all acquired measurements outputted by 3D-tracked devices.

[00459] In some embodiments, a decision step 6102 can include a determination of whether patient anatomy/imaging has been registered relative to a 3D tracking camera axis. In some embodiments, for a positive answer, the process can include step 6104 including a tracked DRF that serves as a reference for patient cross-sectional imaging fusion with a navigation camera, step 6106, including where the orientation of anatomical planes is interpreted, and step 6126 that can include camera coordinates interpreted within anatomical axis.

[00460] In some embodiments, a negative for step 6102 can lead to step 6108 where the position of anatomical planes is indicated relative to camera axis, including, but not limited to step 6110, including adjusting position of a DRF such that it's reference plane labels align with the patient's anatomical planes. Further, step 6112 including tapping two points in space with a tracked probe to represent each anatomical axis aligned with the patient. Further, step 6114, including temporarily holding a tracked probe in instructed orientation. In some embodiments, step 6116 (reached from step 6110 or decision step 6118 from a positive) can include rigidly transforming camera axis to the DRF-referenced anatomical axes, and to step 6126, where camera coordinates are interpreted with anatomical axes.

[00461] In some embodiments, from decision step 6118, including checking if a dedicated DRF is used to indicate patient anatomy, a negative can proceed to step 6120 of rigidly transforming camera axes to referenced anatomical axes and to decision step 6122. From step 6122, a positive can lead to step 6124 including a return to step 6108, and a negative can include moving to step 6126 (described above).

[00462] In some embodiments, any of the above processes, methods, or procedures related to the workflow 6200 can include or be accomplished with one or more of steps or processes 6102, 6104, 6106, 6108, 6110, 6112, 6114, 6116, 6118, 6120, 6122, 6124, and 6126. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 6102 or 6122), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 6100 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 6100 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 6100 can be skipped.

[00463] Some embodiments in the acquisition and interpretation of spinal contour via tracing body surfaces with a 3D-tracked probe and interfacing with previously initialized skin fiducial markers as described previously. In this embodiment, the tracing can be performed with a trigger-equipped probe, as described previously in relation to FIGS. 10A-10G, and FIGS. 15A-15C, to indicate the body surface type that is being traced (e.g., skin, lamina, etc.) and to ensure the probe is only in an active state when in contact with body surfaces as described below in reference to FIG. 69. The acquired tracing data obtained from this embodiment can then be used to automatically compute spinal alignment parameters as described below in reference to FIGS. 66A-66B, and 67.

[00464] FIG. 62A displays one embodiment of the invention which consists of acquiring information regarding the contour of the spine via tracing over body surfaces using a tracked probe. This embodiment consists of spine bony anatomy 6211, overlying skin 6215 interrupted to represent a surgical site 6220, skin-mounted fiducials 6226, 6228 applied to two regions outside of the surgical site with overlying surgical drapes 6208 and over-the- drape-mating fiducials 6225, 6227. Using a 3D-tracked probe, tracing coordinates are acquired over the skin of the cervicothoracic spine 6202, surgical site 6204, and skin of the lumbosacral spine 6205. After acquiring this traced data, the acquisition system software can interpret it with the aid of fiducial initialization data, previously described in relation to FIGS. 4A-4I, and 58 to represent one complete bony surface contour from which spinal alignment parameters can be calculated, as described below in reference to FIGS. 67, and 69.

[00465] FIG. 62B displays on embodiment of the invention which is a display of the acquired body surface contours via tracing with a 3D-tracked probe within the optical 3D- tracking camera's axes, containing the 3D coordinates of the over-the-drape-mating fiducials 6251, cervicothoracic skin tracing 6253, surgical site tracing 6255, and lumbosacral skin tracing 6257. In order to properly interpret this data, the acquisition software has to rigidly transform the data such that it is represented within anatomical reference axes rather than camera axes. The mechanism of establishing anatomical reference axes was previously described in relation to FIGS. 12 and 61 and the transformed data is shown below in reference to FIG. 62C. [00466] FIG. 62C displays one embodiment of the invention which is transforming the acquired tracing data as described previously in relation to FIGS. 62A-B, to be interpreted and displayed within anatomical reference axes including the coordinates of the over-the- drape-mating fiducials 6261, cervicothoracic skin tracing 6263, surgical site tracing 6205, and lumbosacral tracing 6267. Interpreting and displaying the acquired 3D-tracing data in this way enables subsequent manipulation and calculations as described below in relation to FIGS. 62D and 67.

[00467] FIG. 62D displays one embodiment of the invention which is the translation of the acquired tracing data previously described in relation to FIGS. 62A-62C. In this embodiment, based on the displacement vector between the initialized skin fiducial and anatomical regions of interest, and based on the displacement vectors between the skin tracing locations most closely approximating the surgical site tracing and the end points of the surgical site tracing, any skin-surface tracing is translated to represent one continuous tracing of bony anatomy. As shown in the figure, this embodiment consists of the translated coordinates for the cervical fiducial 6281, cervicothoracic skin tracing 6283, lumbosacral tracing 6285, and lumbosacral fiducial 6287. From the data coupling the translated tracings to the surgical site tracing (if applicable), spinal alignment parameters can then be calculated as described below in reference to FIG. 67. Additionally, if a quantitative assessment of aligning is desired for the surgical site only, that is also achievable with the acquired data in this embodiment, as described in more detail below in reference to FIG. 68.

[00468] Some embodiments of this invention include the use of a tracked mobile stray marker (TMSM) to communicate particular commands to the computer system via its tracked dynamic motion relative to the 3D-tracked tool end effector. For example, FIG. 63 shows a workflow 6300 for analog triggering detection of one or more tracked mobile stray marker (TMSM) relative to a tracked tool with a DRF in accordance with some embodiments of the invention. In some embodiments, other relevant figures related to linear actuation of the TMSM relative to the probe shaft can include, but not be limited to, FIGS. 10A-10E, FIGS. 29A-29C, FIGS. 38C and 38G, FIGS. 39A-39B, FIGS. 44B-44D, FIGS. 45A-45B, FIGS. 51E-51H, FIGS. 53 A, 53C, and FIG. 53D, and FIGS. 57A-57B. In some embodiments, other relevant figures related to rotational actuation of the TMSM on a rigid arm relative to the probe shaft can include, but not be limited to, FIG. 4H, FIGS. 15A-15C, FIGS. 48B-48C, FIGS. 49A-49D, FIGS. 50A-50E, and FIGS. 82A-82B. In some embodiments, some relevant figures related to calculation of angle of TMSM with respect to the probe shaft can include, but not be limited to, FIGS. 64A-64B.

[00469] Some embodiments of the invention involve the use of a TMSM that is mechanically linked to a 3D-tracked tool and tracking its dynamic position relative to the coordinates of the 3D-tracked tool, which is defined by a coupled DRF and its associated tool definition file. Some embodiments involve the use of a depressible tip that actuates a rod that is coaxial to the shaft of a 3D-tracked tool. In some embodiments, the TMSM is attached to the depressible rod and subsequently its distance from the tip of the 3D-tracked tool, or any other defined component relative to the DRF of the tool, can dynamically change upon actuation of the depressible tip, following a linear path of motion. Some embodiments of the system use the 3D location of the TMSM and apply to it a 3D rigid transformation of the 3D location and orientation of the 3D-tracked tool relative to the 3D-tracking acquisition unit. The TMSM location data is now transformed to be relative to the coordinate system of the 3D-tracked tool, and thus does not perturb with respect to moving the 3D-tracked tool in space without triggering the depressible tip to change the location of the TMSM relative to the 3D-tracked tool. In some embodiments, the resulting magnitude of the vector between the transformed TMSM and the 3D-tracked tool end effector is the mathematical that is tracked for the system to detect when an event has occurred to note information or store data produced by the position of the 3D-tracked tool.

[00470] In some embodiments, the dynamic change of the magnitude of the vector between transformed TMSM coordinates and the coordinates of the 3D-tracked tool's end effector can be analyzed for detecting specific thresholds of magnitude for a binary system behavior, or also analyzed at various levels of magnitude across the possible range of motion of the TMSM relative to the 3D-tracked tool's end effector, representing a more analog system behavior. Some example embodiments are depicted in FIG. 10A, FIG. 10B, FIG. 10D, FIG. 10E, FIG. 29A, FIG. 29B, FIG. 29C, FIG. 38C, FIG. 38G, FIG. 39A, FIG. 39B, FIG. 44B, FIG. 44C, FIG. 44D, FIG. 45 A, FIG. 45B, FIG. 5 IE, FIG. 5 IF, FIG. 51G, FIG. 51H, FIG. 53 A, FIG. 53C, FIG. 53D, FIG. 57A, and FIG. 57B. In addition, some embodiments of the system can calculate the angle between two vectors to communicate when the behavior of the TMSM is used to communicate a specific command (e.g., such as the vector between the 3D-tracked tool's end effector and the rotation axis of the arm, which is mechanically linked to the 3D-tracked tool, that the TMSM is rigidly attached to, and the vector between the TMSM and the rotation axis of the arm, which is mechanically linked to the 3D-tracked tool, that the TMSM is rigidly attached to. In some embodiments, the system calculates the angle between these two vectors during the use of the 3D-tracked tool and constantly analyzes the angle of the vectors that are defined with respect to the coordinates of the 3D-tracked tool. In some embodiments, this dynamic angle calculation, such as the example described in FIG. 64A and FIG. 65B, can also be sensed in a binary or analog manner such as described above to enable various commands to be communicated to the 3D- tracking acquisition unit for a variety of applications. One example embodiment involves the use of a 3D-tracked tool with a rotationally-actuating TMSM to trace the spine at select regions and communicate to the system to only store location and orientation data of the 3D- tracked tool while the TMSM-based angle has reached a certain threshold via the actuation of a button on the 3D-tracked tool. Some example embodiments are depicted in FIG. 04H, FIG. 15 A, FIG. 15B, FIG. 15C, FIG. 48B, FIG. 48C, FIG. 49A, FIG. 49B, FIG. 49C, FIG. 49D, FIG. 50A, FIG. 50B, FIG. 50C, FIG. 50D, FIG. 50E, FIG. 82A, and FIG. 82B.

[00471] In some embodiments, any of the above processes, methods, or procedures related to the workflow 6300 can include or be accomplished with one or more of steps or processes 6310, 6312, 6314, 6320, 6318, 6316, 6322, 6324, 6326, 6328, 6330, 6332, 6334, 6336, 6338, 6340, 6342, 6344, 6346, 6350, 6354, and 6356. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 6328), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 6300 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 6300 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 6300 can be skipped.

[00472] FIG. 64A displays one embodiment of the invention consisting of a probe with a tip 6415, tracked DRF 6405, pivot arm 6430 containing a TMSM 6425 and pivoting about a pivot hinge 6410. In this embodiment, the coordinates of the probe tip, pivot hinge, and TMSM are known relative to the tracked DRF axes and the position of the TMSM relative to the DRF can be calculated in terms of relative angles as described below in reference to FIG. 64B. Further, FIG. 64B displays one embodiment of the invention consisting of the interpretation and calculation of the position of a rotating TMSM relative to the DRF on a probe as described previously in relation to FIG. 64A. In this software interpretation, a vector VI is defined from the probe tip 6415 through the pivot hinge 6410 and a vector V2 is defined from the pivot hinge to the TMSM 6425. The angle theta between VI and V2 is calculated as described previously in relation to FIG. 63 and used as a method of communicating analog or binary signals to the 3D-tracking acquisition system. This embodiment can be applied to any embodiment of the invention that involves a TMSM rotating about a hinge relative to a tracked DRF, as in those previously described in reference to FIGS. 15A-15C, 48A-48C, 55A-55I, 56C-56D, and 56F.

[00473] In some embodiments, based on data acquired from cross-sectional imaging (CT shown), a relative body and bony surfaces can be manually or automatically annotated to then calculate relative displacement vectors from points on each surface to one another (e.g., the displacement vector from the midpoint of the lamina to the vertebral body centroid). The acquisition software can utilize this information as input into the manipulation of data created by tracing body-surfaces with a 3D-tracked probe. For example, FIG. 65A illustrates displays of a discrete body surface or bony surface annotations on cross-sectional images used for initialization of patient-specific interpretation of body and bony surface tracings with a 3D-tracked probe in accordance with some embodiments of the invention. FIG. 65A displays a body surface or bony surface annotations on cross-sectional images (6510, 6512) to be used for initialization of patient-specific interpretation of body and bony surface tracings with a 3D-tracked probe. These annotated regions include but are not limited to skin surface, spinous process, lamina, transverse process, pedicle, vertebral body, and vertebral body centroid.

[00474] FIG. 65B illustrates 3D perspective of cross-sectional annotations from the CT scan in accordance with some embodiments of the invention, where based on these annotations, software comparison algorithms have a patient-specific reference to compare 3D-tracked tracing contours over bony surfaces to annotated surfaces from the cross-sectional imaging, and use the comparison to attempt to display a 3D perspective of the spine following a contour assessment tracing. Additionally, in other embodiments this data may be utilized for automatically detecting spinal levels represented by the traced contour within the surgical site.

[00475] FIG. 65C illustrates a plot of coronal projected coordinates in accordance with some embodiments of the invention. FIG. 65C displays coronal projected coordinates of annotated transverse processes (6514, 6520), laminae (6516, 6518), vertebral body centroids, skin surface (not shown), and spinous processes (not shown). This embodiment displays the similarity in coronal contours of annotations over varying bony elements. Additionally, it displays the basis of computing displacement vectors within the coronal plane. Further, FIG. 65D illustrates a plot of sagittal projected coordinates in accordance with some embodiments of the invention, and includes sagittal projected coordinates of annotated transverse processes (6528), laminae (6520), vertebral body centroids, skin surface (6522), and spinous processes (6524). This embodiment displays the similarity in sagittal contours of annotations over laminae, transverse processes, and vertebral body centroids across the length of the spine, which serves as valuable input into the interpretation of 3D-traced data previously described in FIG. 62A-62D as well as in the automated calculation of spinal alignment parameters from the tracings, as described below in reference to FIG. 67.

[00476] FIG. 65E illustrates computed cross-sectional distances between corresponding anatomical landmarks and vertebral body centroids in accordance with some embodiments of the invention. Shown are computed cross-sectional distances between corresponding anatomical landmarks and the vertebral body centroids (e.g., left lamina midpoints (6530), right lamina midpoints (6532), left transverse process midpoints (6534), and right transverse process midpoints (6536) etc.).

[00477] In some embodiments, acquired 3D-tracing data can be interpreted to represent the contour of the vertebral body centroids based on initialization data with or without the aid of fiducials. FIG. 66A illustrates a display of cross-sectional slices of vertebra (6601) in their relative anatomical axes in accordance with some embodiments of the invention, with coordinates (6603) from tracing over surgically exposed left lamina with a 3D-tracked probe, and right lamina (not shown), and the corresponding computed coordinates (6605) representing the vertebral body centroids on cross-sectional imaging.

[00478] Some other embodiments include a display of a vertebral body calculated via bilaterally traced coordinates and patient initialization data in accordance with some embodiments of the invention. For example, FIG. 66B displays one embodiment of the invention in which the location of a cross-section image's (6601) vertebral body centroid (6615) is calculated via bilaterally traced coordinates and patient initialization data. This embodiment also consists of left (6607) and right (6609) lamina coordinates as input from a tracked 3D probe tracing, a line segment (6611) connecting the two laminae coordinates, and an orthogonal line segment (6613) from the midpoint of the laminae-connecting segment and of a distance based on patient initialization information. It should be noted that there are varying embodiments of initialization of patient anatomy in this invention including but not limited to CT imaging annotation, as described in reference to FIGS. 13 and 65A-65E, intraoperative X-ray image annotation, normative patient data sets, fiducial-based initialization as previously described in reference to FIGS. 4A-4I, 6A-6C, 9, 44A-44D, 45 A- 45B, 58-60, and 62A-62D.

[00479] Some embodiments of this invention involve the process of filtering and segmenting a contour tracing produced by a 3D-tracked tool. In some embodiments, calculations can be derived from tracing data that is generated inside and outside of the surgical site, with or without annotations of particular anatomical landmarks of interest. For example, FIG. 67 illustrates a workflow 6700 to calculate spinal alignment parameters based on intraoperative tracing in accordance with some embodiments of the invention. Some relevant other figures can include, but not be limited to, FIGS. 9A-9B, FIGS. 21A-21B, and FIGS. 64A-64B (for initialization of tracing sequence, FIG. 12 (for initialization of patient's anatomical planes), FIG. 86 (for alignment parameter output, FIGS. 62, and 65-66 (for transforming of tracing data via 3D-displacement offset to curves generated by connecting other anatomical landmark locations.

[00480] Some embodiments of the invention involve the use of an electromechanical, 3D- tracking system, as depicted in FIG. 23 A and FIG. 23B. Other embodiments involve the use of an optical, 3D-tracking system, which is depicted in FIG. 5A. Further, some embodiments involve the initialization of the patient's anatomical planes via coordinate transformation references defined by tracked DRFs (e.g., FIG. 12), or tracings of a unique pattern or a plane that defines the orientation, direction, and location of the anatomical plane references that measurements generated by 3D-tracked tools will be transformed relative to after initialization. Further, some embodiments of the invention involve the classification of tracing data based on its relation to specific anatomical regions of interest (e.g., spinous processes, laminae, skin surface, transverse processes, etc.). Some embodiments of this anatomical classification of the tracing data are a result of software-based user inputs, proximity-based detections near registered fiducial markers or anatomical landmarks that have known associated locations relative to a 3D-tracking acquisition system, registration of a unique pattern with known dimensions, or via user-based, selective toggles actuated with 3D-tracked tools or DRFs, such as triggering of a tracked mobile stray marker attached to the 3D-tracked tool. Some examples of these embodiments include FIG. 9 A, FIG. 9B, FIG. 21 A, FIG. 21B, FIG. 64A, and FIG. 64B.

[00481] In some embodiments, once a continuous or discrete series of points is acquired via the 3D-tracked tool used in 3D coordinates relative to the 3D-tracking acquisition system, algorithms of the system can utilize data (e.g., including, but not limited to, fiducial -based 3D-displacement vector to one or more anatomical landmarks of interest, normative data of a patient population, or preoperative imaging annotations that define a 3D-displacement vector between anatomical regions that are traced and anatomical landmarks of interest), to transform the tracing data to approximate the contours produced by connecting points at key anatomical landmarks (e.g., curve generated by fitting line to several vertebral body centroids) across the region of the tracing. Examples of this described transformation process are depicted in FIG. 62A, FIG. 62D, FIG. 65A, FIG. 65B, FIG. 65C, FIG. 65D, FIG. 65E, FIG. 66 A, and FIG. 66B.

[00482] Some embodiments involve the use of first and second derivative calculations of filtered tracing contours to identify maxima, minima, and inflection points of the curves. Some embodiments involve using these calculated inflection points as reference lines used in the calculation of endplate-based coronal measurements (e.g., Cobb angles).

[00483] Some embodiments involve the use of annotation of one or more anatomical landmarks of interest as inputs into which segments of the tracing should the algorithm compute perpendicular lines used to make endplate-based measurements of the alignment of vertebral segments in the specific region, defined by one or more annotated anatomical landmarks. Some embodiments of the annotation process involve the registration of anatomical landmarks using 3D-tracked tools, software-based estimations based on registered references to cross-sectional imaging before or during the procedure, or via the location of registered fiducial markers relative to the tracing data. In some embodiments, from these segmented annotations of the tracing data, some embodiments involve the algorithmic calculation of spinal alignment parameters (e.g., Cobb angle, lumbar lordosis (LL), thoracic kyphosis (TK), C2-C7 sagittal vertical axis (SVA), C7-S1 SVA, C2-S1 SVA, central sacral vertical line (CSVL), Tl pelvic angle (T1PA), pelvic tilt (PT), pelvic incidence (PI), chin- brow to vertical angle (CBVA), Tl slope, sacral slope (SS), Cl-2 lordosis, C2-C7 lordosis, C0-C2 lordosis, C1-C2 lordosis, PI-LL mismatch, C2-pelvic tilt (CPT), C2-T3 angle, spino- pelvic inclination from Tl (Tl SPi) and T9 (T9SPi), CO slope, mismatch between T-1 slope and cervical lordosis (T1 S-CL), and/or global sagittal angle (GSA)). One embodiment of the display of these calculated alignment parameters, along with thresholds pre-defined in the literature for patient-specific surgical goals, is depicted in FIG. 86A, FIG. 86B, and FIG. 86C.

[00484] In some embodiments, any of the above processes, methods, or procedures related to the workflow 6700 can include or be accomplished with one or more of steps or processes 6702, 6704, 6706, 6712, 6710, 6708, 6714, 6716, 6718, 6720, 6722, 6724, 6726, 6728, 6730, 6732, 6738, 6740, 6734, 6736, 6742, 6744, 6746, and 6748 as shown. In some embodiments, the steps of workflow 6700 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 6700 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 6700 can be skipped.

[00485] Some embodiments of this invention involve the process of filtering and segmenting a contour tracing produced by a 3D-tracked tool only registering points within the surgical site. In some embodiments, calculations are derived from tracing data that is generated inside the surgical site, with or without annotations of a particular anatomical landmark of interest, as well as with or without registration of bone-mounted fiducial markers in the surgical site. For example, FIG. 68 illustrates a workflow to acquire a spinal alignment curve using probe-based tracing within only the surgical site in accordance with some embodiments of the invention. Other relevant figures can include those related to registration of bone-mounted fiducial markers with one or more anatomical landmarks of interest (FIGS. 59 and 60), triggering of tracked mobile stray markers attached to 3D-tracked tool (FIG. 63), calculating spinal alignment parameters based on intraoperative tracing (see FIGS. 67).

[00486] Some embodiments involve the use of bone-mounted fiducial markers that are registered to one or more nearby anatomical landmarks of interest via a 3D-displacement vector, such as the processes depicted in FIGS. 59-60. Some embodiments involve the communication of commands to the 3D-tracking acquisition system that a tracing or registration is occurring, such as the processes depicted in FIG. 63. Some embodiments involve the user annotating particular anatomical landmarks, via processes such as tracing or discrete-point tapping of registered fiducial markers, or also mechanically coupling between the 3D-tracked tool and the fiducial marker. Some embodiments involve the computer system only storing data that is generated by the 3D-tracked tool while it traces or discretely registers the contour of the anatomical region of interest that begins and ends with the registration of or proximity-detection event of a bone-mounted fiducial marker. Some embodiments involve the user identifying the tracing region of interest in relation to the anatomical sections of the patient via manual display monitor inputs that define the landmarks that the tracing will span. Some embodiments involve the calculation of spinal alignment parameters based on registered contour of the tracing data and/or annotation of one or more anatomical landmarks of interest. Some examples of this process were described in FIG. 67.

[00487] In some embodiments, any of the above processes, methods, or procedures related to the workflow 6800 can include or be accomplished with one or more of steps or processes such as 6802, 6804, 6806, 6808, 6810, 6812, 6816, 6814, 6816, 6822, 6818, 6820, 6822, 6824, 6826, 6828, 6830, 6832, 6834, 6836, 6838, 6840, 6842, and 6844. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 6814), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 6800 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 6800 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 6800 can be skipped.

[00488] FIG. 69 illustrates a workflow 6900 to acquire a spinal alignment curve using probe-based tracing data spanning beyond the surgical site in accordance with some embodiments of the invention. Some embodiments of the invention involve the process of filtering and segmenting a contour tracing produced by a 3D-tracked tool registering points within and beyond the surgical site. In some embodiments, calculations are derived from tracing data that is generated inside the surgical site, with or without annotations of one or more particular anatomical landmarks of interest, with or without registration of bone- mounted fiducial markers in the surgical site, as well as with or without registration of skin- mounted fiducial markers beyond the surgical site. Some other relevant other figures include FIGS. 59-60 (for registration of bone-mounted fiducial markers with one or more anatomical landmarks of interest), and FIG. 63 (the triggering of tracked mobile stray markers attached to 3D-tracked tool). Others include FIG. 67 (for calculating spinal alignment parameters based on intraoperative tracing), FIG. 68 (outling a process of calculating alignment using tracings and bone-mounted fiducials, FIGS. 6B, 9A-B, 11A-B (related to kin-based fiducial markers), and FIGS. 62A, 62D, 65A-E, 66A-B (related to calculating the displacement offset between tracing data and anatomical landmarks of interest). [00489] Some embodiments of this invention involve initializing the key anatomical landmarks of interest, such as those that are required for spinal alignment parameter calculations. Some embodiments involve depictions that are shown in FIGS. 6B, 9A-B, 11A- 11B, 59, 60, and 68. Some embodiments involve tracing anatomical structures within the surgical site as well as registering landmarks, such as skin-based fiducial markers, beyond the surgical site. Some of these embodiments involve applying offsets based on initialized 3D- displacement vectors, such as the examples depicted in FIGS. 62A, 62D, 65A-65E, and 66A- 66B. Further, some embodiments of communicating when to store tracing data and classifying particular tracings as related to an anatomical region involve example embodiments depicted in FIGS. 9A-9B, 62A-62D, 59, and 63.

[00490] In some embodiments, any of the above processes, methods, or procedures related to the workflow 6900 can include or be accomplished with one or more of steps or processes such as 6902, 6904, 6906, 6908, 6910, 6912, 6914, 6916, 6918, 6920, 6922, 6924, 6926, 6928, 6930, 6932, and 6934. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 6924), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 6900 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 6900 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 6900 can be skipped.

[00491] Some embodiments of this invention involve the process of calculating the flexibility or range of motion of a particular anatomical region of interest. Some embodiments enable the user to mechanically manipulate the conformation of the spine while calculating the quantitative flexibility of a region of the spine. For example, FIG. 70 illustrates a workflow 7000 to assess flexibility of the spine intraoperatively using flexibility assessment device in accordance with some embodiments of the invention. Other relevant figures (e.g., such as in relation to a flexibility assessment device can include FIGS. 34A- 34G, FIGS. 35A-35F, FIGS. 36A-36I, FIGS. 37A-37G, FIGS. 39A-39F, and FIGS. 40A-40C. Further, flexibility assessment devices on spine, including during set-and-hold manipulation of adjusting the correction of the spine include FIGS. 42A-42F, and FIG. 70.

[00492] Some embodiments of this invention involve the rigid fixation of a 3D-tracked tool, which can be arranged in adjustable configurations, with vertebrae in the exposed surgical site via attachment rigid landmarks, such as the pedicle screws. Further, some embodiments of the system involve the ability of the 3D-tracked tool to rigidly attach to more than one pedicle screw on a vertebra at once. Examples of some embodiments in various applications and forms, but not exhaustive to all possible and developed design permutations, include those depicted in at least FIGS. 34A-34G, 35A-35F, 36A-36I, 37A-37G, 39A-39F, and 40A-40C.

[00493] Some embodiments involve the x-ray-based registration of the vertebral endplate angle with respect to the 3D-tracked tool side surface. Some embodiments of the system involve the use of one or more of the specified 3D-tracked tools to manipulate multiple regions of the anatomy and store location and orientation information detected by the 3D- tracking acquisition system. Some embodiments of the system involve the calculation of relative angles between two or more 3D-tracked tools rigidly attached to vertebra at the end of the assessment region of interest. In some embodiments, this angle can provide an assessment of the flexibility of the spine, as the system is able to measure the relative angle between two or more 3D-tracked tools during manipulations that explore the full range of motion of the attached vertebrae. Some examples of this manipulation and measurement process are depicted in FIGS. 42A-F.

[00494] In some embodiments, any of the above processes, methods, or procedures related to the workflow 7000 can include or be accomplished with one or more of steps or processes such as 7002, 7004, 7006, 7008, 7010, 7012, 7014, 7016, 7018, 7020, 7022, 7024, 7026, and 7028. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 7014), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 7000 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 7000 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 7000 can be skipped.

[00495] Some embodiments of this invention involve the process of overlaying a surgical instrument using 3D-tracking dynamic reference markers to approximate the 2D, projected shape of the instrument on the 2D radiograph of an anatomical region of interest. For example, FIG. 71 illustrates a workflow of producing real-time overlays of surgical instruments over intraoperative x-rays in accordance with some embodiments of the invention. Some other figures, for example as related to a process of overlay illustration using 3D-tracked tool and C-arm X-ray images are described in relation to FIGS. 46A-46G. [00496] Some embodiments of the invention involve utilizing a 3D-tracked tool with a coupled tracked DRF. Some embodiments also involve the use of a DRF rigidly attached to the emitter of an x-ray imaging system, such as a C-arm. Further, some embodiments involve using the relative distance and orientation of the 3D-tracked tool with respect to the x-ray imaging system to calculate the appropriate size and 2D-projected shape of the surgical tool with the attached DRF on the x-ray image.

[00497] In some embodiments, the system utilizes the known distance of the 3D-tracked surgical tool away from the x-ray imaging system, the size and dimensions of the surgical tool, the location and orientation of the surgical tool, and the location and orientation of the imaging system, all with respect to the coordinates of the 3D-tracking acquisition system, to produce an accurate 2D projection of the tracked surgical tool with appropriate scaling and pose with respect to the x-ray imaging system. Some embodiments include computing the rigid transformation between the tracked surgical tool and the imaging system to transform the tool's location and orientation to be outputted with respect to the imaging system coordinates. Further, some embodiments of the system enable for the visual overlay of the computed 2D-projection of 3D-tracked surgical tool based on its distance and pose in relation to the volume of the cone beam of the x-ray imaging system.

[002160] In some embodiments, any of the above processes, methods, or procedures related to the workflow 7100 can include or be accomplished with one or more of steps or processes such as 7102, 7104, 7106, 7108, 7110, 7112, 7114, 7116, 7118, 7120, 7122, 7124, 7126, 7128, 7130, 7132, 7134, 7136, 7138, 7140, and 7142. In some embodiments, the steps of workflow 7000 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 7000 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 7000 can be skipped.

[00498] Some embodiments of this invention involve the process of registering the location and orientation with accessible fiducial markers, surgical implants, or anatomical landmarks, that are registered to the vertebrae and surrounding anatomical landmarks of interest. For example, FIG. 72 shows a workflow 7200 to rapidly re-register a surgical navigation system after a navigated/registered screw insertion in accordance with some embodiments of the invention. The workflow 7200 describes methods for producing 3D renderings of the vertebrae of interest by registering the location and pose of the vertebrae of interest with respect to known landmarks that are registered in 3D-based images acquired of the vertebra (e.g., CT scan). Some other relevant figures include FIGS. 44A-44D (for a method of registering a rigidly-attached landmark of a vertebra, and FIGS. 45A-45B (for a process of re-registering a manipulated vertebra via a known landmark (e.g., pedicle screw shaft)).

[00499] Some embodiments of the system involve the use of navigated pedicle screws to register the relationship between the pedicle screw shaft and the vertebral body. Some embodiments of the system involve the use of registered bone-mounted fiducials that are associated with a 3D-displacement vector to anatomical landmarks of interest of the attached vertebra. One example embodiment is depicted in FIGS. 44A-D.

[00500] Some embodiments involve the registration of landmarks of interest of the vertebra with a volumetric 3D reconstruction of the anatomy via modalities such as a CT scan or O-arm scan. Further, some embodiments involve the system registering one or more accessible fiducial markers, surgical implants, or anatomical landmarks as associated components of a 3D reconstruction of the vertebrae. In this way, each time one or more of the described items are registered by a 3D-tracking acquisition system with location and orientation outputs, the system can calculate the updated position and orientation of anatomical objects of interest that have associated 3D reconstructions. One example embodiments is depicted in FIGS. 45A and 45B.

[00501] In some embodiments, any of the above processes, methods, or procedures related to the workflow 7200 can include or be accomplished with one or more of steps or processes such as 7202, 7204, 7205, 7206, 7208, 7210, 7212, 7214, 7216, 7218, 7220, 7222, 7224, 7226, 7228, 7230, 7232, 7234, 7236, 7238, 7240, 7242, 7244, 7246, and 7248. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 7212), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 7200 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 7200 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 7200 can be skipped.

[00502] FIGS. 73A-73B display one embodiment of the invention which consists of interpretation of the rod contour via interfacing with a rod-centering fork as described previously in relation to FIGS. 47B, 51D-51I, and 53A-53F, and 54A-54D. This acquisition system's calculation is based on the calculated distance from the fork's bifurcation to the rod's cross-sectional center point when a rod of known diameter is fully engaged with the fork of known geometry. For example, FIG. 73A displays one embodiment 7300 of the invention which consists of a rod-centering fork (7315) on the end of a tool shaft (7305) with attached tracked DRF (not shown), bifurcation at point C (7310), and interfacing with a rod (7311). In this configuration, because the fork is not fully engaged with the rod (i.e., the rod is not approximating both side walls of the fork), the tool does not trigger the acquisition system to record the tool's coordinates. This triggering mechanism to indicate the fork is firmly engaged with the rod can be accomplished via a number of varying embodiments including but not limited to a linearly actuated TMSM, rotationally actuated TMSM, electrical conduction through the rod across fork-mounted electrical contact terminals, wireless or wired electronic communication, and optically signaled via visible or infrared lights.

[00503] FIG. 73B illustrates the fork of FIG. 73 A fully engaged with a rod represented as embodiment 7301 in accordance with some embodiments of the invention. For example, FIG. 73B displays rod-centering fork (7315) on a tool shaft (7305) fully engaged with a rod 7317 such that both inner walls of the fork 7315 are approximating the rod surface. In this embodiment, point C 7310 indicating the bifurcation of the fork is known relative to the tracked DRF (not shown) attached to the tool. Based on the known diameter of the rod and geometry of the fork, a vector VI (7319) is produced to point from C 7310 to the calculated center point of the rod, C (7318), located along the line that bisects the fork. After interpreting the location of point C 7318 relative to the tracked DRF attached to the fork- equipped tool, the coordinates of C 7318 undergo a rigid body transformation to be represented within the coordinates of a DRF-equipped end cap, if applicable. For embodiments that do not involve a coupled end-cap as described previously in relation to FIGS. 52A-52D, 53A-53F, and 54A-54D, the rod coordinates are interpreted relative to the camera coordinates or anatomical reference marker if present.

[00504] Some embodiments of this invention involve the process of registering the contour of a rod implant via a combination of 3D-tracked tools. For example, FIG. 74 illustrates a workflow to assess the contour of a rod prior to implantation using two handheld tracked tools in accordance with some embodiments of the invention. Some other relevant other figures (e.g., such as tools used for assessing rod contour include FIGS. 48A-48C, 49D, 50D- 50E, 51H-51I, 53C-53D, and 54C-54D). Further, other figures and descriptions for tools using a tracked mobile stray marker as a trigger include FIG. 63.

[00505] Some embodiments of this invention involve the use of one or more 3D-tracked tools that have a rigidly attached tracked DRF. Some embodiments of the system involve using a 3D-tracked tool that rigidly attaches to one end of a surgical rod. Some example embodiments are depicted in FIGS. 48A-C, and 49D. Some embodiments involve selecting a rod diameter via various communication signals (e.g., FIGS. 49D, and 50D-50E) using 3D- tracked tools and rigidly attached tracked mobile stray markers (TMSMs) that the computer system can detect as a trigger, as depicted in FIG. 63.

[00506] Some embodiments involve using a second 3D-tracked tool with an end-effector that conforms to a rod surface and contains a depressible shaft that is coaxial with the shaft of the 3D-tracked tool. In some embodiments, when the 3D-tracked tool is pressed against the rod surface, the depressible tip actuates up the 3D-tracked tool and translates a TMSM that is rigidly attached to the depressible shaft, (which signals to the 3D-tracking acquisition system that the rod is being engaged). Some embodiments of this system involve using this 3D- tracked tool in a active/triggered state to trace the contour of the rod, and simultaneously to apply a rigid transformation to each discrete point of tracing data to reference the 3D-tracked end cap tool that has dynamic location coordinates and orientation with respect to the 3D- tracking acquisition system.

[00507] Some embodiments of this system involve the rod, which is attached to the 3D- tracked end cap tool, and inserting the opposite end through a toroid-shaped object that allows for cross-sections of the rod (that are parallel to its entry way) to pass through. In this instance, the dynamic path traveled by the 3D-tracked end cap can be used to calculate the contour of the rod by association of the constraints of the bends causing a travel path for the 3D-tracked end cap. Some example embodiments of this system in various applications and forms are depicted in at least FIGS. 48A-48C, 49D, 50D-50E, 51H-51I, 53C-53D, and 54C- 54D.

[00508] In some embodiments, any of the above processes, methods, or procedures related to the workflow 7400 can include or be accomplished with one or more of steps or processes such as 7402, 7404, 7406, 7408, 7410, 7412, 7414, 7416, 7418, 7420, 7422, 7424, 7426, 7428, 7430, 7432, 7442, 7443, 7440, 7438, 7434, and 7436. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 7404 and 7422), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 7400 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 7400 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 7400 can be skipped.

[00509] Some embodiments of this invention involve the process of registering the contour of a rod implant via a combination of 3D-tracked tools and stationary objects. FIG. 75 illustrates a workflow 7500 to assess the contour of a rod prior to implantation using one handheld tracked tool and one rigidly fixed ring in accordance with some embodiments of the invention. In some embodiments, other relevant figures include tools used for assessing rod contour (FIGS. 48A-C, 50B-C), a ring-based tracing tool (FIGS. 49A-49D), and similar tracked end cap-based process of rod contour assessments (e.g., such as FIGS. 74-75).

[00510] Some embodiments of this system involve a similar process to that described in FIG. 74, in which a 3D-tracked end cap tool with a rigidly tracked DRF is used to serve as a tracked coordinate system reference for the rod contour. Some embodiments of this system involve inserting the rod's opposite end through a toroid-shaped object that is fixed in space, (and that allows for cross-sections of the rod that are parallel to its entry way) to pass through. In this instance, the dynamic path traveled by the 3D-tracked end cap tool is used to calculate the contour of the rod by association of the constraints of the bends causing a travel path for the 3D-tracked end cap.

[00511] Some embodiments involve the use of one or more tracked mobile stray markers (TMSMs) attached to a fixed toroid-shaped object, where one hinge-based TMSM is actuated relative to a fixed TMSM to indicate to the 3D-tracking acquisition system when a rod is being inserted through its passage way. Some example embodiments include FIGS. 49A- 49D.

[00512] Some embodiments involve applying a rigid transformation to the fixed toroid- shaped object's location and orientation, which is relative to the 3D-tracked acquisition unit, and transforming its position to be relative to the location and orientation of the 3D-tracked end cap tool. Some examples of embodiments in various applications and forms are depicted in FIGS. 48A-C and 50B-C. [00513] In some embodiments, any of the above processes, methods, or procedures related to the workflow 7500 can include or be accomplished with one or more of steps or processes such as 7502, 7504, 7506, 7508, 7510, 7512, 7514, 7516, 7518, 7520, 7522, 7524, 7526, 7528, 7530, 7532, 7534, 7536, 7538, 7540, 7542, 7544, 7546, 7548, 7550. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 7504 or 7532), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 7500 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 7500 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 7500 can be skipped.

[00514] Some embodiments of this invention involve the process of registering the contour of a rod implant via a combination of 3D-tracked tools after the rod has been implanted into the spinal anatomy. FIG. 76 illustrates a workflow 7600 to assess the contour of a rod after implantation in accordance with some embodiments of the invention. In some embodiments, other elevant figures include those that relate to rod contour triggering of a 3D-tracked tool (FIGS. 53A, and 53C-53D, 54A-54D, and 73A-73B), and rod contour assessment process while rod is implanted (FIG. 77A-77C).

[00515] Some embodiments involve designs with a depressible shaft that is coaxial to the shaft of a 3D-tracked tool, where the depressible shaft is mechanically linked to a tracked mobile stray marker (TMSM) that can signal to the 3D-tracking acquisition system that a rod is being traced when the TMSM is actuated relative to the 3D-tracking tool's end effector. Some examples of embodiments of this process are depicted in FIGS. 53A, and 53C-53D. Other embodiments for sensing when the 3D-tracked tool is pressed against the rod surface are depicted in FIGS. 54A-D and 73A-B.

[00516] Some embodiments involve using the described rod-sensing, 3D-tracked tool to trace the contour of a rod while it is implanted and collecting the 3D location and pose of the tool during the process. Some embodiments involve the computer system fitting a line between the interruptions in the tracing caused by other surgical implants (e.g., pedicle screw heads) to estimate the full contour of the rod that is implanted. Some examples of embodiments of this system are depicted in FIGS. 77A-C. [00517] In some embodiments, any of the above processes, methods, or procedures related to the workflow 7600 can include or be accomplished with one or more of steps or processes such as 7602, 7604, 7606, 7608, 7610, 7612, 7614, 7620, 7618, 7616, 7622, and 7624. In some embodiments, any of the steps of the workflow 7600 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 7600 can be skipped.

[00518] Some embodiments include interpretation of data generated by the assessment of a rod contour after a rod has been implanted to the tulip heads within the surgical site, including any data from embodiments previously described in relation to FIGS. 52A-52D, 53A-53F, 54A-54D, 73A-73B, and 76.

[00519] FIG. 77A displays one embodiment of the invention which involves spinal vertebra 7740 that have been instrumented with pedicle screws 7745 and a rod 7720 implanted into their tulip heads 7722. The contour of this rod is able to be assessed while implanted within the surgical site in this way via utilization of the embodiments described previously. FIG. 77B displays one embodiment of the invention which consists of an implanted rod and surrounding elements described previously in relation to FIG. 77A and use of a post-implantation rod contour assessment device 7780, described previously in relation to FIGS. 52A-52D, 53A-53F, 54A-54D to interface with and trace the coordinates of the implanted rod such that the coordinates of the activated device 7728 are recorded while the inactive coordinates 7782 are discarded. The contour assessment device is designed in such a way to trigger only when the device is fully engaged with the rod, so when the device is removed from the rod to navigate around path-obstructing hardware, it is not triggering to the acquisition system to record its coordinates. The embodiments describing the acquisition process and interpretation of an implanted rod's coordinates based on the coordinates of the assessment device were previously described in relation to FIGS. 73 and 76. Further, FIG. 77C displays one embodiment of the invention for interpreting the data obtained from an implanted rod's contour assessment with a device as previously described in FIGS. 77A-B consisting of the plotted coordinates representing the rods contour from actively-triggered assessment device 7790 and the reconstructed rod contour 7792 based on the interpretation of the recorded rod data points. In one embodiment, this reconstructed contour is produced via a spline defined by the inputs of the recorded rod coordinates. Other embodiments of producing this reconstructed rod include but are not limited to variable order polynomial fitting and smoothing filters applied to the recorded rod coordinates.

[00520] Some embodiments of this invention involve the process of projecting an overlay of a registered 3D contour of a spinal rod onto patient imaging on a display monitor and allowing the user to interactively place and adjust the position of the rod overlay. For example, FIG. 78 illustrates a workflow 7800 for interactive user placement of a registered rod as an overlay on patient images on a display monitor in accordance with some embodiments of the invention. Some other relevant figures and descriptions include FIGS. 74-76 (for processes for assessing the contour of a rod, pre- and post-implantation), and FIGS. 87F-87G (for interactive overlay of registered rod contour on patient imaging).

[00521] Some embodiments of the invention involve maintaining usage of the 3D-tracked end cap tool that is rigidly attached to a previously-registered rod contour. Some embodiments of the invention involve the user confirming the coordinates of the overlay interaction by pointing the 3D-tracked end cap tool with the registered rod at the display monitor and triggering via a tracked mobile stray marker (TMSM) when the orientation of the 3D-tracked end cap tool matches the up/down and left/right motions that map the overlay in an intuitive manner for the user to manipulate on the display monitor.

[00522] Some embodiments involve the user manipulating the 2D projections of the registered contour of the rod via the movement of the 3D-tracked end cap tool along the preselected orientation of the tool relative to the orientation of the display monitor. Some embodiments involve the patient preoperative or intraoperative imaging being scaled in physical units (e.g., millimeters) and enabling for the accurate scaling of the overlay of the registered rod contour. Some further embodiments involve the user being able to select two or more points on the image that the rod contour overlay should intersect with and manipulate its contour position and orientation to meet those point intersection constraints. Some examples of embodiments of this invention in various applications and form are depicted in FIGS. 74-76, with the interactive overlay of the rod contour on a display monitor with patient imaging depicted in FIGS. 87F-87G.

[00523] In some embodiments, any of the above processes, methods, or procedures related to the workflow 7800 can include or be accomplished with one or more of steps or processes such as 7802, 7804, 7806, 7808, 7810, 7812, 7814, 7816, 7822, 7828, 7830, 7832, 7834, 7836, 7838, 7818, 7820, 7826, 7824, 7844, 7840, 7846, 7848, 7842, and 7850. In some embodiments, any of the steps of the workflow 7800 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 7800 can be skipped.

[00524] FIGS. 79A-79G relate to an embodiment of the invention which consists of the process of interpreting and calculating a tracked rod bending device, as previously described in relation to FIGS. 55D-55I, 56A-56D, and 56F, interfacing with a rod which has had its contour previously registered via embodiments previously described in relation to FIGS. 49D, 50E, and 51H-51I, and enables the interpretation and calculation of the rod's new contour based on acquisition system input from the tracked rod bender as related to the previously registered rod coordinates relative to the tracked-DRF-equipped end cap to which the rod is secured.

[00525] FIG. 79A displays one embodiment of the invention consisting of the coordinates of a previously registered contour of rod 7900 with known diameter, projected onto the 2D plan of the rod bending tool, defined by the middle of the three rod-interface points on the rod bender. FIG. 79B displays one embodiment of the invention consisting of the previously registered rod contour 7900, described previously in relation to FIG. 79A, and the relative locations of the rod bender's left outer roller 7904, center rod contouring surface 7906, and right outer roller 7905. As shown in this embodiment, the three rod-interface components of the bender are engaged with the rod, indicated by being displayed tangential to the previously registered rod contour.

[00526] FIG. 79C displays one embodiment of the invention consisting of the previously registered rod coordinates divided into three segments: the left unengaged rod segment 7901, bender-engaged segment 7903, and right unengaged segment 7902. In addition, this embodiment includes lines connecting the center rod contouring surface to the left outer roller 7920 and right outer roller 7922 from which the angle between them 7924 can be calculated. When the bender is engaged with a straight rod, this angle will be at a minimum, as opposed to when the bender is applying maximum curvature to the rod, this reference angle will be at a maximum.

[00527] FIG. 79D displays one embodiment of the invention in which the rod bender's handles are approximated to induce a bend in previously registered rod such that the angle 7952 between lines (7920, 7922) previously described in relation to FIG. 79C, is increased. From the known current bend configuration of the tracked bender, the bender's known geometry, and the known rod diameter, the acquisition system software then computes rod contact points (displayed as solid circles) on the left outer roller 7948, center contour surface 7951, and right outer roller 7953 by solving for tangent lines between each rod-interface surface.

[00528] FIG. 79E displays one embodiment of the invention which the rod contact points calculated and described previously in relation to FIG. 79D are used as constraints for defining a spline connecting each of them, and producing the newly computed bender- engaged segment of the rod contour 7903 a and based on the path length of the spline, (which is longer when the bender is in the bent configuration than straight configuration), updated left 7901a and right 7901b unengaged segments of the rod are interpreted. Further. FIG. 79F displays one embodiment of the invention which involves tangentially re-approximating the left 7971 and right 7972 unengaged segments of the rod contour as previously described in relation to FIG. 79E, by undergoing a rigid body transformation to both translate and rotate to tangentially approximate the spline-produced bender-engaged contour of the rod.

[00529] FIG. 79G displays one embodiment of the invention in which the embodiments described previously in relation to FIG. 79A-F are utilized to produce updated projected coordinates of the rod's contour 7999 after bending with a tracked bender and combined with 3D contour coordinates prior to the bend to compute and update the registered 3D-curvature of the rod. It should be noted that the embodiments described previously in relation to FIGS. 79A-G can be applied to calculate and update pre-registered rod contours when interfacing with tracked rod benders previously described in FIGS. 55D-55I, 56A-56D, and 56F.

[00530] Some embodiments of this invention involve the process of tracking the dynamic contour of a registered rod that is being contoured into a new shape prior to implantation of the rod. For example, FIG. 80 illustrates a workflow for manually bending a rod prior to its implantation with real-time feedback of its dynamic contour in accordance with some embodiments of the invention. Other relevant figures and descriptions can include FIGS. 55A-55I, 56A-56F (devices used to bend registered rod and track changes in its contour), FIGS. 79A-G (for calculation of rod bending of of a registered rod contour), and FIGS. 87A- G, 88A-F (for display of rod bending feedback of a registered rod contour), and FIGS. 74-76 (for processes for assessing the contour of a rod, pre- and post-implantation). In some embodiments, the workflow 80 can comprise steps 8002, 8004, 8006, 8008, 8010, 8014, 8016, 8018, 8020, 8022, 8024, 8026, 8028, 8030, 8032, 8034, 8036, 8040, 8044, 8038, 8042, and 8046.

[00531] Some embodiments of this invention involve tracking the dynamic changes of a registered rod contour that has maintained rigid fixation to a 3D-tracked end cap tool that has a coupled tracked DRF. Some embodiments of this invention involve processes for previously registering the rod, for which some examples are depicted in FIGS. 74-76.

[00532] Some embodiments of this system involve using a mobile, 3D-tracked rod bender and a tracked mobile stray marker (TMSM) rigidly attached to the opposite end of the registered rod to that of the 3D-tracked end cap tool attached to the rod. Some embodiments interpret the angle between the handles of the 3D-tracked rod bender's bending points, the position of the rod bender along the contour of the rod, and the orientation of the rod bender relative to that of the 3D-tracked end cap tool relative to the 3D-tracking acquisition system, to calculate the approximate new contour of the registered rod based on the deflected segments of the rod. One example of this algorithmic calculation process is depicted in FIGS. 79A-G. Some, but not all, example embodiments and permutations of the system that can assess, manipulate, and update the contour of the registered rod are depicted in FIGS. 55A-I, 56A-F. Some embodiments of the system involve an interactive, quantitative-feedback display of the registered rod, an overlay of the 3D-tracked rod bender in its active, relative position and orientation with respect to the 3D-tracked end cap tool. Some examples of these embodiments are depicted in FIGS. 87A-G, 88A-F.

[00533] In some embodiments, any of the above processes, methods, or procedures related to the workflow 8000 can include or be accomplished with one or more of steps or processes such as 8002, 8004, 8006, 8008, 8010, 8014, 8016, 8018, 8020, 8022, 8024, 8026, 8028, 8030, 8032, 8034, 8036, 8040, 8044, 8038, 8042, and 8046. In some embodiments, any of the steps of the workflow 8000 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 8000 can be skipped.

[00534] Some embodiments of this invention involve the process of tracking the dynamic contour of a registered rod that is being contoured into a new shape prior to implantation of the rod and providing directed software interactive feedback based on surgical planning inputs. For example, FIG. 81 shows a workflow 8100 for manually bending a rod prior to its implantation with directed software input to overlay a projection of the dynamic rod contour onto an intraoperative x-ray image in accordance with some embodiments of the invention. Some other relevant figures include FIG. 80 (e.g., a process for manually bending registered rod contour and outputting adjusted form, and FIGS. 88A-88F (for a display of rod bending feedback of a registered rod contour).

[00535] Some embodiments of this system involve directed software feedback that aids the user in determining where along the rod contour a rod bender must be placed, in which orientation with respect to the 3D-tracked end cap tool, and by how much of a bend angle the 3D-tracked rod bender must apply contouring forces and shapes to the registered rod contour. Some embodiments of the system involve a real-time feedback of the rod contouring process of the registered rod and projections of the rod bender in space relative to the position and orientation of the registered rod contour. Some embodiments of the system involve an interactive feedback display that depicts the amount of bending that is occurring, relative to the angle between the handles of the 3D-tracked rod bender, and how much the user should bend the rod contour at that location and orientation to produce the optimal final new contour of the rod that best matches the surgical planning goals for the procedure.

[00536] Some examples of these embodiments in various applications and forms, including the interactive software-based display of the dynamic rod contouring process are depicted in FIGS. 88A-F.

[00537] In some embodiments, any of the above processes, methods, or procedures related to the workflow 8100 can include or be accomplished with one or more of steps or processes such as 8102, 8104, 8106, 8108, 8110, 8112, 8114, 8116, 8118, 8120, 8122, 8124, 8126, 8128, 8130, 8132, 8134, 8136, 8138, 8140, 8142. In some embodiments, any of the steps of the workflow 8100 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 8100 can be skipped.

[00538] Some embodiments include a tracked probe with triggering capability, as described previously in relation to FIGS. 10A-10G, and 15A-15C, can be utilized as a user interface device with a non-tracked display monitor via the calibration process described in this figure coupled with the calculations described in detail below in reference to FIG. 83.

[00539] FIG. 82A displays one embodiment of the invention in which a non-tracked display monitor 8210 communicates calibration instructions 8205 and displays calibration markers 8230 on the display monitor to guide a user holding a tracked probe with triggering capability 8240 to calibrate the probe to the screen dimensions and location in space relative to the 3D-tracking camera by sequentially orienting the probe tip and its computed line of trajectory 8245 to each indicated marker on the display monitor (directed to center marker as shown). The workflow of interpreting this calibration process is described in detail below in reference to FIG. 83. It should be noted that utilizing a tracked probe with triggering capability to interface as a laser-pointer analog with a non-tracked display monitor is only one embodiment of the invention. Other embodiments include using a tracked probe with triggering capability to interface as a laser-pointer analog with a tracked monitor as described in detail below in reference to FIGS. 84A-84B, and others involve using a tracked probe with triggering capability to create a user defined trackpad analog to interface with an untracked display monitor as described in detail below in reference to FIG. 85. Further, FIG. 82B displays one embodiment of the invention previously described in relation to FIG. 82A, in which the computed line of trajectory 8247 of the tracked probe is directed toward the top left calibration marker on the display monitor.

[00540] Some embodiments of this invention involve the process of using a 3D-tracked tool with attached 3D-tracked triggers to interact with a display monitor and use the tool as a selection cursor. For example, FIG. 83 illustrates a workflow to utilize a trigger-equipped probe to serve as a laser pointer analog for a user-interface system with a non-tracked display in accordance with some embodiments of the invention. Some other relevant figures can include FIGS. 82A-B (for interactive display of trigger-equipped tool with a display monitor), FIGS. 15A-15C (for a trigger-equipped 3D-tracked tool that can be used for interactive display cursor control), and FIG. 63 (for a process of using tracked mobile stray marker (TMSM) as a toggling attachment to a 3D-tracked tool).

[00541] Some embodiments of this system involve the use of a 3D-tracked tool with a coupled tracked DRF, as well as a mechanically-linked tracked mobile stray marker (TMSM), that can be used as software-based inputs of location, orientation, and state of tool relative to a 3D-tracking acquisition system. One example of this embodiment is depicted in FIG. 63.

[00542] Some embodiments involve the 3D-tracked tool pointing at one or more markers at different locations of a display monitor and signaling a selection at each point once the user is confident that the 3D-tracked tool's shaft is most appropriately aligned for pointing a virtual ray at one or more markers displayed on the screen. Some example embodiments of the 3D-tracked tool in various forms and states of use are depicted in FIGS. 15A-C. Further, some embodiments involve determining the mapping of the movement, locations, and orientations of the 3D-tracked tool between registered marker points on the display monitor by calculating the lines formed by coupled locations and orientations of the 3D-tracked tool at these registered marker points. Some embodiments also involve using the dimensions and pixel resolution of the display monitor to provide more appropriate mapping of the 3D- tracked tool's motion relative to the display monitor. Further, some embodiments of the system enable the user to be able to use the 3D-tracked tool as a virtual cursor and input- selection tool for the software system visualized by the display monitor. Some examples of these embodiments in various applications and forms are depicted in FIGS. 82A-B.

[00543] In some embodiments, any of the above processes, methods, or procedures related to the workflow 8300 can include or be accomplished with one or more of steps or processes 8302, 8304, 8306, 8308, 8310, 8312, 8314, 8316, 8318, 8320, 8322, 8324, 8326, 8328, 8330, 8334, 8336, 8338. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 8318 or 8328), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 8300 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 8300 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 8300 can be skipped.

[00544] Some embodiments of this invention involve the process of using a 3D-tracked tool with attached 3D-tracked triggers to interact with a display monitor and use the tool as a selection cursor, while the display monitor has a coupled 3D-tracked DRF. For example, FIGS. 84A-84B illustrates a workflow to utilize a trigger-equipped probe to serve as a laser pointer analog for a user-interface with a 3D-tracked display monitor in accordance with some embodiments of the invention. Some other elevant figures include FIGS. 82A-82B (interactive display of trigger-equipped tool with a display monitor), FIGS. 15A-15C (for a trigger-equipped 3D-tracked tool that can be used for interactive display cursor control), and FIG. 63 (a process of using tracked mobile stray marker (TMSM) as a toggling attachment to a 3D-tracked tool), and FIG. 83 (a process of using a 3D-tracking tool as an interface display monitor cursor. Some embodiments of this system involve the processes and references made by FIG. 83. [00545] Some embodiments of the system involve rigidly attaching a 3D-tracked DRF to a display monitor that will be used for interactive software purposes. Further, some embodiments of the system involve using the DRF-equipped display monitor as a reference tool in the tracking volume of the 3D-tracking acquisition system. Other embodiments involve processes outlined in FIG. 83, which describe examples of a process for calibrating a display monitor's dimensions according to the movement, location, and orientation of a trigger-equipped 3D-tracked tool. Further, example embodiments of this system are depicted in FIGS. 82A-B.

[00546] In reference specifically to FIG. 84B, some embodiments of this system are dependent on process described in FIG. 84A. Some embodiments of this system utilize processes described in FIGS. 83 and 63. Some embodiments of this system involve rigidly attaching a 3D-tracked DRF to a display monitor that will be used for interactive software purposes. Further, some embodiments of this system involve algorithmic calculations of the relative locations and orientations of the 3D-tracked, trigger-equipped tool (e.g., FIGS. 15A- 15C) with respect to the 3D-tracking acquisition system to calculate the appropriate ray intersection of the 3D-tracked tool's probe shaft direction and the orientation of the display monitor. Some embodiments involve using the dimensions and pixel resolution of the display monitor to provide more appropriate mapping of the 3D-tracked tool's motion relative to the display monitor. Some embodiment examples, but not all exhaustive permutations, including the attachment of a DRF to the display monitor, are depicted in FIGS. 82A-B.

[00547] In some embodiments, any of the above processes, methods, or procedures related to the workflow 8400 can include or be accomplished with one or more of steps or processes 8402, 8404, 8406, 8408, 8410, 8412, 8414, 8416, 8418, 8420, 8422, 8424, 8426, 8428, 8430, 8454, 8454, 8456, 8458, 8464, 8466, 8468, 8470, 8462, and 8460. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 8402), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 8400 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 8400 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 8400 can be skipped.

[00548] Some embodiments of this invention involve the process of using a 3D-tracked tool with attached 3D-tracked triggers to interact with a display monitor and use the tool as a selection cursor, via the calibration of a non-tracked surface. For example, FIG. 85 illustrates a workflow 8500 to utilize a trigger-equipped probe to serve as an interface device for a non- tracked display via a user-defined trackpad analog in accordance with some embodiments of the invention. Some other relevant figures include FIG. 63 (a process of using tracked mobile stray marker (TMSM) as a toggling attachment to a 3D-tracked tool), FIG. 83 (a process of using a 3D-tracking tool as an interface display monitor cursor), FIGS. 15A-C (a trigger-equipped, 3D-tracked tool that can be used for interactive display cursor control), and FIGS. 82A-B (an interactive display of trigger-equipped tool with a display monitor). For example, some embodiments of this system utilize processes described in FIGS. 63 and 83. Some embodiments involve the 3D-tracked tool pointing at one or more markers at different locations of a display monitor and signaling a selection at each point once the user is confident that the 3D-tracked tool's shaft is most appropriately aligned to be pointing a virtual ray at the marker(s) displayed on the screen. Some example embodiments of the 3D- tracked tool in various forms and states of use are depicted in FIGS. 15A-C.

[00549] Some embodiments involve the use of the 3D-tracked tool to either trace the border of a rigid, non-tracked object or register multiple discrete points on the border surface of a rigid, non-tracked object in order to register its border dimensions and the orientation of the frame relative to the 3D-tracking acquisition system. Further, some embodiments involve using the dimensions and pixel resolution of the display monitor to provide more appropriate mapping of the 3D-tracked tool's motion relative to the display monitor. Some embodiments involve calculating the mapping between the registered rigid, non-tracked object dimensions and orientation and the dimensions of the display monitor. Some embodiments algorithmically calculate the interactive placement of a cursor on the display monitor based on the location of the 3D-tracked tool end effector on the rigid, non-tracked, registered object surface within its border boundaries. Some analogous examples of some of these system embodiments in various applications and forms are depicted in FIGS. 82A-B, and 83.

[00550] In some embodiments, any of the above processes, methods, or procedures related to the workflow 8500 can include or be accomplished with one or more of steps or processes 8502, 8504, 8506, 8508, 8510, 8512, 8514, 8516, 8518, 8520, 8522, 8524, 8526, 8528, and 8530. In some embodiments, any of the steps of the workflow 8500 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 8500 can be skipped. [00551] Some embodiments of the system described herein can generate output displays for the alignment assessments performed with embodiments of the invention previously described in relation to at least FIGS. 62A-62D, and 65A-65E, 66A-66B, and 67-69.

[00552] FIG. 86A displays one embodiment of the invention consisting of drawings 8600 of computed spinal alignment parameters and their current value displayed beneath each one as calculated from the alignment assessment. Other embodiments include these displays and/or their quantified values changing colors based on proximity to predetermined surgical goals, enabling the user to visualize and focus on parameters that are farthest away from the predetermined ranges. Additional embodiments include the ability of the user to view previously-acquired assessments, and dynamically-responsive spine drawings that change their contour to accurately represent their most recently measured values. It should be noted that this figure displays only one embodiment which does not contain all the spinal alignment parameters for all embodiments. The display as shown and described can be applied to any measurement value between two regions of the spine or between one anatomical region and the spine or pelvis. The data acquisition and interpretation processes to generate these parameters are described previously as described earlier.

[00553] FIG. 86B displays one embodiment of the invention which is an output display of a patient image in the sagittal 8650a and coronal 8650b planes with the option to remove any software overlays. Further, FIG. 86C displays one embodiment of the invention which consists of sagittal and coronal patient images with sagittal and coronal overlays (8651a, 8651b respectively) of the patient's spinal anatomy representing their current spinal alignment based on intraoperative assessments. To generate these overlays, manual or automated segmentation of previously-acquired patient images is used to isolate the elements of the spine which is then anchored at a reference point to the prior image, and then both rotated and distorted to provide a qualitative representation of the measured alignment. In other embodiments of the invention, rather than an overlay of a dynamically modified segmented image, an overlay of a line representing the contour of the spine is displayed on the patient image. This curve can be with or without discrete spinal level indications and the user is able to toggle previously acquired tracing contour assessments on and off.

[00554] FIG. 86D displays one embodiment of the invention which is an output display of the measured spinal alignment parameters represented by discrete vertebra that both individually translate and rotate to align tangentially with the measured spinal alignment. In this way, the output can dynamically adjust to localized measurements, such as lumbar lordosis, shown going from 10 degrees 8675 to 30 degrees 8681 which include altering the alignment between the related endplates within the output display. This embodiment also consists of this dynamic display shown in the coronal plane (not shown) and 3D perspective view. Another component of the embodiment is the display of discrete spinal level labels 8683 relative to the output image.

[00555] Some embodiments include a rod with previously registered contour fixed to a tracked DRF-equipped end cap and interacting with a tracked rod bender in accordance with some embodiments of the invention. For example, FIG. 87A displays one embodiment of the invention previously described in relation to FIGS. 55D-I, 56A-D, and 56F, consisting of a rod 8715 with previously registered contour fixed to a tracked DRF-equipped end cap 8710 and interacting with a tracked rod bender 8730.

[00556] FIG. 87B displays one embodiment of the invention consisting of a sagittal projection of the registered rod contour 8735, a display indicating the current sagittal location of the tracked rod bender 8755 relative to the registered rod contour as referenced to the end cap DRF axes, and labels 8717 for the anatomical axes for ease of user-interpretation. With this embodiment, the user is able to visualize where the rod bender is located relative to the 2D anatomical projection of the rod, allowing for improved interpretation of complex rod contours as well as interpretation relative to the patient imaging as described below in reference to FIGS. 87F-87G. It should be noted that the rod contour registration process, which takes place prior to utilizing this embodiment of the invention, is described above in relation to FIGS. 47A-47B, 51A-51G, and 73A-73B, and 74-75.

[00557] FIG. 87C displays one embodiment of the invention consisting of a coronal projection of the registered rod contour 8765, a display indicating the current coronal location of the tracked rod bender 8760 relative to the registered rod contour as referenced to the end cap DRF axes, and labels 8723 for the anatomical axes for ease of user interpretation. In this embodiment, the location of the rod bender is displayed as a projection of the bender onto the displayed plane. As shown, in this figure, the rod bender is located orthogonal to both the segment of the rod with which it is engaged and the coronal plane, as indicated by the narrow rectangle in this projection. When the bender is bending within the displayed plane, it is displayed as it is shown in relation to FIG. 87B. [00558] FIG. 87D displays one embodiment of the invention which displays the location of the bender's center rod contouring surface 8730 relative to a cross-sectional view of the rod 8725 with labels for the anatomical axes 8727. This embodiment allows for interpretation of the location of tracked rod bender's interface components, as rotated about the long axis of each segment of the rod.

[00559] FIG. 87E displays one embodiment of the invention which displays a sagittal projection of the registered rod contour 8735, and generated orthogonal lines from the superior rod endpoint 8740, and the inferior rod endpoint 8745 along with the calculated angle between them 8750 in addition to labels 8733 for the anatomical axes. In other embodiments, the user can modify and select discrete locations on the rod between which orthogonal lines will be drawn and angles calculated. In other embodiments of this invention, the rod and corresponding measurements between orthogonal lines can be projected onto the coronal plane. Additionally, in other embodiments these projections and measured angles can be performed after assessing the rod contour both prior to implantation and after implantations, and need not necessitate interfacing with a tracked bender to do so.

[00560] FIG. 87F displays a sagittal patient image 8775 with an overlay of a registered rod contour 8777 as well as an overlay display of the location of a tracked rod bender 8779 relative to the previously registered rod. The placement location of the registered rod's contour can be achieved via embodiments described previously in relation to FIG. 78.

[00561] FIG. 87G displays a sagittal patient image adjusted for operative planning 8781 with an overlay of a registered rod contour 8783 as well as an overlay display of the location of a tracked rod bender 8785 relative to the previously registered rod. The placement location of the registered rod's contour over this adjusted patient image can be achieved via embodiments described previously in relation to FIG. 78. By overlaying the registered rod contour over the image adjusted to mimic operative goals, the contour of the rod can be adjusted with real-time display feedback to a point where it superimposes over the adjusted patient image in such a way that it is located where it would be on a postoperative image, secured to the tulip heads of implanted pedicle screws.

[00562] FIG. 87H displays one embodiment of the invention in which the rod bender's location on the display monitor is represented as an arrow 8786 and the rod is represented as a single colored, solid line 8787. [00563] FIG. 871 displays one embodiment of the invention in which the rod bender's location on the display monitor is represented as an arrow 8786 and the segment of the rod engaged with the rod bender is a different color 8789 than the segments of the rod not engaged with the bender 8788, as described previously in relation to FIG. 79. In other embodiments, rather than a change in color, the engaged segment of rod can be differentiated from the unengaged segment of rod via a change in stroke weight of the line, or changing from dashed to solid lines.

[00564] FIG. 87J displays one embodiment of the invention in which the rod bender's location on the display monitor is represented as an outline of the manual rod bender with profile outlines 8795 of the handles and rod interface regions adapting the display based on the current orientation of the handles to one another. In this figure, it is displayed with the handles fully open (i.e., at the largest angle between them) to accommodate interfacing with a straight rod 8793.

[00565] FIG. 87K displays one embodiment of the invention in which the rod bender's location on the display monitor is represented as an outline of the manual rod bender with profile outlines 8796 of the handles and rod interface regions adapting the display based on the current orientation of the handles to one another. In this figure, it is displayed with the handles fully closed (i.e., at the smallest angle between them) and therefore interfacing with a bent region of the rod 8794.

[00566] FIG. 87L displays one embodiment of the invention in which the rod bender's location on the display monitor is represented as three filled circles to represent the left outer roller 8789, center rod contouring surface 8790 and right outer roller 8791 engaged with a straight rod 8787. Further, FIG. 87M displays one embodiment of the invention in which the rod bender's location on the display monitor is represented as three filled circles with an outline 8792 to represent the left outer roller 8789, center rod contouring surface 8790 and right outer roller 8791 engaged with a straight rod 8787.

[00567] Some embodiments include display monitor interfaces to allow for software- directed bending of a previously registered rod rigidly fixed to a tracked DRF-equipped end cap and interfacing with a tracked rod bender as previously described in relation to FIG. 87A- 87M. These embodiments enable mechanisms of instructing the user where and how to bend the rod with a tracked rod bender in order for the rod's final contour to match preset inputs. It should be noted that these preset inputs are embodied in varying forms and can be based on preoperative imaging, preoperative planning, preset measurement inputs, and intraoperative alignment measures among others. The workflow associated with these embodiments is described previously in reference to FIGS. 80-81.

[00568] Some embodiments include a sagittal projection of a registered rod contour, a display of the current location of the rod bender relative to the registered rod contour, a display of the software-instructed location where the user should place the rod-bender, and anatomical axes labels in accordance with some embodiments of the invention.

[00569] FIG. 88A displays one embodiment of the invention consisting of a sagittal projection of a registered rod contour 8801, a display of the current location of the rod bender 8803 relative to the registered rod contour, a display of the software-instructed location where the user should place the rod-bender 8805, and anatomical axes labels 8825. This embodiment allows for visual display and feedback showing where the rod bender is relative to where the software is instructing the user to place the rod bender on the rod. In other embodiments of this invention, the appearance of the software-instructed location of the bender changes via color, line weight, or shape, to indicate when the user has successfully overlaid the current location of the bender onto the software-instructed location for the bender relative to the registered rod.

[00570] FIG. 88B illustrates a display of FIG. 88A as applied to the coronal plane in accordance with some embodiments of the invention, with coronal projection of registered rod contour 8807, coronal display overlay of current bender location relative to rod 8809, software-instructed bending indicator of bender placement location 8811, and anatomical axes labels 8827

[00571] FIG. 88C illustrates a cross-sectional display of the rod, the current location of the rod bender's center contouring surface, the software-instructed location of where the rod bender's center contouring surface should be placed, and anatomical axes labels in accordance with some embodiments of the invention. Shown are the cross-sectional display of rod 8813, current orientation of bender 8815, software-instructed indicator of bender placement location 8817, anatomical axes labels 8829. [00572] FIG. 88D displays one embodiment of the invention consisting of a display representation of the current relative position of the bender's handles 8852, directly related to the degree of bending induced on a rod of known diameter. In this embodiment, the angle between the handles is adaptive and changes based on the detected conformation of the tracked rod bender. Further, FIG. 88E illustrates a display representation of the software- instructed relative position of the bender's handles 8854, directly related to the degree of bending induced on a rod of known diameter in accordance with some embodiments of the invention. The display representation of the software-instructed relative position of the bender's handles 8854, directly related to the degree of bending induced on a rod of known diameter. In this embodiment, the rod bender is displayed in its state of maximum bending (i.e., minimum angle between handles) and any angle within the achievable range of motion of the rod bender's handles can be displayed as the software-instructed degree of bending for the user to match once the bender is placed in the indicated location along the length of the rod, as described in FIGS. 88A-B, and once the bender is located at the right angle relative to the rod's cross section, as described in FIG. 88C.

[00573] FIG. 88F represents one embodiment of the invention consisting of a display representation of an angle gauge 8866 within which the current angle between the tracked rod bender's handles 862 is shown in addition to the software-instructed indicator 8864 of what angle is necessary at that point of engagement between the previously registered rod and tracked rod bender. With this embodiment, the user is able to watch the current bend angle of the tracked bender changes as the handles are moved closer to or farther from one another. The user adjusts the angle between handles until the current angle indicator is superimposed over the software-instructed angle indicator, at which point the user-interface displays the next location of bending required to achieve the desired rod contour that was input to the system.

[00574] In some embodiments, any of the systems and software can be applied with rod cutters to instruct the user where to cut the rod as mentioned above. Other embodiments of the invention also include indications of where a tracked rod-cutting device is relative to a previously registered rod that is still connected with the tracked DRF-equipped end cap. Both live tracking of the cutter relative to the previously registered rod, as well as software- instructed placement of a cutting device relative to the rod, is included in other embodiments of the invention. [00575] Some embodiments of this invention involve the process of interactively providing instructions of how to manipulate and position an adjustable spine phantom model to approximate orientations and relations available in imaging of the model. For example, FIG. 89 shows a workflow to match the adjustable benchtop spinal model to mimic alignment parameters from patient-specific imaging in accordance with some embodiments of the invention. Other relevant figures include FIGS. 90A-90D (a display and interactive adjustable components of benchtop spine model).

[00576] Some embodiments of the system involve the annotation of spinal vertebrae levels of the benchtop spine model based on visualization of the anatomy by imaging technologies (e.g., CT, MRI, 2D x-ray radiograph, ultrasound, etc.) Further, some embodiments of the system involve rigidly attaching an arrangement of adjustable, incrementally-measured levers that both rigidly fix the conformation of the spine model in space, and provide quantitative feedback for the user to interpret the position of each multi-lever, adjustable fixation device. One example embodiment of the multi-lever, adjustable fixation device is depicted in FIG. 90C.

[00577] Some embodiments involve the rigid attachment of the multi-lever, adjustable fixation device to each spinal vertebra level. Other embodiments involve attaching select levels of the spine model to rigidly attach to a multi-lever, adjustable fixation device. Some embodiments of the system involve instructing the user to adjust specific segments of the spine via the manipulation of one or more multi-lever, adjustable fixation devices to configure the conformation of the spine model in a manner that matches the configuration of anatomies as visualized in the imaging registration of the spine model. Some further embodiments involve produced transformed 3D CT-based reconstructions or cross-sectional visualization estimates of the spine model anatomy as it is currently positioned on the benchtop, assuming that the user followed software directions correctly to adjust the spine model in a specific conformation.

[00578] In some embodiments, any of the above processes, methods, or procedures related to the workflow 8900 can include or be accomplished with one or more of steps or processes 8902, 8904, 8906, 8908, 8910, 8912, 8914, 8916, 8918, 8920, 8922, 8924, 8926, 8928, 8930, 8932, 8934, 8936. In some embodiments, at least one of the steps can include a decision step (e.g., such as step 8918), where one or more following steps depend on a status, decision, state, or other condition. In some embodiments, the steps of workflow 8900 can proceed in the order as shown. In some embodiments, any of the steps of the workflow 8900 can proceed out of the order as shown. In some embodiments, one or more of the steps of the workflow 8900 can be skipped.

[00579] Some embodiments relate to patient images that are analyzed to indicate their spinal alignment contour and parameters as well as output instructions of how to position adjustable mounts coupled to an anatomical model of the spine in order to mimic the spinal alignment parameters displayed in the patient images. Other embodiments of this device include inputting desired discrete alignment parameter values (e.g., lumbar lordosis of 30 degrees) to the software which then outputs instructions for how to orient the adjustable mounts to configure the anatomical model to possess the input parameters. Another embodiment of the device consists of a user positioning the anatomical model and then inputting all coordinates of the adjustable mounts into the software for it to then output patient images closely matching the alignment parameters of the anatomical model.

[00580] FIG. 90 A illustrates sagittal and coronal patient images with overlaid sagittal and coronal contour tracings of the spine, discrete software-instructed placement of adjustable mounts onto the anatomical model, and instructions for the coordinates of each of those adjustable mounts to be positioned on the adjustable benchtop model in accordance with some embodiments of the invention. The sagittal 9001 and coronal 9005 patient images are shown with overlaid sagittal 9003 and coronal 9009 contour tracings of the spine, discrete software-instructed placement of adjustable mounts (9005, 9011) onto the anatomical model, and instructions for the coordinates of each of those adjustable mounts to be positioned on the adjustable benchtop model. The software description for this embodiment is described previously in relation to FIG. 89. Further, FIG. 90B illustrates an anatomical model mounting exploded assembly in accordance with some embodiments of the invention.

[00581] FIG. 90B displays one embodiment of the invention consisting of a table top base 9020, side-rail 9022 equipped with distance indicators 9024 and meant to interface with a cross rail 9026 equipped with distance indicators 9028 and designed to interface with a cross- rail sliding piece 9034 within its cross-rail mating slot 9038, which is equipped with a slot 9039 for mating with a height-adjustment slider 9032, which mates with an angular adjustment piece 9030 via a fastener 9036 which interfaces with an individual vertebra on an anatomical spine model (not shown). This embodiment allows for positioning of the coupled anatomical model (not shown) in specific locations anywhere over the table top base. [00582] FIG. 90C displays one embodiment of the invention previously described in relation to FIG. 90B, in its assembled form with the anatomical model interface surface 9040 more easily visualized. In the embodiment shown, this interface is achieved via a through hole for a fastener (not shown) to rigidly couple to the anterior aspect of the anatomical model's vertebral body. In other embodiments, this interface includes a ball joint to allow for the anatomical model to pivot about the interface point. In other embodiments, the fastener to the anatomical model is achieved via a clipping mechanism to pre-installed receptacles on each vertebra of the anatomical model to enable rapid-exchange of interface points.

[00583] FIG. 90D displays one embodiment of the invention in which a spine anatomical model 9050 is positioned in a discrete alignment configuration with the adjustable mounts described previously in relation to FIGS. 90B-C. In this embodiment, each mount is positioned based on software-instructed parameters including: location along the side rail, location along the cross-rail, height from the base piece, angle from the height-adjustment slider, and vertebral level with which it should interface. In other embodiments, the cross rails are cylindrical, allowing for rotation of the base piece about the cross bar. In other embodiments, rather than mating only with select vertebral levels, each vertebra is equipped with an adjustable mount, to allow for matching contours with higher precision.

[00584] Some embodiments enable different probe-like extensions to be added or interchanged to a tracked DRF, while indicating to the acquisition software which extension is currently coupled, and therefore which tool definition file to reference when tracking the associated DRF. For example, FIG. 91 A illustrates an engaged, straight probe extension as the selected modular tool tip and its associated, unique TMSM position relative to the DRF when engaged, in accordance with some embodiments of the invention.

[00585] FIG. 91A illustrates one embodiment of the invention that involves a tracked dynamic reference frame (DRF) 9101 with a mating extension containing a slot in which a spring-loaded (not shown) TMSM 9103 slides due to protrusions 9111 (FIG. 91B) of discrete distances attached to unique probe extension pieces 9105. When the TMSM 9103 is detected in a preset location relative to the tracked DRF 9101, the acquisition system registers which probe extension tip is coupled and updates the tool definition file for the DRF 9101 accordingly. The algorithmic process to detect the motion of a TMSM 9103 relative to a DRF 9101 was described previously in relation to FIG. 63. [00586] FIG. 91B illustrates the embodiment of the invention previously described in FIG. 91 A with the probe extension unengaged from the tracked DRF 9101. In this image, the spring-loaded TMSM 9107 fastened to a sliding insert 9109 is not depressed by the unique mating protrusion 9111 of the probe extension, and the mating pin 9113 and its associated mating slot 9115 are visible. In this embodiment, the mating pin securely fastens to the DRF within the mating slot via a spring-loaded plunger (not shown).

[00587] FIG. 91C illustrates an embodiment of the invention previously described in relation to FIGS. 91A-91B, wherein this figure demonstrates coupling an alternate probe extension 9117 with its own unique mating protrusion 9119 that results in the TMSM 9121 being slid to a different position relative to the 9101 than when other probe extensions are engaged. In this embodiment shown, a curved probe tip is utilized, and when the acquisition system detects the 9107 in this particular position relative to the 9101, it can then load the appropriate tool definition file according to the curved probe extension shown.

[00588] Some other embodiments include multiple, permanently coupled probe extensions to one DRF, and with one or more TMSM moved to discrete positions relative to the DRF to communicate with the acquisition system, which probe extension is being utilized and therefore which tool definition file it should load.

[00589] Further embodiments include systems compatible with TMSM-equipped systems: It should be noted that other embodiments of this invention are compatible with previously described, TMSM-equipped probes for triggering, in reference to FIGS. 10A-10G and 15A- 15C. In these embodiments, the acquisition system distinguishes between the individual stray markers.

[00590] Some other embodiments include TSM on the extensions: It should be noted that other embodiments of this invention can comprise of the probe extensions possessing one or more of their own tracked stray markers (TSMs) such that when the extension engages with the DRF, the TSM(s) are in preset locations. This is an alternative to the sliding, TMSM equipped on the DRF itself.

[00591] Some embodiments of the modular probe extension types include, but are not limited to: a traight probe, a curved probe, a probe with unique mating features for coupling with a fiducial or another accessory device, a screwdriver head, a rod-centering fork, a ring structure or other closed-loop designs.

[00592] Some other embodiments of the mating mechanism between the modular probe extensions and the DRF include, but are not limited to: quarter-turn, threaded, spring-loaded snap arms, and retractable spring plunger.

[00593] Any of the operations described herein that form part of the invention are useful machine operations. The invention also relates to a device or an apparatus for performing these operations. The apparatus can be specially constructed for the required purpose, such as a special purpose computer. When defined as a special purpose computer, the computer can also perform other processing, program execution or routines that are not part of the special purpose, while still being capable of operating for the special purpose. Alternatively, the operations can be processed by a general-purpose computer selectively activated or configured by one or more computer programs stored in the computer memory, cache, or obtained over a network. When data is obtained over a network the data can be processed by other computers on the network, e.g. a cloud of computing resources.

[00594] The embodiments of the present invention can also be defined as a machine that transforms data from one state to another state. The data can represent an article, that can be represented as an electronic signal and electronically manipulate data. The transformed data can, in some cases, be visually depicted on a display, representing the physical object that results from the transformation of data. The transformed data can be saved to storage generally, or in particular formats that enable the construction or depiction of a physical and tangible object. In some embodiments, the manipulation can be performed by a processor. In such an example, the processor thus transforms the data from one thing to another. Still further, some embodiments include methods can be processed by one or more machines or processors that can be coupled over a network. Each machine can transform data from one state or thing to another, and can also process data, save data to storage, transmit data over a network, display the result, or communicate the result to another machine. Computer- readable storage media, as used herein, refers to physical or tangible storage (as opposed to signals) and includes without limitation volatile and non-volatile, removable and nonremovable storage media implemented in any method or technology for the tangible storage of information such as computer-readable instructions, data structures, program modules or other data. [00595] Although method operations can be described in a specific order, it should be understood that other housekeeping operations can be performed in between operations, or operations can be adjusted so that they occur at slightly different times, or can be distributed in a system which allows the occurrence of the processing operations at various intervals associated with the processing, as long as the processing of the overlay operations are performed in the desired way.

[00596] It will be appreciated by those skilled in the art that while the invention has been described above in connection with particular embodiments and examples, the invention is not necessarily so limited, and that numerous other embodiments, examples, uses, modifications and departures from the embodiments, examples and uses are intended to be encompassed by the claims attached hereto. The entire disclosure of each patent and publication cited herein is incorporated by reference, as if each such patent or publication were individually incorporated by reference herein. Various features and advantages of the invention are set forth in the following claims.