Patent Publication Number: US-2023148896-A1

Title: Apparatus and method for recording probe movement

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation of U.S. patent application Ser. No. 15/609,680 filed on May 31, 2017, which is a continuation-in-part of U.S. patent application Ser. No. 15/157,444, filed May 18, 2016, which is a continuation-in-part of U.S. patent application Ser. No. 15/095,883, filed Apr. 11, 2016, which is a continuation-in-part of U.S. patent application Ser. No. 14/062,707, filed on Oct. 24, 2013, which is a continuation-in-part application of U.S. patent application Ser. No. 13/924,505, filed on Jun. 21, 2013, which claims priority to provisional application No. 61/662,702 filed on Jun. 21, 2012 and claims priority to provisional application No. 61/800,527 filed on Mar. 15, 2013, all of which are incorporated by reference herein in their entireties for all purposes. 
    
    
     FIELD 
     The present disclosure relates to a position recognition system, and in particular, a probing system for determining an extent of matter in a targeted anatomical structure. 
     BACKGROUND 
     Certain surgical procedures require a surgeon to remove matter, i.e. bone or tissue, from a patient. During spinal implant surgeries, a surgeon typically must first remove a disk, including primarily ligament and cartilage, from the patient&#39;s spine to provide a clear installation site for attaching an implant or replacement disk to the spine. Surgeons typically perform this removal process without the aid of any real-time indicator to demonstrate how much matter remains in the patient&#39;s targeted anatomical structure. The surgeon must develop a tactile feel for how an instrument navigates through the targeted anatomical structure, and rely on this tactile feel to make a determination regarding how much matter remains in the targeted anatomical structure. The surgeon must also develop a mental image or map of the targeted anatomical structure based on how the instrument feels while being navigated through the targeted anatomical structure. Due to potential “blind spots,” the surgeon can navigate an instrument through the targeted anatomical structure and mistakenly conclude that the proposed installation site is clear of extraneous bone or tissue. This false conclusion can result in the surgeon proceeding with attempting to install an implant despite the installation site not being sufficiently cleared. Alternatively, the surgeon may begin the installation procedure, only to realize that the installation site is not cleared, causing the installation procedure to be delayed until additional matter is removed from the installation site. 
     It would be desirable to provide a more dependable way for a surgeon to ensure that a targeted anatomical structure is sufficiently clear of matter following a targeted removal procedure. 
     SUMMARY 
     To meet this and other needs, devices, systems, and methods for determining an extent of matter remaining within a targeted anatomical structure are provided. 
     In one embodiment, a method for determining an extent of matter removed from a targeted anatomical structure is provided. The method includes acquiring an initial representation of a targeted anatomical structure and then removing matter from the targeted anatomical structure. An instrument is then navigated within the targeted anatomical structure. The instrument includes a tracking array, and a relative position of the instrument within the targeted anatomical structure is determined by the tracking array. The method includes recording the relative position of the instrument within the targeted anatomical structure to determine a final representation of the targeted anatomical structure. Finally, the method includes determining an extent of matter removed from the targeted anatomical structure by comparing the initial representation of the targeted anatomical structure with the final representation of the targeted anatomical structure. 
     In one embodiment, a tracking system for determining an extent of matter remaining in a targeted anatomical structure is provided. The system includes an instrument including a tracking array, and the instrument is configured to be received within a targeted anatomical structure. The system includes at least one camera that detects a relative position of the instrument within the targeted anatomical structure via the tracking array. A computer system includes a display, and the computer system records the relative position of the instrument within the targeted anatomical structure. The display illustrates a path of the instrument within the targeted anatomical structure relative to an initial representation of the targeted anatomical structure. A surgeon can rely on this mapped path of the instrument to conclude how much matter has been removed from the targeted anatomical structure. 
    
    
     
       DESCRIPTION OF THE DRAWINGS 
         FIG.  1    is an overhead view of a potential arrangement for locations of the robotic system, patient, surgeon, and other medical personnel during a surgical procedure; 
         FIG.  2    illustrates the robotic system including positioning of the surgical robot and the camera relative to the patient according to one embodiment; 
         FIG.  3    illustrates a surgical robotic system in accordance with an exemplary embodiment; 
         FIG.  4    illustrates a portion of a surgical robot in accordance with an exemplary embodiment; 
         FIG.  5    illustrates a block diagram of a surgical robot in accordance with an exemplary embodiment; 
         FIG.  6    illustrates a surgical robot in accordance with an exemplary embodiment; 
         FIGS.  7 A- 7 C  illustrate an end-effector in accordance with an exemplary embodiment; 
         FIG.  8    illustrates a surgical instrument and the end-effector, before and after, inserting the surgical instrument into the guide tube of the end-effector according to one embodiment; 
         FIGS.  9 A- 9 C  illustrate portions of an end-effector and robot arm in accordance with an exemplary embodiment; 
         FIG.  10    illustrates a dynamic reference array, an imaging array, and other components in accordance with an exemplary embodiment; 
         FIG.  11    illustrates a method of registration in accordance with an exemplary embodiment; 
         FIG.  12 A- 12 B  illustrate embodiments of imaging devices according to exemplary embodiments; 
         FIG.  13 A  illustrates a portion of a robot including the robot arm and an end-effector in accordance with an exemplary embodiment; 
         FIG.  13 B  is a close-up view of the end-effector, with a plurality of tracking markers rigidly affixed thereon, shown in  FIG.  13 A ; 
         FIG.  13 C  is a tool or instrument with a plurality of tracking markers rigidly affixed thereon according to one embodiment; 
         FIG.  14 A  is an alternative version of an end-effector with moveable tracking markers in a first configuration; 
         FIG.  14 B  is the end-effector shown in  FIG.  14 A  with the moveable tracking markers in a second configuration; 
         FIG.  14 C  shows the template of tracking markers in the first configuration from  FIG.  14 A ; 
         FIG.  14 D  shows the template of tracking markers in the second configuration from  FIG.  14 B ; 
         FIG.  15 A  shows an alternative version of the end-effector having only a single tracking marker affixed thereto; 
         FIG.  15 B  shows the end-effector of  FIG.  15 A  with an instrument disposed through the guide tube; 
         FIG.  15 C  shows the end-effector of  FIG.  15 A  with the instrument in two different positions, and the resulting logic to determine if the instrument is positioned within the guide tube or outside of the guide tube; 
         FIG.  15 D  shows the end-effector of  FIG.  15 A  with the instrument in the guide tube at two different frames and its relative distance to the single tracking marker on the guide tube; 
         FIG.  15 E  shows the end-effector of  FIG.  15 A  relative to a coordinate system; 
         FIG.  16    is a block diagram of a method for navigating and moving the end-effector of the robot to a desired target trajectory; 
         FIGS.  17 A- 17 B  depict an instrument for inserting an expandable implant having fixed and moveable tracking markers in contracted and expanded positions, respectively; and 
         FIGS.  18 A- 18 B  depict an instrument for inserting an articulating implant having fixed and moveable tracking markers in insertion and angled positions, respectively. 
         FIG.  19    illustrates a method of determining an extent of matter remaining in a targeted anatomical structure according to one embodiment. 
         FIGS.  20 A and  20 B  illustrate a system of determining an extent of matter remaining in a targeted anatomical structure according to an embodiment in which a tip of the instrument is tracked. 
         FIGS.  21 A- 21 D  illustrate a system of determining an extent of matter remaining in a targeted anatomical structure according to one embodiment in which a shaft of the instrument is tracked.  FIG.  21 A  shows the beginning of the tracing of a path around the perimeter of the disc, progressing through  FIG.  21 B  and  FIG.  21 C  and ending at  FIG.  21 D  with the perimeter fully traced. The space that was occupied by the shaft during tracing is illustrated in black. 
         FIGS.  22 A and  22 B  illustrate a system of determining an extent of matter remaining in a targeted anatomical structure according to an embodiment in which a tip of the instrument is enlarged. 
         FIGS.  23 A and  23 B  illustrate a system of determining an extent of matter remaining in a targeted anatomical structure according to an embodiment in which the instrument includes an articulable joint. 
     
    
    
     DETAILED DESCRIPTION 
     It is to be understood that the present disclosure is not limited in its application to the details of construction and the arrangement of components set forth in the description herein or illustrated in the drawings. The teachings of the present disclosure may be used and practiced in other embodiments and practiced or 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. 
     The following discussion is presented to enable a person skilled in the art to make and use embodiments of the present disclosure. Various modifications to the illustrated embodiments will be readily apparent to those skilled in the art, and the principles herein can be applied to other embodiments and applications without departing from embodiments of the present disclosure. Thus, the embodiments 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 the embodiments. Skilled artisans will recognize the examples provided herein have many useful alternatives and fall within the scope of the embodiments. 
     Turning now to the drawing,  FIGS.  1  and  2    illustrate a surgical robot system  100  in accordance with an exemplary embodiment. Surgical robot system  100  may include, for example, a surgical robot  102 , one or more robot arms  104 , a base  106 , a display  110 , an end-effector  112 , for example, including a guide tube  114 , and one or more tracking markers  118 . The surgical robot system  100  may include a patient tracking device  116  also including one or more tracking markers  118 , which is adapted to be secured directly to the patient  210  (e.g., to the bone of the patient  210 ). The surgical robot system  100  may also utilize a camera  200 , for example, positioned on a camera stand  202 . The camera stand  202  can have any suitable configuration to move, orient, and support the camera  200  in a desired position. The camera  200  may include any suitable camera or cameras, such as one or more infrared cameras (e.g., bifocal or stereophotogrammetric cameras), able to identify, for example, active and passive tracking markers  118  in a given measurement volume viewable from the perspective of the camera  200 . The camera  200  may scan the given measurement volume and detect the light that comes from the markers  118  in order to identify and determine the position of the markers  118  in three-dimensions. For example, active markers  118  may include infrared-emitting markers that are activated by an electrical signal (e.g., infrared light emitting diodes (LEDs)), and passive markers  118  may include retro-reflective markers that reflect infrared light (e.g., they reflect incoming IR radiation into the direction of the incoming light), for example, emitted by illuminators on the camera  200  or other suitable device. 
       FIGS.  1  and  2    illustrate a potential configuration for the placement of the surgical robot system  100  in an operating room environment. For example, the robot  102  may be positioned near or next to patient  210 . Although depicted near the head of the patient  210 , it will be appreciated that the robot  102  can be positioned at any suitable location near the patient  210  depending on the area of the patient  210  undergoing the operation. The camera  200  may be separated from the robot system  100  and positioned at the foot of patient  210 . This location allows the camera  200  to have a direct visual line of sight to the surgical field  208 . Again, it is contemplated that the camera  200  may be located at any suitable position having line of sight to the surgical field  208 . In the configuration shown, the surgeon  120  may be positioned across from the robot  102 , but is still able to manipulate the end-effector  112  and the display  110 . A surgical assistant  126  may be positioned across from the surgeon  120  again with access to both the end-effector  112  and the display  110 . If desired, the locations of the surgeon  120  and the assistant  126  may be reversed. The traditional areas for the anesthesiologist  122  and the nurse or scrub tech  124  remain unimpeded by the locations of the robot  102  and camera  200 . 
     With respect to the other components of the robot  102 , the display  110  can be attached to the surgical robot  102  and in other exemplary embodiments, display  110  can be detached from surgical robot  102 , either within a surgical room with the surgical robot  102 , or in a remote location. End-effector  112  may be coupled to the robot arm  104  and controlled by at least one motor. In exemplary embodiments, end-effector  112  can comprise a guide tube  114 , which is able to receive and orient a surgical instrument  608  (described further herein) used to perform surgery on the patient  210 . As used herein, the term “end-effector” is used interchangeably with the terms “end-effectuator” and “effectuator element.” Although generally shown with a guide tube  114 , it will be appreciated that the end-effector  112  may be replaced with any suitable instrumentation suitable for use in surgery. In some embodiments, end-effector  112  can comprise any known structure for effecting the movement of the surgical instrument  608  in a desired manner. 
     The surgical robot  102  is able to control the translation and orientation of the end-effector  112 . The robot  102  is able to move end-effector  112  along x-, y-, and z-axes, for example. The end-effector  112  can be configured for selective rotation about one or more of the x-, y-, and z-axis, and a Z Frame axis (such that one or more of the Euler Angles (e.g., roll, pitch, and/or yaw) associated with end-effector  112  can be selectively controlled). In some exemplary embodiments, selective control of the translation and orientation of end-effector  112  can permit performance of medical procedures with significantly improved accuracy compared to conventional robots that utilize, for example, a six degree of freedom robot arm comprising only rotational axes. For example, the surgical robot system  100  may be used to operate on patient  210 , and robot arm  104  can be positioned above the body of patient  210 , with end-effector  112  selectively angled relative to the z-axis toward the body of patient  210 . 
     In some exemplary embodiments, the position of the surgical instrument  608  can be dynamically updated so that surgical robot  102  can be aware of the location of the surgical instrument  608  at all times during the procedure. Consequently, in some exemplary embodiments, surgical robot  102  can move the surgical instrument  608  to the desired position quickly without any further assistance from a physician (unless the physician so desires). In some further embodiments, surgical robot  102  can be configured to correct the path of the surgical instrument  608  if the surgical instrument  608  strays from the selected, preplanned trajectory. In some exemplary embodiments, surgical robot  102  can be configured to permit stoppage, modification, and/or manual control of the movement of end-effector  112  and/or the surgical instrument  608 . Thus, in use, in exemplary embodiments, a physician or other user can operate the system  100 , and has the option to stop, modify, or manually control the autonomous movement of end-effector  112  and/or the surgical instrument  608 . Further details of surgical robot system  100  including the control and movement of a surgical instrument  608  by surgical robot  102  can be found in co-pending U.S. patent application Ser. No. 13/924,505, which is incorporated herein by reference in its entirety. 
     The robotic surgical system  100  can comprise one or more tracking markers  118  configured to track the movement of robot arm  104 , end-effector  112 , patient  210 , and/or the surgical instrument  608  in three dimensions. In exemplary embodiments, a plurality of tracking markers  118  can be mounted (or otherwise secured) thereon to an outer surface of the robot  102 , such as, for example and without limitation, on base  106  of robot  102 , on robot arm  104 , or on the end-effector  112 . In exemplary embodiments, at least one tracking marker  118  of the plurality of tracking markers  118  can be mounted or otherwise secured to the end-effector  112 . One or more tracking markers  118  can further be mounted (or otherwise secured) to the patient  210 . In exemplary embodiments, the plurality of tracking markers  118  can be positioned on the patient  210  spaced apart from the surgical field  208  to reduce the likelihood of being obscured by the surgeon, surgical tools, or other parts of the robot  102 . Further, one or more tracking markers  118  can be further mounted (or otherwise secured) to the surgical tools  608  (e.g., a screw driver, dilator, implant inserter, or the like). Thus, the tracking markers  118  enable each of the marked objects (e.g., the end-effector  112 , the patient  210 , and the surgical tools  608 ) to be tracked by the robot  102 . In exemplary embodiments, system  100  can use tracking information collected from each of the marked objects to calculate the orientation and location, for example, of the end-effector  112 , the surgical instrument  608  (e.g., positioned in the tube  114  of the end-effector  112 ), and the relative position of the patient  210 . 
     In exemplary embodiments, one or more of markers  118  may be optical markers. In some embodiments, the positioning of one or more tracking markers  118  on end-effector  112  can maximize the accuracy of the positional measurements by serving to check or verify the position of end-effector  112 . Further details of surgical robot system  100  including the control, movement and tracking of surgical robot  102  and of a surgical instrument  608  can be found in co-pending U.S. patent application Ser. No. 13/924,505, which is incorporated herein by reference in its entirety. 
     Exemplary embodiments include one or more markers  118  coupled to the surgical instrument  608 . In exemplary embodiments, these markers  118 , for example, coupled to the patient  210  and surgical instruments  608 , as well as markers  118  coupled to the end-effector  112  of the robot  102  can comprise conventional infrared light-emitting diodes (LEDs) or an Optotrak® diode capable of being tracked using a commercially available infrared optical tracking system such as Optotrak®. Optotrak® is a registered trademark of Northern Digital Inc., Waterloo, Ontario, Canada. In other embodiments, markers  118  can comprise conventional reflective spheres capable of being tracked using a commercially available optical tracking system such as Polaris Spectra. Polaris Spectra is also a registered trademark of Northern Digital, Inc. In an exemplary embodiment, the markers  118  coupled to the end-effector  112  are active markers which comprise infrared light-emitting diodes which may be turned on and off, and the markers  118  coupled to the patient  210  and the surgical instruments  608  comprise passive reflective spheres. 
     In exemplary embodiments, light emitted from and/or reflected by markers  118  can be detected by camera  200  and can be used to monitor the location and movement of the marked objects. In alternative embodiments, markers  118  can comprise a radio-frequency and/or electromagnetic reflector or transceiver and the camera  200  can include or be replaced by a radio-frequency and/or electromagnetic transceiver. 
     Similar to surgical robot system  100 ,  FIG.  3    illustrates a surgical robot system  300  and camera stand  302 , in a docked configuration, consistent with an exemplary embodiment of the present disclosure. Surgical robot system  300  may comprise a robot  301  including a display  304 , upper arm  306 , lower arm  308 , end-effector  310 , vertical column  312 , casters  314 , cabinet  316 , tablet drawer  318 , connector panel  320 , control panel  322 , and ring of information  324 . Camera stand  302  may comprise camera  326 . These components are described in greater with respect to  FIG.  5   .  FIG.  3    illustrates the surgical robot system  300  in a docked configuration where the camera stand  302  is nested with the robot  301 , for example, when not in use. It will be appreciated by those skilled in the art that the camera  326  and robot  301  may be separated from one another and positioned at any appropriate location during the surgical procedure, for example, as shown in  FIGS.  1  and  2   . 
       FIG.  4    illustrates a base  400  consistent with an exemplary embodiment of the present disclosure. Base  400  may be a portion of surgical robot system  300  and comprise cabinet  316 . Cabinet  316  may house certain components of surgical robot system  300  including but not limited to a battery  402 , a power distribution module  404 , a platform interface board module  406 , a computer  408 , a handle  412 , and a tablet drawer  414 . The connections and relationship between these components is described in greater detail with respect to  FIG.  5   . 
       FIG.  5    illustrates a block diagram of certain components of an exemplary embodiment of surgical robot system  300 . Surgical robot system  300  may comprise platform subsystem  502 , computer subsystem  504 , motion control subsystem  506 , and tracking subsystem  532 . Platform subsystem  502  may further comprise battery  402 , power distribution module  404 , platform interface board module  406 , and tablet charging station  534 . Computer subsystem  504  may further comprise computer  408 , display  304 , and speaker  536 . Motion control subsystem  506  may further comprise driver circuit  508 , motors  510 ,  512 ,  514 ,  516 ,  518 , stabilizers  520 ,  522 ,  524 ,  526 , end-effector  310 , and controller  538 . Tracking subsystem  532  may further comprise position sensor  540  and camera converter  542 . System  300  may also comprise a foot pedal  544  and tablet  546 . 
     Input power is supplied to system  300  via a power source  548  which may be provided to power distribution module  404 . Power distribution module  404  receives input power and is configured to generate different power supply voltages that are provided to other modules, components, and subsystems of system  300 . Power distribution module  404  may be configured to provide different voltage supplies to platform interface module  406 , which may be provided to other components such as computer  408 , display  304 , speaker  536 , driver  508  to, for example, power motors  512 ,  514 ,  516 ,  518  and end-effector  310 , motor  510 , ring  324 , camera converter  542 , and other components for system  300  for example, fans for cooling the electrical components within cabinet  316 . 
     Power distribution module  404  may also provide power to other components such as tablet charging station  534  that may be located within tablet drawer  318 . Tablet charging station  534  may be in wireless or wired communication with tablet  546  for charging table  546 . Tablet  546  may be used by a surgeon consistent with the present disclosure and described herein. 
     Power distribution module  404  may also be connected to battery  402 , which serves as temporary power source in the event that power distribution module  404  does not receive power from input power  548 . At other times, power distribution module  404  may serve to charge battery  402  if necessary. 
     Other components of platform subsystem  502  may also include connector panel  320 , control panel  322 , and ring  324 . Connector panel  320  may serve to connect different devices and components to system  300  and/or associated components and modules. Connector panel  320  may contain one or more ports that receive lines or connections from different components. For example, connector panel  320  may have a ground terminal port that may ground system  300  to other equipment, a port to connect foot pedal  544  to system  300 , a port to connect to tracking subsystem  532 , which may comprise position sensor  540 , camera converter  542 , and cameras  326  associated with camera stand  302 . Connector panel  320  may also include other ports to allow USB, Ethernet, HDMI communications to other components, such as computer  408 . 
     Control panel  322  may provide various buttons or indicators that control operation of system  300  and/or provide information regarding system  300 . For example, control panel  322  may include buttons to power on or off system  300 , lift or lower vertical column  312 , and lift or lower stabilizers  520 - 526  that may be designed to engage casters  314  to lock system  300  from physically moving. Other buttons may stop system  300  in the event of an emergency, which may remove all motor power and apply mechanical brakes to stop all motion from occurring. Control panel  322  may also have indicators notifying the user of certain system conditions such as a line power indicator or status of charge for battery  402 . 
     Ring  324  may be a visual indicator to notify the user of system  300  of different modes that system  300  is operating under and certain warnings to the user. 
     Computer subsystem  504  includes computer  408 , display  304 , and speaker  536 . Computer  504  includes an operating system and software to operate system  300 . Computer  504  may receive and process information from other components (for example, tracking subsystem  532 , platform subsystem  502 , and/or motion control subsystem  506 ) in order to display information to the user. Further, computer subsystem  504  may also include speaker  536  to provide audio to the user. 
     Tracking subsystem  532  may include position sensor  504  and converter  542 . Tracking subsystem  532  may correspond to camera stand  302  including camera  326  as described with respect to  FIG.  3   . Position sensor  504  may be camera  326 . Tracking subsystem may track the location of certain markers that are located on the different components of system  300  and/or instruments used by a user during a surgical procedure. This tracking may be conducted in a manner consistent with the present disclosure including the use of infrared technology that tracks the location of active or passive elements, such as LEDs or reflective markers, respectively. The location, orientation, and position of structures having these types of markers may be provided to computer  408  which may be shown to a user on display  304 . For example, a surgical instrument  608  having these types of markers and tracked in this manner (which may be referred to as a navigational space) may be shown to a user in relation to a three dimensional image of a patient&#39;s anatomical structure. 
     Motion control subsystem  506  may be configured to physically move vertical column  312 , upper arm  306 , lower arm  308 , or rotate end-effector  310 . The physical movement may be conducted through the use of one or more motors  510 - 518 . For example, motor  510  may be configured to vertically lift or lower vertical column  312 . Motor  512  may be configured to laterally move upper arm  308  around a point of engagement with vertical column  312  as shown in  FIG.  3   . Motor  514  may be configured to laterally move lower arm  308  around a point of engagement with upper arm  308  as shown in  FIG.  3   . Motors  516  and  518  may be configured to move end-effector  310  in a manner such that one may control the roll and one may control the tilt, thereby providing multiple angles that end-effector  310  may be moved. These movements may be achieved by controller  538  which may control these movements through load cells disposed on end-effector  310  and activated by a user engaging these load cells to move system  300  in a desired manner. 
     Moreover, system  300  may provide for automatic movement of vertical column  312 , upper arm  306 , and lower arm  308  through a user indicating on display  304  (which may be a touchscreen input device) the location of a surgical instrument or component on three dimensional image of the patient&#39;s anatomy on display  304 . The user may initiate this automatic movement by stepping on foot pedal  544  or some other input means. 
       FIG.  6    illustrates a surgical robot system  600  consistent with an exemplary embodiment. Surgical robot system  600  may comprise end-effector  602 , robot arm  604 , guide tube  606 , instrument  608 , and robot base  610 . Instrument tool  608  may be attached to a tracking array  612  including one or more tracking markers (such as markers  118 ) and have an associated trajectory  614 . Trajectory  614  may represent a path of movement that instrument tool  608  is configured to travel once it is positioned through or secured in guide tube  606 , for example, a path of insertion of instrument tool  608  into a patient. In an exemplary operation, robot base  610  may be configured to be in electronic communication with robot arm  604  and end-effector  602  so that surgical robot system  600  may assist a user (for example, a surgeon) in operating on the patient  210 . Surgical robot system  600  may be consistent with previously described surgical robot system  100  and  300 . 
     A tracking array  612  may be mounted on instrument  608  to monitor the location and orientation of instrument tool  608 . The tracking array  612  may be attached to an instrument  608  and may comprise tracking markers  804 . As best seen in  FIG.  8   , tracking markers  804  may be, for example, light emitting diodes and/or other types of reflective markers (e.g., markers  118  as described elsewhere herein). The tracking devices may be one or more line of sight devices associated with the surgical robot system. As an example, the tracking devices may be one or more cameras  200 ,  326  associated with the surgical robot system  100 ,  300  and may also track tracking array  612  for a defined domain or relative orientations of the instrument  608  in relation to the robot arm  604 , the robot base  610 , end-effector  602 , and/or the patient  210 . The tracking devices may be consistent with those structures described in connection with camera stand  302  and tracking subsystem  532 . 
       FIGS.  7 A,  7 B, and  7 C  illustrate a top view, front view, and side view, respectively, of end-effector  602  consistent with an exemplary embodiment. End-effector  602  may comprise one or more tracking markers  702 . Tracking markers  702  may be light emitting diodes or other types of active and passive markers, such as tracking markers  118  that have been previously described. In an exemplary embodiment, the tracking markers  702  are active infrared-emitting markers that are activated by an electrical signal (e.g., infrared light emitting diodes (LEDs)). Thus, tracking markers  702  may be activated such that the infrared markers  702  are visible to the camera  200 ,  326  or may be deactivated such that the infrared markers  702  are not visible to the camera  200 ,  326 . Thus, when the markers  702  are active, the end-effector  602  may be controlled by the system  100 ,  300 ,  600 , and when the markers  702  are deactivated, the end-effector  602  may be locked in position and unable to be moved by the system  100 ,  300 ,  600 . 
     Markers  702  may be disposed on or within end-effector  602  in a manner such that the markers  702  are visible by one or more cameras  200 ,  326  or other tracking devices associated with the surgical robot system  100 ,  300 ,  600 . The camera  200 ,  326  or other tracking devices may track end-effector  602  as it moves to different positions and viewing angles by following the movement of tracking markers  702 . The location of markers  702  and/or end-effector  602  may be shown on a display  110 ,  304  associated with the surgical robot system  100 ,  300 ,  600 , for example, display  110  as shown in  FIG.  2    and/or display  304  shown in  FIG.  3   . This display  110 ,  304  may allow a user to ensure that end-effector  602  is in a desirable position in relation to robot arm  604 , robot base  610 , the patient  210 , and/or the user. 
     For example, as shown in  FIG.  7 A , markers  702  may be placed around the surface of end-effector  602  so that a tracking device placed away from the surgical field  208  and facing toward the robot  102 ,  301  and the camera  200 ,  326  is able to view at least 3 of the markers  702  through a range of common orientations of the end-effector  602  relative to the tracking device  100 ,  300 ,  600 . For example, distribution of markers  702  in this way allows end-effector  602  to be monitored by the tracking devices when end-effector  602  is translated and rotated in the surgical field  208 . 
     In addition, in exemplary embodiments, end-effector  602  may be equipped with infrared (IR) receivers that can detect when an external camera  200 ,  326  is getting ready to read markers  702 . Upon this detection, end-effector  602  may then illuminate markers  702 . The detection by the IR receivers that the external camera  200 ,  326  is ready to read markers  702  may signal the need to synchronize a duty cycle of markers  702 , which may be light emitting diodes, to an external camera  200 ,  326 . This may also allow for lower power consumption by the robotic system as a whole, whereby markers  702  would only be illuminated at the appropriate time instead of being illuminated continuously. Further, in exemplary embodiments, markers  702  may be powered off to prevent interference with other navigation tools, such as different types of surgical instruments  608 . 
       FIG.  8    depicts one type of surgical instrument  608  including a tracking array  612  and tracking markers  804 . Tracking markers  804  may be of any type described herein including but not limited to light emitting diodes or reflective spheres. Markers  804  are monitored by tracking devices associated with the surgical robot system  100 ,  300 ,  600  and may be one or more of the line of sight cameras  200 ,  326 . The cameras  200 ,  326  may track the location of instrument  608  based on the position and orientation of tracking array  612  and markers  804 . A user, such as a surgeon  120 , may orient instrument  608  in a manner so that tracking array  612  and markers  804  are sufficiently recognized by the tracking device or camera  200 ,  326  to display instrument  608  and markers  804  on, for example, display  110  of the exemplary surgical robot system. 
     The manner in which a surgeon  120  may place instrument  608  into guide tube  606  of the end-effector  602  and adjust the instrument  608  is evident in  FIG.  8   . The hollow tube or guide tube  114 ,  606  of the end-effector  112 ,  310 ,  602  is sized and configured to receive at least a portion of the surgical instrument  608 . The guide tube  114 ,  606  is configured to be oriented by the robot arm  104  such that insertion and trajectory for the surgical instrument  608  is able to reach a desired anatomical target within or upon the body of the patient  210 . The surgical instrument  608  may include at least a portion of a generally cylindrical instrument. Although a screw driver is exemplified as the surgical tool  608 , it will be appreciated that any suitable surgical tool  608  may be positioned by the end-effector  602 . By way of example, the surgical instrument  608  may include one or more of a guide wire, cannula, a retractor, a drill, a reamer, a screw driver, an insertion tool, a removal tool, or the like. Although the hollow tube  114 ,  606  is generally shown as having a cylindrical configuration, it will be appreciated by those of skill in the art that the guide tube  114 ,  606  may have any suitable shape, size and configuration desired to accommodate the surgical instrument  608  and access the surgical site. 
       FIGS.  9 A- 9 C  illustrate end-effector  602  and a portion of robot arm  604  consistent with an exemplary embodiment. End-effector  602  may further comprise body  1202  and clamp  1204 . Clamp  1204  may comprise handle  1206 , balls  1208 , spring  1210 , and lip  1212 . Robot arm  604  may further comprise depressions  1214 , mounting plate  1216 , lip  1218 , and magnets  1220 . 
     End-effector  602  may mechanically interface and/or engage with the surgical robot system and robot arm  604  through one or more couplings. For example, end-effector  602  may engage with robot arm  604  through a locating coupling and/or a reinforcing coupling. Through these couplings, end-effector  602  may fasten with robot arm  604  outside a flexible and sterile barrier. In an exemplary embodiment, the locating coupling may be a magnetically kinematic mount and the reinforcing coupling may be a five bar over center clamping linkage. 
     With respect to the locating coupling, robot arm  604  may comprise mounting plate  1216 , which may be non-magnetic material, one or more depressions  1214 , lip  1218 , and magnets  1220 . Magnet  1220  is mounted below each of depressions  1214 . Portions of clamp  1204  may comprise magnetic material and be attracted by one or more magnets  1220 . Through the magnetic attraction of clamp  1204  and robot arm  604 , balls  1208  become seated into respective depressions  1214 . For example, balls  1208  as shown in  FIG.  9 B  would be seated in depressions  1214  as shown in  FIG.  9 A . This seating may be considered a magnetically-assisted kinematic coupling. Magnets  1220  may be configured to be strong enough to support the entire weight of end-effector  602  regardless of the orientation of end-effector  602 . The locating coupling may be any style of kinematic mount that uniquely restrains six degrees of freedom. 
     With respect to the reinforcing coupling, portions of clamp  1204  may be configured to be a fixed ground link and as such clamp  1204  may serve as a five bar linkage. Closing clamp handle  1206  may fasten end-effector  602  to robot arm  604  as lip  1212  and lip  1218  engage clamp  1204  in a manner to secure end-effector  602  and robot arm  604 . When clamp handle  1206  is closed, spring  1210  may be stretched or stressed while clamp  1204  is in a locked position. The locked position may be a position that provides for linkage past center. Because of a closed position that is past center, the linkage will not open absent a force applied to clamp handle  1206  to release clamp  1204 . Thus, in a locked position end-effector  602  may be robustly secured to robot arm  604 . 
     Spring  1210  may be a curved beam in tension. Spring  1210  may be comprised of a material that exhibits high stiffness and high yield strain such as virgin PEEK (poly-ether-ether-ketone). The linkage between end-effector  602  and robot arm  604  may provide for a sterile barrier between end-effector  602  and robot arm  604  without impeding fastening of the two couplings. 
     The reinforcing coupling may be a linkage with multiple spring members. The reinforcing coupling may latch with a cam or friction based mechanism. The reinforcing coupling may also be a sufficiently powerful electromagnet that will support fastening end-effector  102  to robot arm  604 . The reinforcing coupling may be a multi-piece collar completely separate from either end-effector  602  and/or robot arm  604  that slips over an interface between end-effector  602  and robot arm  604  and tightens with a screw mechanism, an over center linkage, or a cam mechanism. 
     Referring to  FIGS.  10  and  11   , prior to or during a surgical procedure, certain registration procedures may be conducted in order to track objects and a target anatomical structure of the patient  210  both in a navigation space and an image space. In order to conduct such registration, a registration system  1400  may be used as illustrated in  FIG.  10   . 
     In order to track the position of the patient  210 , a patient tracking device  116  may include a patient fixation instrument  1402  to be secured to a rigid anatomical structure of the patient  210  and a dynamic reference base (DRB)  1404  may be securely attached to the patient fixation instrument  1402 . For example, patient fixation instrument  1402  may be inserted into opening  1406  of dynamic reference base  1404 . Dynamic reference base  1404  may contain markers  1408  that are visible to tracking devices, such as tracking subsystem  532 . These markers  1408  may be optical markers or reflective spheres, such as tracking markers  118 , as previously discussed herein. 
     Patient fixation instrument  1402  is attached to a rigid anatomy of the patient  210  and may remain attached throughout the surgical procedure. In an exemplary embodiment, patient fixation instrument  1402  is attached to a rigid area of the patient  210 , for example, a bone that is located away from the targeted anatomical structure subject to the surgical procedure. In order to track the targeted anatomical structure, dynamic reference base  1404  is associated with the targeted anatomical structure through the use of a registration fixture that is temporarily placed on or near the targeted anatomical structure in order to register the dynamic reference base  1404  with the location of the targeted anatomical structure. 
     A registration fixture  1410  is attached to patient fixation instrument  1402  through the use of a pivot arm  1412 . Pivot arm  1412  is attached to patient fixation instrument  1402  by inserting patient fixation instrument  1402  through an opening  1414  of registration fixture  1410 . Pivot arm  1412  is attached to registration fixture  1410  by, for example, inserting a knob  1416  through an opening  1418  of pivot arm  1412 . 
     Using pivot arm  1412 , registration fixture  1410  may be placed over the targeted anatomical structure and its location may be determined in an image space and navigation space using tracking markers  1420  and/or fiducials  1422  on registration fixture  1410 . Registration fixture  1410  may contain a collection of markers  1420  that are visible in a navigational space (for example, markers  1420  may be detectable by tracking subsystem  532 ). Tracking markers  1420  may be optical markers visible in infrared light as previously described herein. Registration fixture  1410  may also contain a collection of fiducials  1422 , for example, such as bearing balls, that are visible in an imaging space (for example, a three dimension CT image). As described in greater detail with respect to  FIG.  11   , using registration fixture  1410 , the targeted anatomical structure may be associated with dynamic reference base  1404  thereby allowing depictions of objects in the navigational space to be overlaid on images of the anatomical structure. Dynamic reference base  1404 , located at a position away from the targeted anatomical structure, may become a reference point thereby allowing removal of registration fixture  1410  and/or pivot arm  1412  from the surgical area. 
       FIG.  11    provides an exemplary method  1500  for registration consistent with the present disclosure. Method  1500  begins at step  1502  wherein a graphical representation (or image(s)) of the targeted anatomical structure may be imported into system  100 ,  300   600 , for example computer  408 . The graphical representation may be three dimensional CT or a fluoroscope scan of the targeted anatomical structure of the patient  210  which includes registration fixture  1410  and a detectable imaging pattern of fiducials  1420 . 
     At step  1504 , an imaging pattern of fiducials  1420  is detected and registered in the imaging space and stored in computer  408 . Optionally, at this time at step  1506 , a graphical representation of the registration fixture  1410  may be overlaid on the images of the targeted anatomical structure. 
     At step  1508 , a navigational pattern of registration fixture  1410  is detected and registered by recognizing markers  1420 . Markers  1420  may be optical markers that are recognized in the navigation space through infrared light by tracking subsystem  532  via position sensor  540 . Thus, the location, orientation, and other information of the targeted anatomical structure is registered in the navigation space. Therefore, registration fixture  1410  may be recognized in both the image space through the use of fiducials  1422  and the navigation space through the use of markers  1420 . At step  1510 , the registration of registration fixture  1410  in the image space is transferred to the navigation space. This transferal is done, for example, by using the relative position of the imaging pattern of fiducials  1422  compared to the position of the navigation pattern of markers  1420 . 
     At step  1512 , registration of the navigation space of registration fixture  1410  (having been registered with the image space) is further transferred to the navigation space of dynamic registration array  1404  attached to patient fixture instrument  1402 . Thus, registration fixture  1410  may be removed and dynamic reference base  1404  may be used to track the targeted anatomical structure in both the navigation and image space because the navigation space is associated with the image space. 
     At steps  1514  and  1516 , the navigation space may be overlaid on the image space and objects with markers visible in the navigation space (for example, surgical instruments  608  with optical markers  804 ). The objects may be tracked through graphical representations of the surgical instrument  608  on the images of the targeted anatomical structure. 
       FIGS.  12 A- 12 B  illustrate imaging devices  1304  that may be used in conjunction with robot systems  100 ,  300 ,  600  to acquire pre-operative, intra-operative, post-operative, and/or real-time image data of patient  210 . Any appropriate subject matter may be imaged for any appropriate procedure using the imaging system  1304 . The imaging system  1304  may be any imaging device such as imaging device  1306  and/or a C-arm  1308  device. It may be desirable to take x-rays of patient  210  from a number of different positions, without the need for frequent manual repositioning of patient  210  which may be required in an x-ray system. As illustrated in  FIG.  12 A , the imaging system  1304  may be in the form of a C-arm  1308  that includes an elongated C-shaped member terminating in opposing distal ends  1312  of the “C” shape. C-shaped member  1130  may further comprise an x-ray source  1314  and an image receptor  1316 . The space within C-arm  1308  of the arm may provide room for the physician to attend to the patient substantially free of interference from x-ray support structure  1318 . As illustrated in  FIG.  12 B , the imaging system may include imaging device  1306  having a gantry housing  1324  attached to a support structure imaging device support structure  1328 , such as a wheeled mobile cart  1330  with wheels  1332 , which may enclose an image capturing portion, not illustrated. The image capturing portion may include an x-ray source and/or emission portion and an x-ray receiving and/or image receiving portion, which may be disposed about one hundred and eighty degrees from each other and mounted on a rotor (not illustrated) relative to a track of the image capturing portion. The image capturing portion may be operable to rotate three hundred and sixty degrees during image acquisition. The image capturing portion may rotate around a central point and/or axis, allowing image data of patient  210  to be acquired from multiple directions or in multiple planes. Although certain imaging systems  1304  are exemplified herein, it will be appreciated that any suitable imaging system may be selected by one of ordinary skill in the art. 
     Turning now to  FIGS.  13 A- 13 C , the surgical robot system  100 ,  300 ,  600  relies on accurate positioning of the end-effector  112 ,  602 , surgical instruments  608 , and/or the patient  210  (e.g., patient tracking device  116 ) relative to the desired surgical area. In the embodiments shown in  FIGS.  13 A- 13 C , the tracking markers  118 ,  804  are rigidly attached to a portion of the instrument  608  and/or end-effector  112 . 
       FIG.  13 A  depicts part of the surgical robot system  100  with the robot  102  including base  106 , robot arm  104 , and end-effector  112 . The other elements, not illustrated, such as the display, cameras, etc. may also be present as described herein.  FIG.  13 B  depicts a close-up view of the end-effector  112  with guide tube  114  and a plurality of tracking markers  118  rigidly affixed to the end-effector  112 . In this embodiment, the plurality of tracking markers  118  are attached to the guide tube  112 .  FIG.  13 C  depicts an instrument  608  (in this case, a probe  608 A) with a plurality of tracking markers  804  rigidly affixed to the instrument  608 . As described elsewhere herein, the instrument  608  could include any suitable surgical instrument, such as, but not limited to, guide wire, cannula, a retractor, a drill, a reamer, a screw driver, an insertion tool, a removal tool, or the like. 
     When tracking an instrument  608 , end-effector  112 , or other object to be tracked in 3D, an array of tracking markers  118 ,  804  may be rigidly attached to a portion of the tool  608  or end-effector  112 . Preferably, the tracking markers  118 ,  804  are attached such that the markers  118 ,  804  are out of the way (e.g., not impeding the surgical operation, visibility, etc.). The markers  118 ,  804  may be affixed to the instrument  608 , end-effector  112 , or other object to be tracked, for example, with an array  612 . Usually three or four markers  118 ,  804  are used with an array  612 . The array  612  may include a linear section, a cross piece, and may be asymmetric such that the markers  118 ,  804  are at different relative positions and locations with respect to one another. For example, as shown in  FIG.  13 C , a probe  608 A with a 4-marker tracking array  612  is shown, and  FIG.  13 B  depicts the end-effector  112  with a different 4-marker tracking array  612 . 
     In  FIG.  13 C , the tracking array  612  functions as the handle  620  of the probe  608 A. Thus, the four markers  804  are attached to the handle  620  of the probe  608 A, which is out of the way of the shaft  622  and tip  624 . Stereophotogrammetric tracking of these four markers  804  allows the instrument  608  to be tracked as a rigid body and for the tracking system  100 ,  300 ,  600  to precisely determine the position of the tip  624  and the orientation of the shaft  622  while the probe  608 A is moved around in front of tracking cameras  200 ,  326 . 
     To enable automatic tracking of one or more tools  608 , end-effector  112 , or other object to be tracked in 3D (e.g., multiple rigid bodies), the markers  118 ,  804  on each tool  608 , end-effector  112 , or the like, are arranged asymmetrically with a known inter-marker spacing. The reason for asymmetric alignment is so that it is unambiguous which marker  118 ,  804  corresponds to a particular location on the rigid body and whether markers  118 ,  804  are being viewed from the front or back, i.e., mirrored. For example, if the markers  118 ,  804  were arranged in a square on the tool  608  or end-effector  112 , it would be unclear to the system  100 ,  300 ,  600  which marker  118 ,  804  corresponded to which corner of the square. For example, for the probe  608 A, it would be unclear which marker  804  was closest to the shaft  622 . Thus, it would be unknown which way the shaft  622  was extending from the array  612 . Accordingly, each array  612  and thus each tool  608 , end-effector  112 , or other object to be tracked should have a unique marker pattern to allow it to be distinguished from other tools  608  or other objects being tracked. Asymmetry and unique marker patterns allow the system  100 ,  300 ,  600  to detect individual markers  118 ,  804  then to check the marker spacing against a stored template to determine which tool  608 , end effector  112 , or other object they represent. Detected markers  118 ,  804  can then be sorted automatically and assigned to each tracked object in the correct order. Without this information, rigid body calculations could not then be performed to extract key geometric information, for example, such as tool tip  624  and alignment of the shaft  622 , unless the user manually specified which detected marker  118 ,  804  corresponded to which position on each rigid body. These concepts are commonly known to those skilled in the methods of 3D optical tracking. 
     Turning now to  FIGS.  14 A- 14 D , an alternative version of an end-effector  912  with moveable tracking markers  918 A- 918 D is shown. In  FIG.  14 A , an array with moveable tracking markers  918 A- 918 D are shown in a first configuration, and in  FIG.  14 B  the moveable tracking markers  918 A- 918 D are shown in a second configuration, which is angled relative to the first configuration.  FIG.  14 C  shows the template of the tracking markers  918 A- 918 D, for example, as seen by the cameras  200 ,  326  in the first configuration of  FIG.  14 A ; and  FIG.  14 D  shows the template of tracking markers  918 A- 918 D, for example, as seen by the cameras  200 ,  326  in the second configuration of  FIG.  14 B . 
     In this embodiment, 4-marker array tracking is contemplated wherein the markers  918 A- 918 D are not all in fixed position relative to the rigid body and instead, one or more of the array markers  918 A- 918 D can be adjusted, for example, during testing, to give updated information about the rigid body that is being tracked without disrupting the process for automatic detection and sorting of the tracked markers  918 A- 918 D. 
     When tracking any tool, such as a guide tube  914  connected to the end effector  912  of a robot system  100 ,  300 ,  600 , the tracking array&#39;s primary purpose is to update the position of the end effector  912  in the camera coordinate system. When using the rigid system, for example, as shown in  FIG.  13 B , the array  612  of reflective markers  118  rigidly extend from the guide tube  114 . Because the tracking markers  118  are rigidly connected, knowledge of the marker locations in the camera coordinate system also provides exact location of the centerline, tip, and tail of the guide tube  114  in the camera coordinate system. Typically, information about the position of the end effector  112  from such an array  612  and information about the location of a target trajectory from another tracked source are used to calculate the required moves that must be input for each axis of the robot  102  that will move the guide tube  114  into alignment with the trajectory and move the tip to a particular location along the trajectory vector. 
     Sometimes, the desired trajectory is in an awkward or unreachable location, but if the guide tube  114  could be swiveled, it could be reached. For example, a very steep trajectory pointing away from the base  106  of the robot  102  might be reachable if the guide tube  114  could be swiveled upward beyond the limit of the pitch (wrist up-down angle) axis, but might not be reachable if the guide tube  114  is attached parallel to the plate connecting it to the end of the wrist. To reach such a trajectory, the base  106  of the robot  102  might be moved or a different end effector  112  with a different guide tube attachment might be exchanged with the working end effector. Both of these solutions may be time consuming and cumbersome. 
     As best seen in  FIGS.  14 A and  14 B , if the array  908  is configured such that one or more of the markers  918 A- 918 D are not in a fixed position and instead, one or more of the markers  918 A- 918 D can be adjusted, swiveled, pivoted, or moved, the robot  102  can provide updated information about the object being tracked without disrupting the detection and tracking process. For example, one of the markers  918 A- 918 D may be fixed in position and the other markers  918 A- 918 D may be moveable; two of the markers  918 A- 918 D may be fixed in position and the other markers  918 A- 918 D may be moveable; three of the markers  918 A- 918 D may be fixed in position and the other marker  918 A- 918 D may be moveable; or all of the markers  918 A- 918 D may be moveable. 
     In the embodiment shown in  FIGS.  14 A and  14 B , markers  918 A,  918 B are rigidly connected directly to a base  906  of the end-effector  912 , and markers  918 C,  918 D are rigidly connected to the tube  914 . Similar to array  612 , array  908  may be provided to attach the markers  918 A- 918 D to the end-effector  912 , instrument  608 , or other object to be tracked. In this case, however, the array  908  is comprised of a plurality of separate components. For example, markers  918 A,  918 B may be connected to the base  906  with a first array  908 A, and markers  918 C,  918 D may be connected to the guide tube  914  with a second array  908 B. Marker  918 A may be affixed to a first end of the first array  908 A and marker  918 B may be separated a linear distance and affixed to a second end of the first array  908 A. While first array  908  is substantially linear, second array  908 B has a bent or V-shaped configuration, with respective root ends, connected to the guide tube  914 , and diverging therefrom to distal ends in a V-shape with marker  918 C at one distal end and marker  918 D at the other distal end. Although specific configurations are exemplified herein, it will be appreciated that other asymmetric designs including different numbers and types of arrays  908 A,  908 B and different arrangements, numbers, and types of markers  918 A- 918 D are contemplated. 
     The guide tube  914  may be moveable, swivelable, or pivotable relative to the base  906 , for example, across a hinge  920  or other connector to the base  906 . Thus, markers  918 C,  918 D are moveable such that when the guide tube  914  pivots, swivels, or moves, markers  918 C,  918 D also pivot, swivel, or move. As best seen in  FIG.  14 A , guide tube  914  has a longitudinal axis  916  which is aligned in a substantially normal or vertical orientation such that markers  918 A- 918 D have a first configuration. Turning now to  FIG.  14 B , the guide tube  914  is pivoted, swiveled, or moved such that the longitudinal axis  916  is now angled relative to the vertical orientation such that markers  918 A- 918 D have a second configuration, different from the first configuration. 
     In contrast to the embodiment described for  FIGS.  14 A- 14 D , if a swivel existed between the guide tube  914  and the arm  104  (e.g., the wrist attachment) with all four markers  918 A- 918 D remaining attached rigidly to the guide tube  914  and this swivel was adjusted by the user, the robotic system  100 ,  300 ,  600  would not be able to automatically detect that the guide tube  914  orientation had changed. The robotic system  100 ,  300 ,  600  would track the positions of the marker array  908  and would calculate incorrect robot axis moves assuming the guide tube  914  was attached to the wrist (the robot arm  104 ) in the previous orientation. By keeping one or more markers  918 A- 918 D (e.g., two markers  918 C,  918 D) rigidly on the tube  914  and one or more markers  918 A- 918 D (e.g., two markers  918 A,  918 B) across the swivel, automatic detection of the new position becomes possible and correct robot moves are calculated based on the detection of a new tool or end-effector  112 ,  912  on the end of the robot arm  104 . 
     One or more of the markers  918 A- 918 D are configured to be moved, pivoted, swiveled, or the like according to any suitable means. For example, the markers  918 A- 918 D may be moved by a hinge  920 , such as a clamp, spring, lever, slide, toggle, or the like, or any other suitable mechanism for moving the markers  918 A- 918 D individually or in combination, moving the arrays  908 A,  908 B individually or in combination, moving any portion of the end-effector  912  relative to another portion, or moving any portion of the tool  608  relative to another portion. 
     As shown in  FIGS.  14 A and  14 B , the array  908  and guide tube  914  may become reconfigurable by simply loosening the clamp or hinge  920 , moving part of the array  908 A,  908 B relative to the other part  908 A,  908 B, and retightening the hinge  920  such that the guide tube  914  is oriented in a different position. For example, two markers  918 C,  918 D may be rigidly interconnected with the tube  914  and two markers  918 A,  918 B may be rigidly interconnected across the hinge  920  to the base  906  of the end-effector  912  that attaches to the robot arm  104 . The hinge  920  may be in the form of a clamp, such as a wing nut or the like, which can be loosened and retightened to allow the user to quickly switch between the first configuration ( FIG.  14 A ) and the second configuration ( FIG.  14 B ). 
     The cameras  200 ,  326  detect the markers  918 A- 918 D, for example, in one of the templates identified in  FIGS.  14 C and  14 D . If the array  908  is in the first configuration ( FIG.  14 A ) and tracking cameras  200 ,  326  detect the markers  918 A- 918 D, then the tracked markers match Array Template  1  as shown in  FIG.  14 C . If the array  908  is the second configuration ( FIG.  14 B ) and tracking cameras  200 ,  326  detect the same markers  918 A- 918 D, then the tracked markers match Array Template  2  as shown in  FIG.  14 D . Array Template  1  and Array Template  2  are recognized by the system  100 ,  300 ,  600  as two distinct tools, each with its own uniquely defined spatial relationship between guide tube  914 , markers  918 A- 918 D, and robot attachment. The user could therefore adjust the position of the end-effector  912  between the first and second configurations without notifying the system  100 ,  300 ,  600  of the change and the system  100 ,  300 ,  600  would appropriately adjust the movements of the robot  102  to stay on trajectory. 
     In this embodiment, there are two assembly positions in which the marker array matches unique templates that allow the system  100 ,  300 ,  600  to recognize the assembly as two different tools or two different end effectors. In any position of the swivel between or outside of these two positions (namely, Array Template  1  and Array Template  2  shown in  FIGS.  14 C and  14 D , respectively), the markers  918 A- 918 D would not match any template and the system  100 ,  300 ,  600  would not detect any array present despite individual markers  918 A- 918 D being detected by cameras  200 ,  326 , with the result being the same as if the markers  918 A- 918 D were temporarily blocked from view of the cameras  200 ,  326 . It will be appreciated that other array templates may exist for other configurations, for example, identifying different instruments  608  or other end-effectors  112 ,  912 , etc. 
     In the embodiment described, two discrete assembly positions are shown in  FIGS.  14 A and  14 B . It will be appreciated, however, that there could be multiple discrete positions on a swivel joint, linear joint, combination of swivel and linear joints, pegboard, or other assembly where unique marker templates may be created by adjusting the position of one or more markers  918 A- 918 D of the array relative to the others, with each discrete position matching a particular template and defining a unique tool  608  or end-effector  112 ,  912  with different known attributes. In addition, although exemplified for end effector  912 , it will be appreciated that moveable and fixed markers  918 A- 918 D may be used with any suitable instrument  608  or other object to be tracked. 
     When using an external 3D tracking system  100 ,  300 ,  600  to track a full rigid body array of three or more markers attached to a robot&#39;s end effector  112  (for example, as depicted in  FIGS.  13 A and  13 B ), it is possible to directly track or to calculate the 3D position of every section of the robot  102  in the coordinate system of the cameras  200 ,  326 . The geometric orientations of joints relative to the tracker are known by design, and the linear or angular positions of joints are known from encoders for each motor of the robot  102 , fully defining the 3D positions of all of the moving parts from the end effector  112  to the base  116 . Similarly, if a tracker were mounted on the base  106  of the robot  102  (not shown), it is likewise possible to track or calculate the 3D position of every section of the robot  102  from base  106  to end effector  112  based on known joint geometry and joint positions from each motor&#39;s encoder. 
     In some situations, it may be desirable to track the positions of all segments of the robot  102  from fewer than three markers  118  rigidly attached to the end effector  112 . Specifically, if a tool  608  is introduced into the guide tube  114 , it may be desirable to track full rigid body motion of the robot  902  with only one additional marker  118  being tracked. 
     Turning now to  FIGS.  15 A- 15 E , an alternative version of an end-effector  1012  having only a single tracking marker  1018  is shown. End-effector  1012  may be similar to the other end-effectors described herein, and may include a guide tube  1014  extending along a longitudinal axis  1016 . A single tracking marker  1018 , similar to the other tracking markers described herein, may be rigidly affixed to the guide tube  1014 . This single marker  1018  can serve the purpose of adding missing degrees of freedom to allow full rigid body tracking and/or can serve the purpose of acting as a surveillance marker to ensure that assumptions about robot and camera positioning are valid. 
     The single tracking marker  1018  may be attached to the robotic end effector  1012  as a rigid extension to the end effector  1012  that protrudes in any convenient direction and does not obstruct the surgeon&#39;s view. The tracking marker  1018  may be affixed to the guide tube  1014  or any other suitable location of on the end-effector  1012 . When affixed to the guide tube  1014 , the tracking marker  1018  may be positioned at a location between first and second ends of the guide tube  1014 . For example, in  FIG.  15 A , the single tracking marker  1018  is shown as a reflective sphere mounted on the end of a narrow shaft  1017  that extends forward from the guide tube  1014  and is positioned longitudinally above a mid-point of the guide tube  1014  and below the entry of the guide tube  1014 . This position allows the marker  1018  to be generally visible by cameras  200 ,  326  but also would not obstruct vision of the surgeon  120  or collide with other tools or objects in the vicinity of surgery. In addition, the guide tube  1014  with the marker  1018  in this position is designed for the marker array on any tool  608  introduced into the guide tube  1014  to be visible at the same time as the single marker  1018  on the guide tube  1014  is visible. 
     As shown in  FIG.  15 B , when a snugly fitting tool or instrument  608  is placed within the guide tube  1014 , the instrument  608  becomes mechanically constrained in 4 of 6 degrees of freedom. That is, the instrument  608  cannot be rotated in any direction except about the longitudinal axis  1016  of the guide tube  1014  and the instrument  608  cannot be translated in any direction except along the longitudinal axis  1016  of the guide tube  1014 . In other words, the instrument  608  can only be translated along and rotated about the centerline of the guide tube  1014 . If two more parameters are known, such as (1) an angle of rotation about the longitudinal axis  1016  of the guide tube  1014 ; and (2) a position along the guide tube  1014 , then the position of the end effector  1012  in the camera coordinate system becomes fully defined. 
     Referring now to  FIG.  15 C , the system  100 ,  300 ,  600  should be able to know when a tool  608  is actually positioned inside of the guide tube  1014  and is not instead outside of the guide tube  1014  and just somewhere in view of the cameras  200 ,  326 . The tool  608  has a longitudinal axis or centerline  616  and an array  612  with a plurality of tracked markers  804 . The rigid body calculations may be used to determine where the centerline  616  of the tool  608  is located in the camera coordinate system based on the tracked position of the array  612  on the tool  608 . 
     The fixed normal (perpendicular) distance D F  from the single marker  1018  to the centerline or longitudinal axis  1016  of the guide tube  1014  is fixed and is known geometrically, and the position of the single marker  1018  can be tracked. Therefore, when a detected distance D D  from tool centerline  616  to single marker  1018  matches the known fixed distance D F  from the guide tube centerline  1016  to the single marker  1018 , it can be determined that the tool  608  is either within the guide tube  1014  (centerlines  616 ,  1016  of tool  608  and guide tube  1014  coincident) or happens to be at some point in the locus of possible positions where this distance D D  matches the fixed distance D F . For example, in  FIG.  15 C , the normal detected distance D D  from tool centerline  616  to the single marker  1018  matches the fixed distance D F  from guide tube centerline  1016  to the single marker  1018  in both frames of data (tracked marker coordinates) represented by the transparent tool  608  in two positions, and thus, additional considerations may be needed to determine when the tool  608  is located in the guide tube  1014 . 
     Turning now to  FIG.  15 D , programmed logic can be used to look for frames of tracking data in which the detected distance D D  from tool centerline  616  to single marker  1018  remains fixed at the correct length despite the tool  608  moving in space by more than some minimum distance relative to the single sphere  1018  to satisfy the condition that the tool  608  is moving within the guide tube  1014 . For example, a first frame F1 may be detected with the tool  608  in a first position and a second frame F2 may be detected with the tool  608  in a second position (namely, moved linearly with respect to the first position). The markers  804  on the tool array  612  may move by more than a given amount (e.g., more than 5 mm total) from the first frame F1 to the second frame F2. Even with this movement, the detected distance D D  from the tool centerline vector C′ to the single marker  1018  is substantially identical in both the first frame F1 and the second frame F2. 
     Logistically, the surgeon  120  or user could place the tool  608  within the guide tube  1014  and slightly rotate it or slide it down into the guide tube  1014  and the system  100 ,  300 ,  600  would be able to detect that the tool  608  is within the guide tube  1014  from tracking of the five markers (four markers  804  on tool  608  plus single marker  1018  on guide tube  1014 ). Knowing that the tool  608  is within the guide tube  1014 , all 6 degrees of freedom may be calculated that define the position and orientation of the robotic end effector  1012  in space. Without the single marker  1018 , even if it is known with certainty that the tool  608  is within the guide tube  1014 , it is unknown where the guide tube  1014  is located along the tool&#39;s centerline vector C′ and how the guide tube  1014  is rotated relative to the centerline vector C′. 
     With emphasis on  FIG.  15 E , the presence of the single marker  1018  being tracked as well as the four markers  804  on the tool  608 , it is possible to construct the centerline vector C′ of the guide tube  1014  and tool  608  and the normal vector through the single marker  1018  and through the centerline vector C′. This normal vector has an orientation that is in a known orientation relative to the forearm of the robot distal to the wrist (in this example, oriented parallel to that segment) and intersects the centerline vector C′ at a specific fixed position. For convenience, three mutually orthogonal vectors k′, j′, i′ can be constructed, as shown in  FIG.  15 E , defining rigid body position and orientation of the guide tube  1014 . One of the three mutually orthogonal vectors k′ is constructed from the centerline vector C′, the second vector j′ is constructed from the normal vector through the single marker  1018 , and the third vector i′ is the vector cross product of the first and second vectors k′, j′. The robot&#39;s joint positions relative to these vectors k′, j are known and fixed when all joints are at zero, and therefore rigid body calculations can be used to determine the location of any section of the robot relative to these vectors k′, j′, i′ when the robot is at a home position. During robot movement, if the positions of the tool markers  804  (while the tool  608  is in the guide tube  1014 ) and the position of the single marker  1018  are detected from the tracking system, and angles/linear positions of each joint are known from encoders, then position and orientation of any section of the robot can be determined. 
     In some embodiments, it may be useful to fix the orientation of the tool  608  relative to the guide tube  1014 . For example, the end effector guide tube  1014  may be oriented in a particular position about its axis  1016  to allow machining or implant positioning. Although the orientation of anything attached to the tool  608  inserted into the guide tube  1014  is known from the tracked markers  804  on the tool  608 , the rotational orientation of the guide tube  1014  itself in the camera coordinate system is unknown without the additional tracking marker  1018  (or multiple tracking markers in other embodiments) on the guide tube  1014 . This marker  1018  provides essentially a “clock position” from −180° to +180° based on the orientation of the marker  1018  relative to the centerline vector C′. Thus, the single marker  1018  can provide additional degrees of freedom to allow full rigid body tracking and/or can act as a surveillance marker to ensure that assumptions about the robot and camera positioning are valid. 
       FIG.  16    is a block diagram of a method  1100  for navigating and moving the end-effector  1012  (or any other end-effector described herein) of the robot  102  to a desired target trajectory. Another use of the single marker  1018  on the robotic end effector  1012  or guide tube  1014  is as part of the method  1100  enabling the automated safe movement of the robot  102  without a full tracking array attached to the robot  102 . This method  1100  functions when the tracking cameras  200 ,  326  do not move relative to the robot  102  (i.e., they are in a fixed position), the tracking system&#39;s coordinate system and robot&#39;s coordinate system are co-registered, and the robot  102  is calibrated such that the position and orientation of the guide tube  1014  can be accurately determined in the robot&#39;s Cartesian coordinate system based only on the encoded positions of each robotic axis. 
     For this method  1100 , the coordinate systems of the tracker and the robot must be co-registered, meaning that the coordinate transformation from the tracking system&#39;s Cartesian coordinate system to the robot&#39;s Cartesian coordinate system is needed. For convenience, this coordinate transformation can be a 4×4 matrix of translations and rotations that is well known in the field of robotics. This transformation will be termed Tcr to refer to “transformation—camera to robot”. Once this transformation is known, any new frame of tracking data, which is received as x,y,z coordinates in vector form for each tracked marker, can be multiplied by the 4×4 matrix and the resulting x,y,z coordinates will be in the robot&#39;s coordinate system. To obtain Tcr, a full tracking array on the robot is tracked while it is rigidly attached to the robot at a location that is known in the robot&#39;s coordinate system, then known rigid body methods are used to calculate the transformation of coordinates. It should be evident that any tool  608  inserted into the guide tube  1014  of the robot  102  can provide the same rigid body information as a rigidly attached array when the additional marker  1018  is also read. That is, the tool  608  need only be inserted to any position within the guide tube  1014  and at any rotation within the guide tube  1014 , not to a fixed position and orientation. Thus, it is possible to determine Tcr by inserting any tool  608  with a tracking array  612  into the guide tube  1014  and reading the tool&#39;s array  612  plus the single marker  1018  of the guide tube  1014  while at the same time determining from the encoders on each axis the current location of the guide tube  1014  in the robot&#39;s coordinate system. 
     Logic for navigating and moving the robot  102  to a target trajectory is provided in the method  1100  of  FIG.  16   . Before entering the loop  1102 , it is assumed that the transformation Tcr was previously stored. Thus, before entering loop  1102 , in step  1104 , after the robot base  106  is secured, greater than or equal to one frame of tracking data of a tool inserted in the guide tube while the robot is static is stored; and in step  1106 , the transformation of robot guide tube position from camera coordinates to robot coordinates Tcr is calculated from this static data and previous calibration data. Tcr should remain valid as long as the cameras  200 ,  326  do not move relative to the robot  102 . If the cameras  200 ,  326  move relative to the robot  102 , and Tcr needs to be re-obtained, the system  100 ,  300 ,  600  can be made to prompt the user to insert a tool  608  into the guide tube  1014  and then automatically perform the necessary calculations. 
     In the flowchart of method  1100 , each frame of data collected consists of the tracked position of the DRB  1404  on the patient  210 , the tracked position of the single marker  1018  on the end effector  1014 , and a snapshot of the positions of each robotic axis. From the positions of the robot&#39;s axes, the location of the single marker  1018  on the end effector  1012  is calculated. This calculated position is compared to the actual position of the marker  1018  as recorded from the tracking system. If the values agree, it can be assured that the robot  102  is in a known location. The transformation Tcr is applied to the tracked position of the DRB  1404  so that the target for the robot  102  can be provided in terms of the robot&#39;s coordinate system. The robot  102  can then be commanded to move to reach the target. 
     After steps  1104 ,  1106 , loop  1102  includes step  1108  receiving rigid body information for DRB  1404  from the tracking system; step  1110  transforming target tip and trajectory from image coordinates to tracking system coordinates; and step  1112  transforming target tip and trajectory from camera coordinates to robot coordinates (apply Tcr). Loop  1102  further includes step  1114  receiving a single stray marker position for robot from tracking system; and step  1116  transforming the single stray marker from tracking system coordinates to robot coordinates (apply stored Tcr). Loop  1102  also includes step  1118  determining current location of the single robot marker  1018  in the robot coordinate system from forward kinematics. The information from steps  1116  and  1118  is used to determine step  1120  whether the stray marker coordinates from transformed tracked position agree with the calculated coordinates being less than a given tolerance. If yes, proceed to step  1122 , calculate and apply robot move to target x, y, z and trajectory. If no, proceed to step  1124 , halt and require full array insertion into guide tube  1014  before proceeding; step  1126  after array is inserted, recalculate Tcr; and then proceed to repeat steps  1108 ,  1114 , and  1118 . 
     This method  1100  has advantages over a method in which the continuous monitoring of the single marker  1018  to verify the location is omitted. Without the single marker  1018 , it would still be possible to determine the position of the end effector  1012  using Tcr and to send the end-effector  1012  to a target location but it would not be possible to verify that the robot  102  was actually in the expected location. For example, if the cameras  200 ,  326  had been bumped and Tcr was no longer valid, the robot  102  would move to an erroneous location. For this reason, the single marker  1018  provides value with regard to safety. 
     For a given fixed position of the robot  102 , it is theoretically possible to move the tracking cameras  200 ,  326  to a new location in which the single tracked marker  1018  remains unmoved since it is a single point, not an array. In such a case, the system  100 ,  300 ,  600  would not detect any error since there would be agreement in the calculated and tracked locations of the single marker  1018 . However, once the robot&#39;s axes caused the guide tube  1012  to move to a new location, the calculated and tracked positions would disagree and the safety check would be effective. 
     The term “surveillance marker” may be used, for example, in reference to a single marker that is in a fixed location relative to the DRB  1404 . In this instance, if the DRB  1404  is bumped or otherwise dislodged, the relative location of the surveillance marker changes and the surgeon  120  can be alerted that there may be a problem with navigation. Similarly, in the embodiments described herein, with a single marker  1018  on the robot&#39;s guide tube  1014 , the system  100 ,  300 ,  600  can continuously check whether the cameras  200 ,  326  have moved relative to the robot  102 . If registration of the tracking system&#39;s coordinate system to the robot&#39;s coordinate system is lost, such as by cameras  200 ,  326  being bumped or malfunctioning or by the robot malfunctioning, the system  100 ,  300 ,  600  can alert the user and corrections can be made. Thus, this single marker  1018  can also be thought of as a surveillance marker for the robot  102 . 
     It should be clear that with a full array permanently mounted on the robot  102  (e.g., the plurality of tracking markers  702  on end-effector  602  shown in  FIGS.  7 A- 7 C ) such functionality of a single marker  1018  as a robot surveillance marker is not needed because it is not required that the cameras  200 ,  326  be in a fixed position relative to the robot  102 , and Tcr is updated at each frame based on the tracked position of the robot  102 . Reasons to use a single marker  1018  instead of a full array are that the full array is more bulky and obtrusive, thereby blocking the surgeon&#39;s view and access to the surgical field  208  more than a single marker  1018 , and line of sight to a full array is more easily blocked than line of sight to a single marker  1018 . 
     Turning now to  FIGS.  17 A- 17 B and  18 A- 18 B , instruments  608 , such as implant holders  608 B,  608 C, are depicted which include both fixed and moveable tracking markers  804 ,  806 . The implant holders  608 B,  608 C may have a handle  620  and an outer shaft  622  extending from the handle  620 . The shaft  622  may be positioned substantially perpendicular to the handle  620 , as shown, or in any other suitable orientation. An inner shaft  626  may extend through the outer shaft  622  with a knob  628  at one end. Implant  10 ,  12  connects to the shaft  622 , at the other end, at tip  624  of the implant holder  608 B,  608 C using typical connection mechanisms known to those of skill in the art. The knob  628  may be rotated, for example, to expand or articulate the implant  10 ,  12 . U.S. Pat. Nos. 8,709,086 and 8,491,659, which are incorporated by reference herein, describe expandable fusion devices and methods of installation. 
     When tracking the tool  608 , such as implant holder  608 B,  608 C, the tracking array  612  may contain a combination of fixed markers  804  and one or more moveable markers  806  which make up the array  612  or is otherwise attached to the implant holder  608 B,  608 C. The navigation array  612  may include at least one or more (e.g., at least two) fixed position markers  804 , which are positioned with a known location relative to the implant holder instrument  608 B,  608 C. These fixed markers  804  would not be able to move in any orientation relative to the instrument geometry and would be useful in defining where the instrument  608  is in space. In addition, at least one marker  806  is present which can be attached to the array  612  or the instrument itself which is capable of moving within a pre-determined boundary (e.g., sliding, rotating, etc.) relative to the fixed markers  804 . The system  100 ,  300 ,  600  (e.g., the software) correlates the position of the moveable marker  806  to a particular position, orientation, or other attribute of the implant  10  (such as height of an expandable interbody spacer shown in  FIGS.  17 A- 17 B  or angle of an articulating interbody spacer shown in  FIGS.  18 A- 18 B ). Thus, the system and/or the user can determine the height or angle of the implant  10 ,  12  based on the location of the moveable marker  806 . 
     In the embodiment shown in  FIGS.  17 A- 17 B , four fixed markers  804  are used to define the implant holder  608 B and a fifth moveable marker  806  is able to slide within a pre-determined path to provide feedback on the implant height (e.g., a contracted position or an expanded position).  FIG.  17 A  shows the expandable spacer  10  at its initial height, and  FIG.  17 B  shows the spacer  10  in the expanded state with the moveable marker  806  translated to a different position. In this case, the moveable marker  806  moves closer to the fixed markers  804  when the implant  10  is expanded, although it is contemplated that this movement may be reversed or otherwise different. The amount of linear translation of the marker  806  would correspond to the height of the implant  10 . Although only two positions are shown, it would be possible to have this as a continuous function whereby any given expansion height could be correlated to a specific position of the moveable marker  806 . 
     Turning now to  FIGS.  18 A- 18 B , four fixed markers  804  are used to define the implant holder  608 C and a fifth, moveable marker  806  is configured to slide within a pre-determined path to provide feedback on the implant articulation angle.  FIG.  18 A  shows the articulating spacer  12  at its initial linear state, and  FIG.  18 B  shows the spacer  12  in an articulated state at some offset angle with the moveable marker  806  translated to a different position. The amount of linear translation of the marker  806  would correspond to the articulation angle of the implant  12 . Although only two positions are shown, it would be possible to have this as a continuous function whereby any given articulation angle could be correlated to a specific position of the moveable marker  806 . 
     In these embodiments, the moveable marker  806  slides continuously to provide feedback about an attribute of the implant  10 ,  12  based on position. It is also contemplated that there may be discreet positions that the moveable marker  806  must be in which would also be able to provide further information about an implant attribute. In this case, each discreet configuration of all markers  804 ,  806  correlates to a specific geometry of the implant holder  608 B,  608 C and the implant  10 ,  12  in a specific orientation or at a specific height. In addition, any motion of the moveable marker  806  could be used for other variable attributes of any other type of navigated implant. 
     Although depicted and described with respect to linear movement of the moveable marker  806 , the moveable marker  806  should not be limited to just sliding as there may be applications where rotation of the marker  806  or other movements could be useful to provide information about the implant  10 ,  12 . Any relative change in position between the set of fixed markers  804  and the moveable marker  806  could be relevant information for the implant  10 ,  12  or other device. In addition, although expandable and articulating implants  10 ,  12  are exemplified, the instrument  608  could work with other medical devices and materials, such as spacers, cages, plates, fasteners, nails, screws, rods, pins, wire structures, sutures, anchor clips, staples, stents, bone grafts, biologics, or the like. 
     Referring to  FIGS.  19 ,  20 A, and  20 B , a method  1900  and a system  2000  for determining the extent of matter, i.e. tissue and/or bone, remaining within a targeted anatomical structure  2001  of a patient is provided. In the preferred embodiment, the targeted anatomical space  2001  is preferably the disk space in a patient&#39;s spine. The method  1900  includes acquiring  1910  an initial representation of a targeted anatomical structure  2001 . The acquiring step  1910  can be performed in variety of ways including, but not limited to, any one of the components or steps shown in the registration system  1400  and the procedure  1500  illustrated in  FIGS.  10  and  11   , the imaging devices  1304  shown in  FIGS.  12 A and  12 B , or any other suitable imaging system as understood by one of ordinary skill in the art. The term “representation” as used herein includes any type of imaging, mapping, dataset, or other form of information. 
     Data for the initial representation of the targeted anatomical structure is stored by a computer system  2002 , shown schematically in  FIGS.  20 A and  20 B . The computer system  2002  can include any of the features described herein with respect to the surgical robot system  300 , the computer  408 , or the computer subsystem  504 . The initial representation of the targeted anatomical structure  2001  includes a mapping of the patient&#39;s body. This mapping can include a three-dimensional rendering of the targeted anatomical structure, including indications, such as different colors, to represent bone matter, tissue matter, and vacant space. The initial representation of the targeted anatomical structure  2001  can be displayed by a display or screen of the computer system  2002 , such as the display  110  or the display  304  described herein. 
     After the initial representation of the targeted anatomical structure  2001  is acquired, the method  1900  includes removing  1920  matter from the targeted anatomical structure  2001 . The removal step  1920  is performed by any type of cutting, shaving, or scraping tools. The removal step  1920  is preferably performed by inserting a cutting tool in an incision near the targeted anatomical structure  2001  of the patient. In one embodiment, a surgeon performs the removal step  1920  while monitoring the position of the cutting tool via one of the tracking systems described herein. Alternatively, a robot system  100 ,  300 ,  600  can perform the removal step  1920 . In another embodiment, the removal step  1920  may include the step of simultaneously monitoring and recording the position of the removal tool. As the removal of the tissue if conducted, the tissue removal is recording based on the monitored path of the instrument. Once the removal step  1920  is completed, the initial representation of the targeted anatomical structure  2001  varies from the current condition of the targeted anatomical structure  2001 . 
     After or during the removal step  1920 , the method  1900  includes navigating  1930  an instrument  2008  within the targeted anatomical structure  2001 . To determine how much matter is remaining in the targeted anatomical structure  2001 , The instrument  2008  is preferably a probing tool. One of ordinary skill in the art would recognize from the present disclosure that other types of surgical instruments can be used, such as a cutting tool, scraping tool, or any other type of surgical instrument. In one preferred embodiment, the navigated instrument may also be the tissue removal instrument such as the cutting tool, scraping tool or any tissue removal instrument. A surgeon can manually navigate the instrument  2008  inside the targeted anatomical structure  2001 , or the instrument  2008  can be navigated with the assistance of an automated system, such as a robot system as described herein. The instrument  2008  in other embodiments may include a straight shaft for a curved shaft. In other embodiments, the instrument may include a ball tip at the distal end of the instrument. In yet other embodiments, the shaft or the distal end or both portions of the instrument may be designed to be flexible. 
     The instrument  2008  includes a tracking array  2012 . The tracking array  2012  can include any of the features described herein with respect to the tracking array  612 , or any other suitable tracking component understood by those of ordinary skill in the art. The method  1900  includes determining  1940  a relative position of the instrument  2008  within the targeted anatomical structure  2001  via the tracking array  2012 . A camera  2020  tracks a position of the instrument  2008  by determining a position of the tracking array  2012 . The camera  2020  can include similar features, functionality, and/or components as the cameras  200 ,  326  described herein. 
     The method  1900  includes recording  1950  the relative position of the instrument  2008  within the targeted anatomical structure  2001  to determine a final representation of the targeted anatomical structure  2001 . A recorded path (P) of the instrument  2008  is shown in  FIG.  20 B . The recorded path (P) tracks areas within the targeted anatomical structure  2001  where the tip  2024  of the instrument  2008  has traveled. In other embodiments, any portion of the instrument may be tracked. The computer system  2002  records and processes data regarding the recorded path (P) and provides an updated image, i.e. the final representation of the targeted anatomical structure  2001 . 
     Finally, the method  1900  includes determining  1960  the extent of matter removed from the targeted anatomical structure  2001  by comparing the initial representation of the targeted anatomical structure  2001  with the final representation of the targeted anatomical structure  2001 . Multiple calculations are made regarding the delta between the initial representation and the final representation. These determinations can be performed according to a variety of processes. For example, the initial representation and the final representation of the targeted anatomical structure  2001  can be overlaid with one another by the computer system  2002  to visually illustrate how much matter has been removed. The computer system  2002  can extract data sets from the initial representation and the final representation of the targeted anatomical structure  2001  to determine dimensions, such as a thickness, of matter within the targeted anatomical structure  2001 . These dimensions can be measured from the traced path of the probe, considering the diameter of the probe&#39;s tip and assuming that no volume of matter could share the space occupied by the probe tip. For example, if a probe with a spherical tip is moved in a straight line to assess whether tissue is clear, a volume represented as a cylinder of the same radius as the probe tip&#39;s radius, capped by hemispherical volumes at each end, also with the radius of the probe tip, would be the assumed space calculated to be clear of matter. 
     In one embodiment, the computer system  2002  is configured to provide an indicator to a user based on the relative position of the instrument  2008  within the targeted anatomical structure  2001  when the instrument  2008  approaches or encounters a boundary defined by the initial representation of the targeted anatomical structure  2001 . A user can manually set borders within the targeted anatomical structure  2001  based on the initial representation. The computer system  2002  can provide a tactual, visual or auditory indicator that the instrument is approaching a boundary of the targeted anatomical structure  2001 , a patient&#39;s spinal cord, or any other critical region. The indicator can include a percentage of matter remaining in the targeted anatomical structure  2001 . In one embodiment, the computer system  2002  provides a dynamic indicator of the extent of matter remaining in the targeted anatomical structure  2001  during simultaneous cutting and removal of matter from the targeted anatomical structure  2001 . 
     In another embodiment, the method  1900  includes attaching the instrument  2008  to a robotic component, such as robot arm  104 . The instrument  2008  can be attached to any portion of the robotic systems  100 ,  300 ,  600 . In one embodiment, the instrument  2008  is attached to an end-effector of a robot, such as end-effectors  112 ,  912 ,  1012 , etc. The robotic arm can guide the instrument  2008  within the targeted anatomical structure  2001  based on data from the initial representation of the targeted anatomical structure  2001  or based on user input. The end-effector of the robot can include a guide tube, similar to guide tubes  114 ,  606 , for receiving the instrument  2008 . In one embodiment, the robotic arm can include a secondary tracking array, such as markers  702  associated with the end-effector  602 , and the system  2000  can track movement of the robotic arm to further determine where the instrument  2008  has been with respect to the targeted anatomical structure  2001 . The robotic arm can use data derived from comparing the initial representation of the targeted anatomical structure  2001  to the final representation of the targeted anatomical structure  2001  to navigate the instrument  2008  within the targeted anatomical structure  2001 . 
     In one embodiment shown in  FIGS.  21 A- 21 D , a shaft  2122  of the instrument  2108  is recorded to determine where the instrument  2108  has traveled with respect to the targeted anatomical structure  2101 . One of ordinary skill in the art would recognize from the present disclosure that the tip, shaft, or any other portion of the instrument can be tracked and recorded.  FIG.  21    illustrates the advantage of tracking the shaft of the instrument over tracking only the tip. It can be seen from this figure that although the tip of the tool  2024  progresses around the perimeter of the disc, the central region of the disc (not numbered—shown as hatched) never encounters any portion of the instrument  2108 . The system can record the path traveled by the shaft, calculate the overlap of this path with the anatomical region of interest, and display the region of the disc that is clear of matter. 
     In one embodiment of the system  2200  shown in  FIGS.  22 A and  22 B , a tip  2224  of the instrument  2208  is enlarged relative to a shaft  2222  of the instrument  2208 . As shown in  FIGS.  22 A and  22 B , the tip  2224  has a spherical profile. This enlarged tip  2224  allows a user to more quickly map the targeted anatomical structure  2201  since the tip  2224  has a relatively larger area. One of ordinary skill in the art would recognize from the present disclosure that alternative shapes of the tip  2224  can be used. 
     Another embodiment of the instrument  2308  is illustrated in  FIGS.  23 A and  23 B . A terminal end  2309  of the instrument  2308  includes an articulable joint  2311 . The instrument  2308  includes a secondary tracking marker  2313  configured to move relative to a primary instrument tracking array  2313  based on actuation of the articulable joint  2311 . As shown in  FIG.  23 B , actuation of the articulable joint  2311  of the instrument  2308  pivots the tip  2324  of the instrument  2308  within the targeted anatomical structure. In one embodiment, actuation of the articulable joint  2311  is performed by squeezing a trigger  2329 . One of ordinary skill in the art would recognize from the present disclosure that alternative actuators can be provided. The path traveled by the distal portion of the tool when squeezing the actuator can be traced similarly to tracing the position of the entire tool and overlaid on the anatomy to record all locations occupied by any portion of the tool. Such an articulation would be able to reach around structures and test whether matter occupies regions that are not reachable by a straight instrument. The angular position of the tip  2324  of the instrument  2308  within the targeted anatomical structure is compared to the initial representation of the targeted anatomical structure to determine the extent of matter remaining in the targeted anatomical structure. In one embodiment, the tip  2324  of the instrument  2308  can pivot from 0° to 180°. One of ordinary skill in the art would recognize from the present disclosure that the tip  2324  can have multiple degrees of freedom and could be manipulated via the trigger  2329  or additional actuators to move in multiple directions. In another embodiment, the system enables the monitoring of the position of the pivoting mechanism to determine the current position of the pivoted tip and provides this information continuously to a control unit. In another embodiment, the system is configured to assess the geometric position of the instrument and continuously tracks and records data associated with the path the instrument is moved by the user and the movement of the hinged pivot portion, thereby recording the path the instrument in moved in the x, y and z axis. 
     Although several embodiments of the invention have been disclosed in the foregoing specification, it is understood that many modifications and other embodiments of the invention will come to mind to which the invention pertains, having the benefit of the teaching presented in the foregoing description and associated drawings. It is thus understood that the invention is not limited to the specific embodiments disclosed hereinabove, and that many modifications and other embodiments are intended to be included within the scope of the appended claims. 
     It is further envisioned that features from one embodiment may be combined or used with the features from a different embodiment described herein. Moreover, although specific terms are employed herein, as well as in the claims which follow, they are used only in a generic and descriptive sense, and not for the purposes of limiting the described invention, nor the claims which follow. 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.