Patent Publication Number: US-2023146311-A1

Title: Systems and methods for docking medical instruments

Description:
PRIORITY APPLICATION(S) 
     This application is a continuation of U.S. application Ser. No. 16/586,527, filed Sep. 27, 2019, which claims priority to U.S. Provisional Patent Application No. 62/738,483, filed Sep. 28, 2018, the entirety of which is incorporated herein by reference. Any and all applications for which a foreign or domestic priority claim is identified in the Application Data Sheet as filed with the present application are hereby incorporated by reference under 37 CFR 1.57. 
    
    
     TECHNICAL FIELD 
     The systems and methods disclosed herein are directed to docking medical instruments, and more particularly, to systems and methods for docking robotic medical instruments, which may include pre-tensioned pull wires, to corresponding instrument drive mechanisms. 
     BACKGROUND 
     Robotically-enabled medical systems can be used in a wide variety of medical procedures, including endoscopy, laparoscopy, and others. In some of these procedures, a robotically controlled medical instrument can be docked to an instrument positioning device such as a robotic arm. Once docked, the instrument positioning device can manipulate the medical instrument to perform the procedure. 
     SUMMARY 
     The systems, methods and devices of this disclosure each have several innovative aspects, no single one of which is solely responsible for the desirable attributes disclosed herein. 
     In a first aspect, a robotic medical system includes an instrument drive mechanism comprising a drive output configured to rotate and engage a corresponding drive input on a handle of a robotic medical instrument, wherein the robotic medical instrument comprises a pre-tensioned pull wire actuated by the drive input, a motor associated with the drive output and configured to rotate the drive output, and a torque sensor associated with the drive output and configured to measure torque imparted on the drive output; and at least one computer-readable memory in communication with at least one processor, the memory having stored thereon computer-executable instructions that cause the at least one processor to activate the motor associated with the drive output to rotate the drive output in response to a torque signal from the torque sensor associated with the drive output. 
     In some embodiments, the robotic medical system may include one or more of the following features in any combination: (a) wherein the instructions cause the processor to rotate the drive output to align the drive output with the corresponding drive output; (b) wherein the instructions cause the processor to activate the motor in response to the torque signal exceeding a threshold; (c) wherein the instructions cause the processor to deactivate the motor in response to the torque signal dropping below the threshold; (d) wherein the torque signal is indicative of a direction of a torque imparted on the drive output, and wherein the instructions cause the processor to activate the motor to cause rotation of the motor in a direction that is the same as the direction of the imparted torque; (e) wherein a speed of rotation of the motor is proportional to a measured torque determined based on the torque signal; (f) wherein a speed of rotation of the motor is constant; (g) wherein the drive output is a gear and the drive input is a socket; (h) wherein the drive output is a socket and the drive input is a gear; (i) wherein the instructions cause the processor to activate the motor associated with the drive output to rotate the drive output in response to the torque signal when the system is in a load instrument state; (j) the torque sensor comprises a strain gauge; (k) wherein the strain gauge is positioned between a housing of the instrument drive mechanism and the motor; and/or ( 1 ) wherein the torque sensor is bi-directional. 
     In another aspect, a computer readable medium can include instructions configured to cause at least one processor to receive a torque signal from a torque sensor associated with a drive output of an instrument drive mechanism; activate a motor associated with the drive output to rotate the drive output in response to the torque signal from the torque sensor exceeding a threshold; and deactivate the motor to cause the motor to stop rotating the drive output in response to the torque signal from the torque sensor dropping below the threshold. 
     In some embodiments, the computer readable medium may further include one or more of the following features in any combination: (a) wherein the instructions are configured to cause at least one processor to rotate the drive output to align the drive output with a drive input or a robotic medical instrument, wherein the robotic medical instrument comprises at least one pre-tensioned pull wire associated with the drive input; (b) wherein the torque signal is indicative of a direction of a torque imparted on the drive output, and wherein the instructions cause the at least one processor to activate the motor to cause rotation of the motor in a direction that is the same as the direction of the imparted torque; (c) wherein the instructions are configured to cause the motor to rotate the drive output at a speed of rotation that is proportional to a measured torque determined based on the torque signal; (d) wherein the instructions are configured to cause the motor to rotate the drive output at a speed of rotation that is constant; and/or (e) wherein the instructions cause the at least one processor to activate the motor associated with the drive output to rotate the drive output in response to the torque signal when the system is in a load instrument state. 
     In another aspect, a method for aligning a drive output of an instrument drive mechanism with a drive input of a robotic medical instrument includes receiving a torque signal from a torque sensor associated with the drive output of the instrument drive mechanism, the torque signal indicative of a torque imparted on the drive output; comparing the torque signal to a threshold; activating a motor of the instrument drive mechanism associated with the drive output to cause rotation of the drive output in response to the torque signal exceeding the threshold; and deactivating the motor to cause the motor to stop rotating the drive output in response to the torque signal from the torque sensor dropping below the threshold. 
     In some embodiments, the method can include one or more of the following features in any combination: (a) wherein the drive output is rotated to align the drive output with the drive input of the robotic medical instrument; (b) wherein the robotic medical instrument comprises at least one pre-tensioned pull wire associated with the drive input; (c), wherein the torque signal is indicative of a direction of a torque imparted on the drive output, and wherein the method comprises activating the motor to cause rotation of the motor in a direction that is the same as the direction of the imparted torque; (d) wherein a speed of rotation of the motor is proportional to a measured torque determined based on the torque signal; (e) wherein a speed of rotation of the motor is constant; (f) wherein the drive output is a gear and the drive input is a socket; (g) wherein the drive output is a socket and the drive input is a gear; and/or (h) wherein the activating and deactivating steps occur when in a load instrument state. 
     In another aspect, a robotic medical system includes an instrument drive mechanism comprising a drive output configured to rotate and engage a drive input on a handle of a robotic medical instrument, wherein the robotic medical instrument comprises a pull wire associated with the drive input, a motor associated with the drive output and configured to rotate the drive output, and a torque sensor associated with the drive output and configured to measure torque imparted on the drive output; and at least one computer-readable memory in communication with at least one processor, the memory having stored thereon computer-executable instructions that cause the at least one processor to: activate the motor associated with the drive output to rotate the drive output in a first direction until a first rotational position at which a torque signal measured by the torque sensor associated with the drive output exceeds a threshold, cause the motor to rotate the drive output in a second direction until a second rotational position at which the torque signal measured by the torque sensor exceeds the threshold, and determine a rotational distance between the first rotational position and the second rotational position. 
     In some embodiments, the system may include one or more of the following features in any combination: (a) wherein the rotational distance is indicative of a gap between the drive output and the drive input; (b) wherein the torque signal exceeding the threshold is indicative of the drive output contacting the drive input; (c) wherein the instructions cause the at least one processor to rotate the drive output to articulate an elongated shaft of the medical instrument, and wherein the rotation is based at least in part of the determined rotational distance; (d) wherein the drive output is a gear and the drive input is a socket; (e) wherein the drive output is a socket and the drive input is a gear; (f) wherein the instructions cause the processor to activate the motor associated with the drive output to rotate the drive output to align the drive output with the drive input in response to the torque signal when the system is in a homing state; (g) wherein the system enters the homing state after the medical instrument is docked to the instrument drive mechanism; (h) wherein the torque sensor comprises a strain gauge; (i) wherein the strain gauge is positioned between a housing of the instrument drive mechanism and the motor; and/or (j) wherein the torque sensor is bi-directional. 
     In another aspect, a computer readable medium includes instructions configured to cause at least one processor to: activate a motor associated with a drive output of an instrument drive mechanism to rotate the drive output in a first direction until a first rotational position at which a torque signal measured by a torque sensor associated with the drive output exceeds a threshold; cause the motor to rotate the drive output in a second direction until a second rotational position at which the torque signal measured by the torque sensor exceeds the threshold; and determine a rotational distance between the first rotational position and the second rotational position. 
     In some embodiments, the computer readable instructions may further include one or more of the following features in any combination: (a) wherein the rotational distance is indicative of a gap between the drive output and a drive input of a robotic medical instrument docked to the instrument drive mechanism; (b) wherein the torque signal exceeding the threshold is indicative of the drive output contacting the drive input; (c) wherein the instructions cause the at least one processor to rotate the drive output to articulate an elongated shaft of the medical instrument, and wherein the rotation is based at least in part of the determined rotational distance; (d) wherein the instructions cause the at least one processor to activate the motor associated with the drive output to rotate the drive output to align the drive output with the drive input in response to the torque signal when the system is in a homing state; and/or (e) wherein the system enters the homing state after the medical instrument is docked to the instrument drive mechanism. 
     In another aspect, a method includes: activating a motor associated with a drive output of an instrument drive mechanism to rotate the drive output in a first direction until a first rotational position at which a torque signal measured by a torque sensor associated with the drive output exceeds a threshold, causing the motor to rotate the drive output in a second direction until a second rotational position at which the torque signal measured by the torque sensor exceeds the threshold, and determining a rotational distance between the first rotational position and the second rotational position. 
     The method may include one or more of the following features in any combination: (a) wherein the rotational distance is indicative of a gap between the drive output and a drive input of a robotic medical instrument docked to the instrument drive mechanism; (b) wherein the torque signal exceeding the threshold is indicative of the drive output contacting the drive input; and/or (c) rotating the drive output to articulate an elongated shaft of the medical instrument, and wherein the rotation is based at least in part of the determined rotational distance. 
     In another aspect, a robotic medical system, includes an instrument drive mechanism comprising a drive output configured to rotate and engage a corresponding drive input on a handle of a robotic medical instrument, wherein the robotic medical instrument comprises a pre-tensioned pull wire actuated by the drive input, a motor associated with the drive output and configured to rotate the drive output, and a sensor configured to detect when the handle of the robotic medical instrument is within a threshold loading distance from the instrument drive mechanism. The system also includes at least one computer-readable memory in communication with at least one processor, the memory having stored thereon computer-executable instructions that cause the at least one processor to determine that the robotic medical instrument is within the threshold loading distance of the instrument drive mechanism based on an output of the sensor, and activate the motor associated with the drive output to cause the drive output to oscillate to facilitate alignment of the drive output and the corresponding drive input. 
     The system can include one or more of the following features in any combination: (a) wherein the instructions further configure the processor to place the motor in an admittance mode the robotic medical instrument is within the threshold loading distance of the instrument drive mechanism; (b) wherein the sensor is a proximity sensor; (c) wherein the sensor is a magnetic sensor; (d) wherein the sensor is an RFID reader; (e) wherein oscillation of the drive output comprises rotation of the drive output back and forth in clockwise and counter clockwise directions through a rotational range of at least 30 degrees, at least 20 degrees, at least 15 degrees, at least 10 degrees, at least 5 degrees, at least 3 degrees, or at least 1 degree; (f) wherein oscillation of the drive output comprises rotation of the drive output back and forth in clockwise and counter clockwise directions through a rotational range of no more than 30 degrees, no more than 20 degrees, no more than 15 degrees, no more than 10 degrees, no more than 5 degrees, no more than 3 degrees, or no more than 1 degree; (g) wherein the instructions further configure the processor to determine that the robotic medical instrument has docked to the instrument drive mechanism based on an output of the sensor; and stop causing oscillation of the drive output when the robotic medical instrument has docked; (h) wherein the threshold loading distance is at least 20 cm, at least 15 cm, at least 10 cm, at least 5 cm, or at least 1 cm; and/or (i) wherein the threshold loading distance is no more than 20 cm, no more than 15 cm, no more than 10 cm, no more than 5 cm, or no more than 1 cm. 
     In another aspect, a method includes determining that a robotic medical instrument is within a threshold loading distance of an instrument drive mechanism based on an output of a sensor on the instrument drive mechanism, and activating a motor associated with a drive output of the instrument drive mechanism to cause the drive output to oscillate to facilitate alignment of the drive output and the corresponding drive input when the robotic medical instrument is within the threshold loading distance of the instrument drive mechanism. 
     The method can include one or more of the following features in any combination: (a) placing the motor in an admittance mode the robotic medical instrument is within the threshold loading distance of the instrument drive mechanism; (b) wherein the sensor is a proximity sensor; (c) wherein the sensor is a magnetic sensor; (d) wherein the sensor is an RFID reader; (e) wherein oscillation of the drive output comprises rotation of the drive output back and forth in clockwise and counter clockwise directions through a rotational range of at least 30 degrees, at least 20 degrees, at least 15 degrees, at least 10 degrees, at least 5 degrees, at least 3 degrees, or at least 1 degree; (f) wherein oscillation of the drive output comprises rotation of the drive output back and forth in clockwise and counter clockwise directions through a rotational range of no more than 70 degrees, no more than 20 degrees, no more than 15 degrees, no more than 10 degrees, no more than 5 degrees, no more than 3 degrees, or no more than 1 degree; (g) determining that the robotic medical instrument has docked to the instrument drive mechanism based on an output of the sensor, and stopping oscillation of the drive output when the robotic medical instrument has docked; (h) wherein the threshold loading distance is at least 20 cm, at least 15 cm, at least 10 cm, at least 5 cm, or at least 1 cm; and/or (i) wherein the threshold loading distance is no more than 20 cm, no more than 15 cm, no more than 10 cm, no more than 5 cm, or no more than 1 cm. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The disclosed aspects will hereinafter be described in conjunction with the appended drawings, provided to illustrate and not to limit the disclosed aspects, wherein like designations denote like elements. 
         FIG.  1    illustrates an embodiment of a cart-based robotic system arranged for diagnostic and/or therapeutic bronchoscopy. 
         FIG.  2    depicts further aspects of the robotic system of  FIG.  1   . 
         FIG.  3    illustrates an embodiment of the robotic system of  FIG.  1    arranged for ureteroscopy. 
         FIG.  4    illustrates an embodiment of the robotic system of  FIG.  1    arranged for a vascular procedure. 
         FIG.  5    illustrates an embodiment of a table-based robotic system arranged for a bronchoscopic procedure. 
         FIG.  6    provides an alternative view of the robotic system of  FIG.  5   . 
         FIG.  7    illustrates an example system configured to stow robotic arm(s). 
         FIG.  8    illustrates an embodiment of a table-based robotic system configured for a ureteroscopic procedure. 
         FIG.  9    illustrates an embodiment of a table-based robotic system configured for a laparoscopic procedure. 
         FIG.  10    illustrates an embodiment of the table-based robotic system of  FIGS.  5 - 9    with pitch or tilt adjustment. 
         FIG.  11    provides a detailed illustration of the interface between the table and the column of the table-based robotic system of  FIGS.  5 - 10   . 
         FIG.  12    illustrates an alternative embodiment of a table-based robotic system. 
         FIG.  13    illustrates an end view of the table-based robotic system of  FIG.  12   . 
         FIG.  14    illustrates an end view of a table-based robotic system with robotic arms attached thereto. 
         FIG.  15    illustrates an exemplary instrument driver. 
         FIG.  16    illustrates an exemplary medical instrument with a paired instrument driver. 
         FIG.  17    illustrates an alternative design for an instrument driver and instrument where the axes of the drive units are parallel to the axis of the elongated shaft of the instrument. 
         FIG.  18    illustrates an instrument having an instrument-based insertion architecture. 
         FIG.  19    illustrates an exemplary controller. 
         FIG.  20    depicts a block diagram illustrating a localization system that estimates a location of one or more elements of the robotic systems of  FIGS.  1 - 10   , such as the location of the instrument of  FIGS.  16 - 18   , in accordance to an example embodiment. 
         FIGS.  21 A and  21 B  illustrate isometric and end views, respectively, of an embodiment of an instrument drive mechanism including a plurality of drive outputs configured to engage a corresponding plurality of drive inputs of a medical instrument. 
         FIGS.  22 A and  22 B  illustrate isometric and end views, respectively, of an embodiment of an instrument handle of a medical instrument including a plurality of drive inputs configured to engage a corresponding plurality of drive outputs of an instrument drive mechanism. 
         FIG.  23    illustrates a perspective view of an instrument drive output engaging an instrument drive output during docking of a medical instrument to an instrument drive mechanism. 
         FIG.  24    illustrates an embodiment of a drive output aligned with an embodiment of a drive input. 
         FIGS.  25 A- 25 D  illustrate alignment of a drive output with a drive input. 
         FIG.  25 A  illustrates the drive output and the drive input in a first misaligned position.  FIG.  25 B  illustrates the drive output and the drive input in a second misaligned position.  FIG.  25 C  illustrates the drive input and the drive output in an aligned position.  FIG.  25 D  illustrates an example graph of the output of a torque sensor associated with the drive output during the alignment process illustrated in  FIGS.  25 A- 25 C . 
         FIG.  26    is a block diagram illustrating an embodiment of a medical system configured to align drive outputs of an instrument drive mechanism with drive inputs of a medical instrument. 
         FIG.  27    is a flowchart illustrating an example method for aligning drive outputs of an instrument drive mechanism with drive inputs of a medical instrument. 
         FIGS.  28 A- 28 D  illustrate an example homing process using a drive output and drive input.  FIG.  28 A  illustrates the drive output engaged with the drive input.  FIG.  28 B  illustrates the drive output rotated in a first direction to a first rotational position.  FIG.  28 C  illustrates the drive output rotated in second direction to a second rotational position.  FIG.  28 D  illustrates a graph of the output of a torque sensor associated with the drive output during the homing process illustrated in  FIGS.  28 A- 28 C . 
         FIG.  29    is a flowchart illustrating an example homing method for a medical system. 
         FIG.  30    illustrates an example of a robotic medical system during docking of the medical instrument to an instrument drive mechanism. 
         FIG.  31    is a flowchart illustrating an example alignment method for a robotic medical system. 
     
    
    
     DETAILED DESCRIPTION 
     1. Overview. 
     Aspects of the present disclosure may be integrated into a robotically-enabled medical system capable of performing a variety of medical procedures, including both minimally invasive, such as laparoscopy, and non-invasive, such as endoscopy, procedures. Among endoscopic procedures, the system may be capable of performing bronchoscopy, ureteroscopy, gastroscopy, etc. 
     In addition to performing the breadth of procedures, the system may provide additional benefits, such as enhanced imaging and guidance to assist the physician. Additionally, the system may provide the physician with the ability to perform the procedure from an ergonomic position without the need for awkward arm motions and positions. Still further, the system may provide the physician with the ability to perform the procedure with improved ease of use such that one or more of the instruments of the system can be controlled by a single user. 
     Various embodiments will be described below in conjunction with the drawings for purposes of illustration. It should be appreciated that many other implementations of the disclosed concepts are possible, and various advantages can be achieved with the disclosed implementations. Headings are included herein for reference and to aid in locating various sections. These headings are not intended to limit the scope of the concepts described with respect thereto. Such concepts may have applicability throughout the entire specification. 
     A. Robotic System—Cart. 
     The robotically-enabled medical system may be configured in a variety of ways depending on the particular procedure.  FIG.  1    illustrates an embodiment of a cart-based robotically-enabled system  10  arranged for a diagnostic and/or therapeutic bronchoscopy. During a bronchoscopy, the system  10  may comprise a cart  11  having one or more robotic arms  12  to deliver a medical instrument, such as a steerable endoscope  13 , which may be a procedure-specific bronchoscope for bronchoscopy, to a natural orifice access point (i.e., the mouth of the patient positioned on a table in the present example) to deliver diagnostic and/or therapeutic tools. As shown, the cart  11  may be positioned proximate to the patient&#39;s upper torso in order to provide access to the access point. Similarly, the robotic arms  12  may be actuated to position the bronchoscope relative to the access point. The arrangement in  FIG.  1    may also be utilized when performing a gastro-intestinal (GI) procedure with a gastroscope, a specialized endoscope for GI procedures.  FIG.  2    depicts an example embodiment of the cart in greater detail. 
     With continued reference to  FIG.  1   , once the cart  11  is properly positioned, the robotic arms  12  may insert the steerable endoscope  13  into the patient robotically, manually, or a combination thereof. As shown, the steerable endoscope  13  may comprise at least two telescoping parts, such as an inner leader portion and an outer sheath portion, each portion coupled to a separate instrument driver from the set of instrument drivers  28 , each instrument driver coupled to the distal end of an individual robotic arm. This linear arrangement of the instrument drivers  28 , which facilitates coaxially aligning the leader portion with the sheath portion, creates a “virtual rail”  29  that may be repositioned in space by manipulating the one or more robotic arms  12  into different angles and/or positions. The virtual rails described herein are depicted in the Figures using dashed lines, and accordingly the dashed lines do not depict any physical structure of the system. Translation of the instrument drivers  28  along the virtual rail  29  telescopes the inner leader portion relative to the outer sheath portion or advances or retracts the endoscope  13  from the patient. The angle of the virtual rail  29  may be adjusted, translated, and pivoted based on clinical application or physician preference. For example, in bronchoscopy, the angle and position of the virtual rail  29  as shown represents a compromise between providing physician access to the endoscope  13  while minimizing friction that results from bending the endoscope  13  into the patient&#39;s mouth. 
     The endoscope  13  may be directed down the patient&#39;s trachea and lungs after insertion using precise commands from the robotic system until reaching the target destination or operative site. In order to enhance navigation through the patient&#39;s lung network and/or reach the desired target, the endoscope  13  may be manipulated to telescopically extend the inner leader portion from the outer sheath portion to obtain enhanced articulation and greater bend radius. The use of separate instrument drivers  28  also allows the leader portion and sheath portion to be driven independently of each other. 
     For example, the endoscope  13  may be directed to deliver a biopsy needle to a target, such as, for example, a lesion or nodule within the lungs of a patient. The needle may be deployed down a working channel that runs the length of the endoscope to obtain a tissue sample to be analyzed by a pathologist. Depending on the pathology results, additional tools may be deployed down the working channel of the endoscope for additional biopsies. After identifying a nodule to be malignant, the endoscope  13  may endoscopically deliver tools to resect the potentially cancerous tissue. In some instances, diagnostic and therapeutic treatments can be delivered in separate procedures. In those circumstances, the endoscope  13  may also be used to deliver a fiducial to “mark” the location of the target nodule as well. In other instances, diagnostic and therapeutic treatments may be delivered during the same procedure. 
     The system  10  may also include a movable tower  30 , which may be connected via support cables to the cart  11  to provide support for controls, electronics, fluidics, optics, sensors, and/or power to the cart  11 . Placing such functionality in the tower  30  allows for a smaller form factor cart  11  that may be more easily adjusted and/or re-positioned by an operating physician and his/her staff. Additionally, the division of functionality between the cart/table and the support tower  30  reduces operating room clutter and facilitates improving clinical workflow. While the cart  11  may be positioned close to the patient, the tower  30  may be stowed in a remote location to stay out of the way during a procedure. 
     In support of the robotic systems described above, the tower  30  may include component(s) of a computer-based control system that stores computer program instructions, for example, within a non-transitory computer-readable storage medium such as a persistent magnetic storage drive, solid state drive, etc. The execution of those instructions, whether the execution occurs in the tower  30  or the cart  11 , may control the entire system or sub-system(s) thereof. For example, when executed by a processor of the computer system, the instructions may cause the components of the robotics system to actuate the relevant carriages and arm mounts, actuate the robotics arms, and control the medical instruments. For example, in response to receiving the control signal, the motors in the joints of the robotics arms may position the arms into a certain posture. 
     The tower  30  may also include a pump, flow meter, valve control, and/or fluid access in order to provide controlled irrigation and aspiration capabilities to the system that may be deployed through the endoscope  13 . These components may also be controlled using the computer system of the tower  30 . In some embodiments, irrigation and aspiration capabilities may be delivered directly to the endoscope  13  through separate cable(s). 
     The tower  30  may include a voltage and surge protector designed to provide filtered and protected electrical power to the cart  11 , thereby avoiding placement of a power transformer and other auxiliary power components in the cart  11 , resulting in a smaller, more moveable cart  11 . 
     The tower  30  may also include support equipment for the sensors deployed throughout the robotic system  10 . For example, the tower  30  may include optoelectronics equipment for detecting, receiving, and processing data received from the optical sensors or cameras throughout the robotic system  10 . In combination with the control system, such optoelectronics equipment may be used to generate real-time images for display in any number of consoles deployed throughout the system, including in the tower  30 . Similarly, the tower  30  may also include an electronic subsystem for receiving and processing signals received from deployed electromagnetic (EM) sensors. The tower  30  may also be used to house and position an EM field generator for detection by EM sensors in or on the medical instrument. 
     The tower  30  may also include a console  31  in addition to other consoles available in the rest of the system, e.g., console mounted on top of the cart. The console  31  may include a user interface and a display screen, such as a touchscreen, for the physician operator. Consoles in the system  10  are generally designed to provide both robotic controls as well as preoperative and real-time information of the procedure, such as navigational and localization information of the endoscope  13 . When the console  31  is not the only console available to the physician, it may be used by a second operator, such as a nurse, to monitor the health or vitals of the patient and the operation of the system  10 , as well as to provide procedure-specific data, such as navigational and localization information. In other embodiments, the console  30  is housed in a body that is separate from the tower  30 . 
     The tower  30  may be coupled to the cart  11  and endoscope  13  through one or more cables or connections (not shown). In some embodiments, the support functionality from the tower  30  may be provided through a single cable to the cart  11 , simplifying and de-cluttering the operating room. In other embodiments, specific functionality may be coupled in separate cabling and connections. For example, while power may be provided through a single power cable to the cart  11 , the support for controls, optics, fluidics, and/or navigation may be provided through a separate cable. 
       FIG.  2    provides a detailed illustration of an embodiment of the cart  11  from the cart-based robotically-enabled system shown in  FIG.  1   . The cart  11  generally includes an elongated support structure  14  (often referred to as a “column”), a cart base  15 , and a console  16  at the top of the column  14 . The column  14  may include one or more carriages, such as a carriage  17  (alternatively “arm support”) for supporting the deployment of one or more robotic arms  12  (three shown in  FIG.  2   ). The carriage  17  may include individually configurable arm mounts that rotate along a perpendicular axis to adjust the base of the robotic arms  12  for better positioning relative to the patient. The carriage  17  also includes a carriage interface  19  that allows the carriage  17  to vertically translate along the column  14 . 
     The carriage interface  19  is connected to the column  14  through slots, such as slot  20 , that are positioned on opposite sides of the column  14  to guide the vertical translation of the carriage  17 . The slot  20  contains a vertical translation interface to position and hold the carriage  17  at various vertical heights relative to the cart base  15 . Vertical translation of the carriage  17  allows the cart  11  to adjust the reach of the robotic arms  12  to meet a variety of table heights, patient sizes, and physician preferences. Similarly, the individually configurable arm mounts on the carriage  17  allow the robotic arm base  21  of the robotic arms  12  to be angled in a variety of configurations. 
     In some embodiments, the slot  20  may be supplemented with slot covers that are flush and parallel to the slot surface to prevent dirt and fluid ingress into the internal chambers of the column  14  and the vertical translation interface as the carriage  17  vertically translates. The slot covers may be deployed through pairs of spring spools positioned near the vertical top and bottom of the slot  20 . The covers are coiled within the spools until deployed to extend and retract from their coiled state as the carriage  17  vertically translates up and down. The spring-loading of the spools provides force to retract the cover into a spool when the carriage  17  translates towards the spool, while also maintaining a tight seal when the carriage  17  translates away from the spool. The covers may be connected to the carriage  17  using, for example, brackets in the carriage interface  19  to ensure proper extension and retraction of the cover as the carriage  17  translates. 
     The column  14  may internally comprise mechanisms, such as gears and motors, that are designed to use a vertically aligned lead screw to translate the carriage  17  in a mechanized fashion in response to control signals generated in response to user inputs, e.g., inputs from the console  16 . 
     The robotic arms  12  may generally comprise robotic arm bases  21  and end effectors  22 , separated by a series of linkages  23  that are connected by a series of joints  24 , each joint comprising an independent actuator, each actuator comprising an independently controllable motor. Each independently controllable joint represents an independent degree of freedom available to the robotic arm  12 . Each of the robotic arms  12  may have seven joints, and thus provide seven degrees of freedom. A multitude of joints result in a multitude of degrees of freedom, allowing for “redundant” degrees of freedom. Having redundant degrees of freedom allows the robotic arms  12  to position their respective end effectors  22  at a specific position, orientation, and trajectory in space using different linkage positions and joint angles. This allows for the system to position and direct a medical instrument from a desired point in space while allowing the physician to move the arm joints into a clinically advantageous position away from the patient to create greater access, while avoiding arm collisions. 
     The cart base  15  balances the weight of the column  14 , carriage  17 , and robotic arms  12  over the floor. Accordingly, the cart base  15  houses heavier components, such as electronics, motors, power supply, as well as components that either enable movement and/or immobilize the cart  11 . For example, the cart base  15  includes rollable wheel-shaped casters  25  that allow for the cart  11  to easily move around the room prior to a procedure. After reaching the appropriate position, the casters  25  may be immobilized using wheel locks to hold the cart  11  in place during the procedure. 
     Positioned at the vertical end of the column  14 , the console  16  allows for both a user interface for receiving user input and a display screen (or a dual-purpose device such as, for example, a touchscreen  26 ) to provide the physician user with both preoperative and intraoperative data. Potential preoperative data on the touchscreen  26  may include preoperative plans, navigation and mapping data derived from preoperative computerized tomography (CT) scans, and/or notes from preoperative patient interviews. Intraoperative data on display may include optical information provided from the tool, sensor and coordinate information from sensors, as well as vital patient statistics, such as respiration, heart rate, and/or pulse. The console  16  may be positioned and tilted to allow a physician to access the console  16  from the side of the column  14  opposite the carriage  17 . From this position, the physician may view the console  16 , robotic arms  12 , and patient while operating the console  16  from behind the cart  11 . As shown, the console  16  also includes a handle  27  to assist with maneuvering and stabilizing the cart  11 . 
       FIG.  3    illustrates an embodiment of a robotically-enabled system  10  arranged for ureteroscopy. In a ureteroscopic procedure, the cart  11  may be positioned to deliver a ureteroscope  32 , a procedure-specific endoscope designed to traverse a patient&#39;s urethra and ureter, to the lower abdominal area of the patient. In a ureteroscopy, it may be desirable for the ureteroscope  32  to be directly aligned with the patient&#39;s urethra to reduce friction and forces on the sensitive anatomy in the area. As shown, the cart  11  may be aligned at the foot of the table to allow the robotic arms  12  to position the ureteroscope  32  for direct linear access to the patient&#39;s urethra. From the foot of the table, the robotic arms  12  may insert the ureteroscope  32  along the virtual rail  33  directly into the patient&#39;s lower abdomen through the urethra. 
     After insertion into the urethra, using similar control techniques as in bronchoscopy, the ureteroscope  32  may be navigated into the bladder, ureters, and/or kidneys for diagnostic and/or therapeutic applications. For example, the ureteroscope  32  may be directed into the ureter and kidneys to break up kidney stone build up using a laser or ultrasonic lithotripsy device deployed down the working channel of the ureteroscope  32 . After lithotripsy is complete, the resulting stone fragments may be removed using baskets deployed down the ureteroscope  32 . 
       FIG.  4    illustrates an embodiment of a robotically-enabled system  10  similarly arranged for a vascular procedure. In a vascular procedure, the system  10  may be configured such that the cart  11  may deliver a medical instrument  34 , such as a steerable catheter, to an access point in the femoral artery in the patient&#39;s leg. The femoral artery presents both a larger diameter for navigation as well as a relatively less circuitous and tortuous path to the patient&#39;s heart, which simplifies navigation. As in a ureteroscopic procedure, the cart  11  may be positioned towards the patient&#39;s legs and lower abdomen to allow the robotic arms  12  to provide a virtual rail  35  with direct linear access to the femoral artery access point in the patient&#39;s thigh/hip region. After insertion into the artery, the medical instrument  34  may be directed and inserted by translating the instrument drivers  28 . Alternatively, the cart may be positioned around the patient&#39;s upper abdomen in order to reach alternative vascular access points, such as, for example, the carotid and brachial arteries near the shoulder and wrist. 
     B. Robotic System—Table. 
     Embodiments of the robotically-enabled medical system may also incorporate the patient&#39;s table. Incorporation of the table reduces the amount of capital equipment within the operating room by removing the cart, which allows greater access to the patient.  FIG.  5    illustrates an embodiment of such a robotically-enabled system arranged for a bronchoscopic procedure. System  36  includes a support structure or column  37  for supporting platform  38  (shown as a “table” or “bed”) over the floor. Much like in the cart-based systems, the end effectors of the robotic arms  39  of the system  36  comprise instrument drivers  42  that are designed to manipulate an elongated medical instrument, such as a bronchoscope  40  in  FIG.  5   , through or along a virtual rail  41  formed from the linear alignment of the instrument drivers  42 . In practice, a C-arm for providing fluoroscopic imaging may be positioned over the patient&#39;s upper abdominal area by placing the emitter and detector around the table  38 . 
       FIG.  6    provides an alternative view of the system  36  without the patient and medical instrument for discussion purposes. As shown, the column  37  may include one or more carriages  43  shown as ring-shaped in the system  36 , from which the one or more robotic arms  39  may be based. The carriages  43  may translate along a vertical column interface  44  that runs the length of the column  37  to provide different vantage points from which the robotic arms  39  may be positioned to reach the patient. The carriage(s)  43  may rotate around the column  37  using a mechanical motor positioned within the column  37  to allow the robotic arms  39  to have access to multiples sides of the table  38 , such as, for example, both sides of the patient. In embodiments with multiple carriages, the carriages may be individually positioned on the column and may translate and/or rotate independently of the other carriages. While the carriages  43  need not surround the column  37  or even be circular, the ring-shape as shown facilitates rotation of the carriages  43  around the column  37  while maintaining structural balance. Rotation and translation of the carriages  43  allows the system  36  to align the medical instruments, such as endoscopes and laparoscopes, into different access points on the patient. In other embodiments (not shown), the system  36  can include a patient table or bed with adjustable arm supports in the form of bars or rails extending alongside it. One or more robotic arms  39  (e.g., via a shoulder with an elbow joint) can be attached to the adjustable arm supports, which can be vertically adjusted. By providing vertical adjustment, the robotic arms  39  are advantageously capable of being stowed compactly beneath the patient table or bed, and subsequently raised during a procedure. 
     The robotic arms  39  may be mounted on the carriages  43  through a set of arm mounts  45  comprising a series of joints that may individually rotate and/or telescopically extend to provide additional configurability to the robotic arms  39 . Additionally, the arm mounts  45  may be positioned on the carriages  43  such that, when the carriages  43  are appropriately rotated, the arm mounts  45  may be positioned on either the same side of the table  38  (as shown in  FIG.  6   ), on opposite sides of the table  38  (as shown in  FIG.  9   ), or on adjacent sides of the table  38  (not shown). 
     The column  37  structurally provides support for the table  38 , and a path for vertical translation of the carriages  43 . Internally, the column  37  may be equipped with lead screws for guiding vertical translation of the carriages, and motors to mechanize the translation of the carriages  43  based the lead screws. The column  37  may also convey power and control signals to the carriages  43  and the robotic arms  39  mounted thereon. 
     The table base  46  serves a similar function as the cart base  15  in the cart  11  shown in  FIG.  2   , housing heavier components to balance the table/bed  38 , the column  37 , the carriages  43 , and the robotic arms  39 . The table base  46  may also incorporate rigid casters to provide stability during procedures. Deployed from the bottom of the table base  46 , the casters may extend in opposite directions on both sides of the base  46  and retract when the system  36  needs to be moved. 
     With continued reference to  FIG.  6   , the system  36  may also include a tower (not shown) that divides the functionality of the system  36  between the table and the tower to reduce the form factor and bulk of the table. As in earlier disclosed embodiments, the tower may provide a variety of support functionalities to the table, such as processing, computing, and control capabilities, power, fluidics, and/or optical and sensor processing. The tower may also be movable to be positioned away from the patient to improve physician access and de-clutter the operating room. Additionally, placing components in the tower allows for more storage space in the table base  46  for potential stowage of the robotic arms  39 . The tower may also include a master controller or console that provides both a user interface for user input, such as keyboard and/or pendant, as well as a display screen (or touchscreen) for preoperative and intraoperative information, such as real-time imaging, navigation, and tracking information. In some embodiments, the tower may also contain holders for gas tanks to be used for insufflation. 
     In some embodiments, a table base may stow and store the robotic arms when not in use.  FIG.  7    illustrates a system  47  that stows robotic arms in an embodiment of the table-based system. In the system  47 , carriages  48  may be vertically translated into base  49  to stow robotic arms  50 , arm mounts  51 , and the carriages  48  within the base  49 . Base covers  52  may be translated and retracted open to deploy the carriages  48 , arm mounts  51 , and robotic arms  50  around column  53 , and closed to stow to protect them when not in use. The base covers  52  may be sealed with a membrane  54  along the edges of its opening to prevent dirt and fluid ingress when closed. 
       FIG.  8    illustrates an embodiment of a robotically-enabled table-based system configured for a ureteroscopic procedure. In a ureteroscopy, the table  38  may include a swivel portion  55  for positioning a patient off-angle from the column  37  and table base  46 . The swivel portion  55  may rotate or pivot around a pivot point (e.g., located below the patient&#39;s head) in order to position the bottom portion of the swivel portion  55  away from the column  37 . For example, the pivoting of the swivel portion  55  allows a C-arm (not shown) to be positioned over the patient&#39;s lower abdomen without competing for space with the column (not shown) below table  38 . By rotating the carriage  35  (not shown) around the column  37 , the robotic arms  39  may directly insert a ureteroscope  56  along a virtual rail  57  into the patient&#39;s groin area to reach the urethra. In a ureteroscopy, stirrups  58  may also be fixed to the swivel portion  55  of the table  38  to support the position of the patient&#39;s legs during the procedure and allow clear access to the patient&#39;s groin area. 
     In a laparoscopic procedure, through small incision(s) in the patient&#39;s abdominal wall, minimally invasive instruments may be inserted into the patient&#39;s anatomy. In some embodiments, the minimally invasive instruments comprise an elongated rigid member, such as a shaft, which is used to access anatomy within the patient. After inflation of the patient&#39;s abdominal cavity, the instruments may be directed to perform surgical or medical tasks, such as grasping, cutting, ablating, suturing, etc. In some embodiments, the instruments can comprise a scope, such as a laparoscope.  FIG.  9    illustrates an embodiment of a robotically-enabled table-based system configured for a laparoscopic procedure. As shown in  FIG.  9   , the carriages  43  of the system  36  may be rotated and vertically adjusted to position pairs of the robotic arms  39  on opposite sides of the table  38 , such that instrument  59  may be positioned using the arm mounts  45  to be passed through minimal incisions on both sides of the patient to reach his/her abdominal cavity. 
     To accommodate laparoscopic procedures, the robotically-enabled table system may also tilt the platform to a desired angle.  FIG.  10    illustrates an embodiment of the robotically-enabled medical system with pitch or tilt adjustment. As shown in  FIG.  10   , the system  36  may accommodate tilt of the table  38  to position one portion of the table at a greater distance from the floor than the other. Additionally, the arm mounts  45  may rotate to match the tilt such that the robotic arms  39  maintain the same planar relationship with the table  38 . To accommodate steeper angles, the column  37  may also include telescoping portions  60  that allow vertical extension of the column  37  to keep the table  38  from touching the floor or colliding with the table base  46 . 
       FIG.  11    provides a detailed illustration of the interface between the table  38  and the column  37 . Pitch rotation mechanism  61  may be configured to alter the pitch angle of the table  38  relative to the column  37  in multiple degrees of freedom. The pitch rotation mechanism  61  may be enabled by the positioning of orthogonal axes  1 ,  2  at the column-table interface, each axis actuated by a separate motor  3 ,  4  responsive to an electrical pitch angle command. Rotation along one screw  5  would enable tilt adjustments in one axis  1 , while rotation along the other screw  6  would enable tilt adjustments along the other axis  2 . In some embodiments, a ball joint can be used to alter the pitch angle of the table  38  relative to the column  37  in multiple degrees of freedom. 
     For example, pitch adjustments are particularly useful when trying to position the table in a Trendelenburg position, i.e., position the patient&#39;s lower abdomen at a higher position from the floor than the patient&#39;s upper abdomen, for lower abdominal surgery. The Trendelenburg position causes the patient&#39;s internal organs to slide towards his/her upper abdomen through the force of gravity, clearing out the abdominal cavity for minimally invasive tools to enter and perform lower abdominal surgical or medical procedures, such as laparoscopic prostatectomy. 
       FIGS.  12  and  13    illustrate isometric and end views of an alternative embodiment of a table-based surgical robotics system  100 . The surgical robotics system  100  includes one or more adjustable arm supports  105  that can be configured to support one or more robotic arms (see, for example,  FIG.  14   ) relative to a table  101 . In the illustrated embodiment, a single adjustable arm support  105  is shown, though an additional arm support can be provided on an opposite side of the table  101 . The adjustable arm support  105  can be configured so that it can move relative to the table  101  to adjust and/or vary the position of the adjustable arm support  105  and/or any robotic arms mounted thereto relative to the table  101 . For example, the adjustable arm support  105  may be adjusted one or more degrees of freedom relative to the table  101 . The adjustable arm support  105  provides high versatility to the system  100 , including the ability to easily stow the one or more adjustable arm supports  105  and any robotics arms attached thereto beneath the table  101 . The adjustable arm support  105  can be elevated from the stowed position to a position below an upper surface of the table  101 . In other embodiments, the adjustable arm support  105  can be elevated from the stowed position to a position above an upper surface of the table  101 . 
     The adjustable arm support  105  can provide several degrees of freedom, including lift, lateral translation, tilt, etc. In the illustrated embodiment of  FIGS.  12  and  13   , the arm support  105  is configured with four degrees of freedom, which are illustrated with arrows in  FIG.  12   . A first degree of freedom allows for adjustment of the adjustable arm support  105  in the z-direction (“Z-lift”). For example, the adjustable arm support  105  can include a carriage  109  configured to move up or down along or relative to a column  102  supporting the table  101 . A second degree of freedom can allow the adjustable arm support  105  to tilt. For example, the adjustable arm support  105  can include a rotary joint, which can allow the adjustable arm support  105  to be aligned with the bed in a Trendelenburg position. A third degree of freedom can allow the adjustable arm support  105  to “pivot up,” which can be used to adjust a distance between a side of the table  101  and the adjustable arm support  105 . A fourth degree of freedom can permit translation of the adjustable arm support  105  along a longitudinal length of the table. 
     The surgical robotics system  100  in  FIGS.  12  and  13    can comprise a table supported by a column  102  that is mounted to a base  103 . The base  103  and the column  102  support the table  101  relative to a support surface. A floor axis  131  and a support axis  133  are shown in  FIG.  13   . 
     The adjustable arm support  105  can be mounted to the column  102 . In other embodiments, the arm support  105  can be mounted to the table  101  or base  103 . The adjustable arm support  105  can include a carriage  109 , a bar or rail connector  111  and a bar or rail  107 . In some embodiments, one or more robotic arms mounted to the rail  107  can translate and move relative to one another. 
     The carriage  109  can be attached to the column  102  by a first joint  113 , which allows the carriage  109  to move relative to the column  102  (e.g., such as up and down a first or vertical axis  123 ). The first joint  113  can provide the first degree of freedom (“Z-lift”) to the adjustable arm support  105 . The adjustable arm support  105  can include a second joint  115 , which provides the second degree of freedom (tilt) for the adjustable arm support  105 . The adjustable arm support  105  can include a third joint  117 , which can provide the third degree of freedom (“pivot up”) for the adjustable arm support  105 . An additional joint  119  (shown in  FIG.  13   ) can be provided that mechanically constrains the third joint  117  to maintain an orientation of the rail  107  as the rail connector  111  is rotated about a third axis  127 . The adjustable arm support  105  can include a fourth joint  121 , which can provide a fourth degree of freedom (translation) for the adjustable arm support  105  along a fourth axis  129 . 
       FIG.  14    illustrates an end view of the surgical robotics system  140 A with two adjustable arm supports  105 A,  105 B mounted on opposite sides of a table  101 . A first robotic arm  142 A is attached to the bar or rail  107 A of the first adjustable arm support  105 B. The first robotic arm  142 A includes a base  144 A attached to the rail  107 A. The distal end of the first robotic arm  142 A includes an instrument drive mechanism  146 A that can attach to one or more robotic medical instruments or tools. Similarly, the second robotic arm  142 B includes a base  144 B attached to the rail  107 B. The distal end of the second robotic arm  142 B includes an instrument drive mechanism  146 B. The instrument drive mechanism  146 B can be configured to attach to one or more robotic medical instruments or tools. 
     In some embodiments, one or more of the robotic arms  142 A,  142 B comprises an arm with seven or more degrees of freedom. In some embodiments, one or more of the robotic arms  142 A,  142 B can include eight degrees of freedom, including an insertion axis (1-degree of freedom including insertion), a wrist (3-degrees of freedom including wrist pitch, yaw and roll), an elbow (1-degree of freedom including elbow pitch), a shoulder (2-degrees of freedom including shoulder pitch and yaw), and base  144 A,  144 B (1-degree of freedom including translation). In some embodiments, the insertion degree of freedom can be provided by the robotic arm  142 A,  142 B, while in other embodiments, the instrument itself provides insertion via an instrument-based insertion architecture. 
     C. Instrument Driver &amp; Interface. 
     The end effectors of the system&#39;s robotic arms may comprise (i) an instrument driver (alternatively referred to as “instrument drive mechanism” or “instrument device manipulator”) that incorporates electro-mechanical means for actuating the medical instrument and (ii) a removable or detachable medical instrument, which may be devoid of any electro-mechanical components, such as motors. This dichotomy may be driven by the need to sterilize medical instruments used in medical procedures, and the inability to adequately sterilize expensive capital equipment due to their intricate mechanical assemblies and sensitive electronics. Accordingly, the medical instruments may be designed to be detached, removed, and interchanged from the instrument driver (and thus the system) for individual sterilization or disposal by the physician or the physician&#39;s staff. In contrast, the instrument drivers need not be changed or sterilized, and may be draped for protection. 
       FIG.  15    illustrates an example instrument driver. Positioned at the distal end of a robotic arm, instrument driver  62  comprises one or more drive units  63  arranged with parallel axes to provide controlled torque to a medical instrument via drive shafts  64 . Each drive unit  63  comprises an individual drive shaft  64  for interacting with the instrument, a gear head  65  for converting the motor shaft rotation to a desired torque, a motor  66  for generating the drive torque, an encoder  67  to measure the speed of the motor shaft and provide feedback to the control circuitry, and control circuitry  68  for receiving control signals and actuating the drive unit. Each drive unit  63  being independently controlled and motorized, the instrument driver  62  may provide multiple (e.g., four as shown in  FIG.  15   ) independent drive outputs to the medical instrument. In operation, the control circuitry  68  would receive a control signal, transmit a motor signal to the motor  66 , compare the resulting motor speed as measured by the encoder  67  with the desired speed, and modulate the motor signal to generate the desired torque. 
     For procedures that require a sterile environment, the robotic system may incorporate a drive interface, such as a sterile adapter connected to a sterile drape, that sits between the instrument driver and the medical instrument. The chief purpose of the sterile adapter is to transfer angular motion from the drive shafts of the instrument driver to the drive inputs of the instrument while maintaining physical separation, and thus sterility, between the drive shafts and drive inputs. Accordingly, an example sterile adapter may comprise a series of rotational inputs and outputs intended to be mated with the drive shafts of the instrument driver and drive inputs on the instrument. Connected to the sterile adapter, the sterile drape, comprised of a thin, flexible material such as transparent or translucent plastic, is designed to cover the capital equipment, such as the instrument driver, robotic arm, and cart (in a cart-based system) or table (in a table-based system). Use of the drape would allow the capital equipment to be positioned proximate to the patient while still being located in an area not requiring sterilization (i.e., non-sterile field). On the other side of the sterile drape, the medical instrument may interface with the patient in an area requiring sterilization (i.e., sterile field). 
     D. Medical Instrument. 
       FIG.  16    illustrates an example medical instrument with a paired instrument driver. Like other instruments designed for use with a robotic system, medical instrument  70  comprises an elongated shaft  71  (or elongate body) and an instrument base  72 . The instrument base  72 , also referred to as an “instrument handle” due to its intended design for manual interaction by the physician, may generally comprise rotatable drive inputs  73 , e.g., receptacles, pulleys or spools, that are designed to be mated with drive outputs  74  that extend through a drive interface on instrument driver  75  at the distal end of robotic arm  76 . When physically connected, latched, and/or coupled, the mated drive inputs  73  of the instrument base  72  may share axes of rotation with the drive outputs  74  in the instrument driver  75  to allow the transfer of torque from the drive outputs  74  to the drive inputs  73 . In some embodiments, the drive outputs  74  may comprise splines that are designed to mate with receptacles on the drive inputs  73 . 
     The elongated shaft  71  is designed to be delivered through either an anatomical opening or lumen, e.g., as in endoscopy, or a minimally invasive incision, e.g., as in laparoscopy. The elongated shaft  71  may be either flexible (e.g., having properties similar to an endoscope) or rigid (e.g., having properties similar to a laparoscope) or contain a customized combination of both flexible and rigid portions. When designed for laparoscopy, the distal end of a rigid elongated shaft may be connected to an end effector extending from a jointed wrist formed from a clevis with at least one degree of freedom and a surgical tool or medical instrument, such as, for example, a grasper or scissors, that may be actuated based on force from the tendons as the drive inputs rotate in response to torque received from the drive outputs  74  of the instrument driver  75 . When designed for endoscopy, the distal end of a flexible elongated shaft may include a steerable or controllable bending section that may be articulated and bent based on torque received from the drive outputs  74  of the instrument driver  75 . 
     Torque from the instrument driver  75  is transmitted down the elongated shaft  71  using tendons along the elongated shaft  71 . These individual tendons, such as pull wires, may be individually anchored to individual drive inputs  73  within the instrument handle  72 . From the handle  72 , the tendons are directed down one or more pull lumens along the elongated shaft  71  and anchored at the distal portion of the elongated shaft  71 , or in the wrist at the distal portion of the elongated shaft. During a surgical procedure, such as a laparoscopic, endoscopic or hybrid procedure, these tendons may be coupled to a distally mounted end effector, such as a wrist, grasper, or scissor. Under such an arrangement, torque exerted on drive inputs  73  would transfer tension to the tendon, thereby causing the end effector to actuate in some way. In some embodiments, during a surgical procedure, the tendon may cause a joint to rotate about an axis, thereby causing the end effector to move in one direction or another. Alternatively, the tendon may be connected to one or more jaws of a grasper at the distal end of the elongated shaft  71 , where tension from the tendon causes the grasper to close. 
     In endoscopy, the tendons may be coupled to a bending or articulating section positioned along the elongated shaft  71  (e.g., at the distal end) via adhesive, control ring, or other mechanical fixation. When fixedly attached to the distal end of a bending section, torque exerted on the drive inputs  73  would be transmitted down the tendons, causing the softer, bending section (sometimes referred to as the articulable section or region) to bend or articulate. Along the non-bending sections, it may be advantageous to spiral or helix the individual pull lumens that direct the individual tendons along (or inside) the walls of the endoscope shaft to balance the radial forces that result from tension in the pull wires. The angle of the spiraling and/or spacing therebetween may be altered or engineered for specific purposes, wherein tighter spiraling exhibits lesser shaft compression under load forces, while lower amounts of spiraling results in greater shaft compression under load forces, but limits bending. On the other end of the spectrum, the pull lumens may be directed parallel to the longitudinal axis of the elongated shaft  71  to allow for controlled articulation in the desired bending or articulable sections. 
     In endoscopy, the elongated shaft  71  houses a number of components to assist with the robotic procedure. The shaft  71  may comprise a working channel for deploying surgical tools (or medical instruments), irrigation, and/or aspiration to the operative region at the distal end of the shaft  71 . The shaft  71  may also accommodate wires and/or optical fibers to transfer signals to/from an optical assembly at the distal tip, which may include an optical camera. The shaft  71  may also accommodate optical fibers to carry light from proximally-located light sources, such as light emitting diodes, to the distal end of the shaft  71 . 
     At the distal end of the instrument  70 , the distal tip may also comprise the opening of a working channel for delivering tools for diagnostic and/or therapy, irrigation, and aspiration to an operative site. The distal tip may also include a port for a camera, such as a fiberscope or a digital camera, to capture images of an internal anatomical space. Relatedly, the distal tip may also include ports for light sources for illuminating the anatomical space when using the camera. 
     In the example of  FIG.  16   , the drive shaft axes, and thus the drive input axes, are orthogonal to the axis of the elongated shaft  71 . This arrangement, however, complicates roll capabilities for the elongated shaft  71 . Rolling the elongated shaft  71  along its axis while keeping the drive inputs  73  static results in undesirable tangling of the tendons as they extend off the drive inputs  73  and enter pull lumens within the elongated shaft  71 . The resulting entanglement of such tendons may disrupt any control algorithms intended to predict movement of the flexible elongated shaft  71  during an endoscopic procedure. 
       FIG.  17    illustrates an alternative design for an instrument driver and instrument where the axes of the drive units are parallel to the axis of the elongated shaft of the instrument. As shown, a circular instrument driver  80  comprises four drive units with their drive outputs  81  aligned in parallel at the end of a robotic arm  82 . The drive units, and their respective drive outputs  81 , are housed in a rotational assembly  83  of the instrument driver  80  that is driven by one of the drive units within the assembly  83 . In response to torque provided by the rotational drive unit, the rotational assembly  83  rotates along a circular bearing that connects the rotational assembly  83  to the non-rotational portion  84  of the instrument driver  80 . Power and controls signals may be communicated from the non-rotational portion  84  of the instrument driver  80  to the rotational assembly  83  through electrical contacts that may be maintained through rotation by a brushed slip ring connection (not shown). In other embodiments, the rotational assembly  83  may be responsive to a separate drive unit that is integrated into the non-rotatable portion  84 , and thus not in parallel to the other drive units. The rotational mechanism  83  allows the instrument driver  80  to rotate the drive units, and their respective drive outputs  81 , as a single unit around an instrument driver axis  85 . 
     Like earlier disclosed embodiments, an instrument  86  may comprise an elongated shaft portion  88  and an instrument base  87  (shown with a transparent external skin for discussion purposes) comprising a plurality of drive inputs  89  (such as receptacles, pulleys, and spools) that are configured to receive the drive outputs  81  in the instrument driver  80 . Unlike prior disclosed embodiments, the instrument shaft  88  extends from the center of the instrument base  87  with an axis substantially parallel to the axes of the drive inputs  89 , rather than orthogonal as in the design of  FIG.  16   . 
     When coupled to the rotational assembly  83  of the instrument driver  80 , the medical instrument  86 , comprising instrument base  87  and instrument shaft  88 , rotates in combination with the rotational assembly  83  about the instrument driver axis  85 . Since the instrument shaft  88  is positioned at the center of instrument base  87 , the instrument shaft  88  is coaxial with instrument driver axis  85  when attached. Thus, rotation of the rotational assembly  83  causes the instrument shaft  88  to rotate about its own longitudinal axis. Moreover, as the instrument base  87  rotates with the instrument shaft  88 , any tendons connected to the drive inputs  89  in the instrument base  87  are not tangled during rotation. Accordingly, the parallelism of the axes of the drive outputs  81 , drive inputs  89 , and instrument shaft  88  allows for the shaft rotation without tangling any control tendons. 
       FIG.  18    illustrates an instrument having an instrument based insertion architecture in accordance with some embodiments. The instrument  150  can be coupled to any of the instrument drivers discussed above. The instrument  150  comprises an elongated shaft  152 , an end effector  162  connected to the shaft  152 , and a handle  170  coupled to the shaft  152 . The elongated shaft  152  comprises a tubular member having a proximal portion  154  and a distal portion  156 . The elongated shaft  152  comprises one or more channels or grooves  158  along its outer surface. The grooves  158  are configured to receive one or more wires or cables  180  therethrough. One or more cables  180  thus run along an outer surface of the elongated shaft  152 . In other embodiments, cables  180  can also run through the elongated shaft  152 . Manipulation of the one or more cables  180  (e.g., via an instrument driver) results in actuation of the end effector  162 . 
     The instrument handle  170 , which may also be referred to as an instrument base, may generally comprise an attachment interface  172  having one or more mechanical inputs  174 , e.g., receptacles, pulleys or spools, that are designed to be reciprocally mated with one or more torque couplers on an attachment surface of an instrument driver. In some embodiments, the instrument  150  comprises a series of pulleys or cables that enable the elongated shaft  152  to translate relative to the handle  170 . In other words, the instrument  150  itself comprises an instrument-based insertion architecture that accommodates insertion of the instrument, thereby minimizing the reliance on a robot arm to provide insertion of the instrument  150 . In other embodiments, a robotic arm can be largely responsible for instrument insertion. 
     E. Controller. 
     Any of the robotic systems described herein can include an input device or controller for manipulating an instrument attached to a robotic arm. In some embodiments, the controller can be coupled (e.g., communicatively, electronically, electrically, wirelessly and/or mechanically) with an instrument such that manipulation of the controller causes a corresponding manipulation of the instrument e.g., via master slave control. 
       FIG.  19    is a perspective view of an embodiment of a controller  182 . In the present embodiment, the controller  182  comprises a hybrid controller that can have both impedance and admittance control. In other embodiments, the controller  182  can utilize just impedance or passive control. In other embodiments, the controller  182  can utilize just admittance control. By being a hybrid controller, the controller  182  advantageously can have a lower perceived inertia while in use. 
     In the illustrated embodiment, the controller  182  is configured to allow manipulation of two medical instruments, and includes two handles  184 . Each of the handles  184  is connected to a gimbal  186 . Each gimbal  186  is connected to a positioning platform  188 . 
     As shown in  FIG.  19   , each positioning platform  188  includes a SCARA arm (selective compliance assembly robot arm)  198  coupled to a column  194  by a prismatic joint  196 . The prismatic joints  196  are configured to translate along the column  194  (e.g., along rails  197 ) to allow each of the handles  184  to be translated in the z-direction, providing a first degree of freedom. The SCARA arm  198  is configured to allow motion of the handle  184  in an x-y plane, providing two additional degrees of freedom. 
     In some embodiments, one or more load cells are positioned in the controller. For example, in some embodiments, a load cell (not shown) is positioned in the body of each of the gimbals  186 . By providing a load cell, portions of the controller  182  are capable of operating under admittance control, thereby advantageously reducing the perceived inertia of the controller while in use. In some embodiments, the positioning platform  188  is configured for admittance control, while the gimbal  186  is configured for impedance control. In other embodiments, the gimbal  186  is configured for admittance control, while the positioning platform  188  is configured for impedance control. Accordingly, for some embodiments, the translational or positional degrees of freedom of the positioning platform  188  can rely on admittance control, while the rotational degrees of freedom of the gimbal  186  rely on impedance control. 
     F. Navigation and Control. 
     Traditional endoscopy may involve the use of fluoroscopy (e.g., as may be delivered through a C-arm) and other forms of radiation-based imaging modalities to provide endoluminal guidance to an operator physician. In contrast, the robotic systems contemplated by this disclosure can provide for non-radiation-based navigational and localization means to reduce physician exposure to radiation and reduce the amount of equipment within the operating room. As used herein, the term “localization” may refer to determining and/or monitoring the position of objects in a reference coordinate system. Technologies such as preoperative mapping, computer vision, real-time EM tracking, and robot command data may be used individually or in combination to achieve a radiation-free operating environment. In other cases, where radiation-based imaging modalities are still used, the preoperative mapping, computer vision, real-time EM tracking, and robot command data may be used individually or in combination to improve upon the information obtained solely through radiation-based imaging modalities. 
       FIG.  20    is a block diagram illustrating a localization system  90  that estimates a location of one or more elements of the robotic system, such as the location of the instrument, in accordance to an example embodiment. The localization system  90  may be a set of one or more computer devices configured to execute one or more instructions. The computer devices may be embodied by a processor (or processors) and computer-readable memory in one or more components discussed above. By way of example and not limitation, the computer devices may be in the tower  30  shown in  FIG.  1   , the cart  11  shown in  FIGS.  1 - 4   , the beds shown in  FIGS.  5 - 14   , etc. 
     As shown in  FIG.  20   , the localization system  90  may include a localization module  95  that processes input data  91 - 94  to generate location data  96  for the distal tip of a medical instrument. The location data  96  may be data or logic that represents a location and/or orientation of the distal end of the instrument relative to a frame of reference. The frame of reference can be a frame of reference relative to the anatomy of the patient or to a known object, such as an EM field generator (see discussion below for the EM field generator). 
     The various input data  91 - 94  are now described in greater detail. Preoperative mapping may be accomplished through the use of the collection of low dose CT scans. Preoperative CT scans are reconstructed into three-dimensional images, which are visualized, e.g. as “slices” of a cutaway view of the patient&#39;s internal anatomy. When analyzed in the aggregate, image-based models for anatomical cavities, spaces and structures of the patient&#39;s anatomy, such as a patient lung network, may be generated. Techniques such as center-line geometry may be determined and approximated from the CT images to develop a three-dimensional volume of the patient&#39;s anatomy, referred to as model data  91  (also referred to as “preoperative model data” when generated using only preoperative CT scans). The use of center-line geometry is discussed in U.S. patent application Ser. No. 14/523,760, the contents of which are herein incorporated in its entirety. Network topological models may also be derived from the CT-images, and are particularly appropriate for bronchoscopy. 
     In some embodiments, the instrument may be equipped with a camera to provide vision data (or image data)  92 . The localization module  95  may process the vision data  92  to enable one or more vision-based (or image-based) location tracking modules or features. For example, the preoperative model data  91  may be used in conjunction with the vision data  92  to enable computer vision-based tracking of the medical instrument (e.g., an endoscope or an instrument advance through a working channel of the endoscope). For example, using the preoperative model data  91 , the robotic system may generate a library of expected endoscopic images from the model based on the expected path of travel of the endoscope, each image linked to a location within the model. Intraoperatively, this library may be referenced by the robotic system in order to compare real-time images captured at the camera (e.g., a camera at a distal end of the endoscope) to those in the image library to assist localization. 
     Other computer vision-based tracking techniques use feature tracking to determine motion of the camera, and thus the endoscope. Some features of the localization module  95  may identify circular geometries in the preoperative model data  91  that correspond to anatomical lumens and track the change of those geometries to determine which anatomical lumen was selected, as well as the relative rotational and/or translational motion of the camera. Use of a topological map may further enhance vision-based algorithms or techniques. 
     Optical flow, another computer vision-based technique, may analyze the displacement and translation of image pixels in a video sequence in the vision data  92  to infer camera movement. Examples of optical flow techniques may include motion detection, object segmentation calculations, luminance, motion compensated encoding, stereo disparity measurement, etc. Through the comparison of multiple frames over multiple iterations, movement and location of the camera (and thus the endoscope) may be determined. 
     The localization module  95  may use real-time EM tracking to generate a real-time location of the endoscope in a global coordinate system that may be registered to the patient&#39;s anatomy, represented by the preoperative model. In EM tracking, an EM sensor (or tracker) comprising one or more sensor coils embedded in one or more locations and orientations in a medical instrument (e.g., an endoscopic tool) measures the variation in the EM field created by one or more static EM field generators positioned at a known location. The location information detected by the EM sensors is stored as EM data  93 . The EM field generator (or transmitter), may be placed close to the patient to create a low intensity magnetic field that the embedded sensor may detect. The magnetic field induces small currents in the sensor coils of the EM sensor, which may be analyzed to determine the distance and angle between the EM sensor and the EM field generator. These distances and orientations may be intraoperatively “registered” to the patient anatomy (e.g., the preoperative model) in order to determine the geometric transformation that aligns a single location in the coordinate system with a position in the preoperative model of the patient&#39;s anatomy. Once registered, an embedded EM tracker in one or more positions of the medical instrument (e.g., the distal tip of an endoscope) may provide real-time indications of the progression of the medical instrument through the patient&#39;s anatomy. 
     Robotic command and kinematics data  94  may also be used by the localization module  95  to provide localization data  96  for the robotic system. Device pitch and yaw resulting from articulation commands may be determined during preoperative calibration. Intraoperatively, these calibration measurements may be used in combination with known insertion depth information to estimate the position of the instrument. Alternatively, these calculations may be analyzed in combination with EM, vision, and/or topological modeling to estimate the position of the medical instrument within the network. 
     As  FIG.  20    shows, a number of other input data can be used by the localization module  95 . For example, although not shown in  FIG.  20   , an instrument utilizing shape-sensing fiber can provide shape data that the localization module  95  can use to determine the location and shape of the instrument. 
     The localization module  95  may use the input data  91 - 94  in combination(s). In some cases, such a combination may use a probabilistic approach where the localization module  95  assigns a confidence weight to the location determined from each of the input data  91 - 94 . Thus, where the EM data may not be reliable (as may be the case where there is EM interference) the confidence of the location determined by the EM data  93  can be decrease and the localization module  95  may rely more heavily on the vision data  92  and/or the robotic command and kinematics data  94 . 
     As discussed above, the robotic systems discussed herein may be designed to incorporate a combination of one or more of the technologies above. The robotic system&#39;s computer-based control system, based in the tower, bed and/or cart, may store computer program instructions, for example, within a non-transitory computer-readable storage medium such as a persistent magnetic storage drive, solid state drive, or the like, that, upon execution, cause the system to receive and analyze sensor data and user commands, generate control signals throughout the system, and display the navigational and localization data, such as the position of the instrument within the global coordinate system, anatomical map, etc. 
     2. Docking Medical Instruments. 
     Embodiments of the disclosure relate to systems and techniques for docking medical instruments. Some robotically controllable medical instruments include a base or handle that can be docked with an additional component of a robotic medical system. As an example, a robotically controllable endoscope can include a base or handle that is configured to be docked with an instrument drive mechanism (IDM) on a robotic arm. The instrument drive mechanism can include drive outputs that engage with corresponding drive inputs of the medical instrument to facilitate and enable control of the medical instrument. In some embodiments, the systems and techniques disclosed herein are configured to facilitate alignment between the drive outputs of the instrument drive mechanism and the drive inputs of the medical instrument. Aligning the drive outputs with the drive inputs can facilitate docking the medical instrument to the instrument drive mechanism. For example, aligning the drive outputs and drive inputs can make docking the medical instrument to the instrument drive mechanism quicker and easier. The systems and techniques described herein can be employed, for example, with robotically-enabled medical systems, such as those discussed above with reference to  FIGS.  1 - 20   , as well as those discussed below and other robotic systems. Example medical instruments and instrument drive mechanisms are described above, for example, with reference to  FIGS.  15 - 18   , as well as below. 
     As shown in  FIG.  16   , during a robotic medical procedure, a medical instrument  70  can be docked to an instrument drive mechanism  75 , which can be positioned on a robotic arm  76 . The medical instrument  70  can include an instrument base or handle  72  that is configured to engage with the instrument drive mechanism  75 . As shown, the instrument handle  72  can include a plurality of drive inputs  73  that are configured to engage corresponding drive outputs  74  on the instrument drive mechanism  75 . Detailed example embodiments of drive inputs and drive outputs are shown in  FIGS.  21 A- 23   , which are described below. As discussed above, the drive outputs  74  can be driven by motors within the instrument drive mechanism  75  (see  FIG.  15   ). The drive outputs  74  can transfer the rotation (or other motion) of the motor to the drive inputs  75  to control various functions of the medical instrument  70 , such as articulation of the elongated shaft  71  of the medical instrument  70  or actuation of a tool positioned at the distal end of the elongated shaft  71 . The instrument handle  72  can latch to the instrument drive mechanism  75  to retain the medical instrument  70  for use during the procedure. 
     When attempting to dock the medical instrument  70  to the instrument drive mechanism  75 , the drive inputs  73  of the instrument handle  72  and the drive outputs  74  of the instrument drive mechanism  75  may not be aligned. Misalignment of the drive inputs  73  and the drive outputs  74  can make docking the medical instrument  70  to the instrument drive mechanism  75  difficult or impossible. In order for the medical instrument  70  to dock to the instrument drive mechanism  75 , the drive outputs  74  or the drive inputs  73  may need to be rotated until they are properly aligned. 
     There are several ways by which the drive outputs  74  and the drive inputs  73  can be aligned. For example, in some embodiments, the instrument drive mechanism  75  may be configured such that the motors are back drivable. In such embodiments, the force of docking the medical instrument  70  to the instrument drive mechanism  75  may be sufficient to cause the drive outputs  74  to rotate until they are adequately aligned with the drive inputs  73 . In some embodiments, however, this may require significant force as any resistance in the motors must be overcome as they are back driven. Similarly, in some embodiments, the motors in the instrument drive mechanism  75  may be turned off during docking in order to allow the drive outputs  74  to rotate until they are aligned with the drive inputs  73 . The performance provided by these embodiments may be adjustable. For example, the torque required to rotate the drive outputs  74  may be adjustable. 
     As another example, in some embodiments, the force applied during docking may cause the drive inputs  73  on medical instrument  70  to rotate until they are adequately aligned with the drive outputs  74  of the instrument drive mechanism  75 . Some embodiments of medical instruments  70  may include pull wires that are actuated by the drive inputs  73  that are not pre-tensioned. For medical instruments  70  that do not include pre-tensioned pull wires, the drive inputs  73  may have some tolerance for free motion. That is, for medical instruments  70  that do not include pre-tensioned pull wires it may be possible to rotate the drive inputs  73  (at least for some degree of rotation) without actuating the pull wires. Therefore, in some embodiments, when the drive inputs  73  are misaligned with the drive outputs  74 , the drive inputs  73  may rotate to adjust themselves within this tolerance during docking. 
     Other embodiments of medical instruments  70  may include pre-tensioned pull wires. For some embodiments of these instruments (which include pre-tensioned pull wires) any rotation of the drive inputs  73  can cause a corresponding actuation of the pull wires. For example, where the pre-tensioned pull wires are configured to cause articulation of the elongated shaft  71  of the instrument  70 , any rotation of the drive inputs  73  will cause articulation of the elongated shaft  71 . For these embodiments, it may be undesirable to permit the drive inputs  73  to rotate freely to facilitate alignment during docking. For example, it may be undesirable to permit the drive inputs  73  to rotate freely during docking because this rotation may cause the elongated shaft  71  to articulate, which may not be acceptable because it may desired that the elongated shaft  71  of the medical instrument  70  be maintained straight during docking. Therefore, a methodology to automatically adjust the drive outputs  74  to align with drive inputs  75  may be desirable. Examples of such a methodology are described in greater detail below. 
     In some embodiments, the instrument drive mechanism  75  can include sensors configured to sense torque or force applied on to the drive outputs  74 . During docking of the medical instrument  70 , if the drive outputs  74  and drive inputs  73  are misaligned, the drive inputs  73  can contact and push against the drive outputs  74  as the medical instrument  70  and instrument drive mechanism  75  are brought together. This contact between the drive outputs  74  and the drive inputs  73  that is experienced during misalignment can be determined based on the output of the sensors. For example, the misalignment can cause a torque to be imparted on the drive output  74  by the drive input  73  that can be measured by the sensors. The measured torque can provide an indication that the drive output  74  and the drive input  73  are misaligned. In some embodiments, the system may then activate the motor associated with the drive output  74 , causing the drive output  74  to rotate. The drive output  74  can rotate until it is aligned with the drive input  73 . In some embodiments, the system determines that the drive output  74  is aligned with the drive input  73  when the measured torque imparted on the drive output  74  decreases or drops to zero. When this occurs, the system can stop rotating the drive output  74 . 
     Thus, in some embodiments, the system may be configured to automatically align drive outputs  74  with drive inputs  73  in response to torque or force measured by the sensors associated with the drive outputs  74 , wherein the torque is caused by misalignment of the drive outputs  74  with drive inputs  73 . This may advantageously facilitate docking of the medical instrument  70  to the instrument drive mechanism  75 . In some embodiments, this advantageously enables alignment of drive outputs  74  with drive inputs  73  without requiring the motors associated with the drive outputs  74  be back driven. Further, in some embodiments, this advantageously enables alignment of drive outputs  74  with drive inputs  73  without requiring rotation of the drive inputs  73 . Thus, in some embodiments, the automatic alignment system described herein may advantageously be used with medical instruments that include pre-tensioned pull wires. 
     These and other features and advantages of the disclosed systems and methods, will be described in greater detail below with reference to the examples and embodiments illustrated in  FIGS.  21 A- 29   . These examples and embodiments are provided by way of illustration and are not intended to limit this disclosure. 
       FIGS.  21 A and  21 B  illustrate isometric and end views, respectively, of an embodiment of an instrument drive mechanism  200  including a plurality of drive outputs  208  configured to engage a corresponding plurality of drive inputs of a medical instrument. As illustrated, the instrument drive mechanism  200  can include a housing  202 . The housing  202  can include an attachment face  204  that is configured to dock to the medical instrument. The instrument drive mechanism  200  can include latching mechanisms  206  that secure the medical instrument to the instrument drive mechanism  200  when docked. 
     As illustrated in  FIGS.  21 A- 21 B , the instrument drive mechanism  200  can include drive outputs  208 . The drive outputs  208  can be, for example, rotatable elements configured to be driven by motors that are positioned, for example, within the housing. In the illustrated embodiment, the drive outputs  208  are configured as splines or gears that protrude from the attachment face  204 , although other configurations for the drive outputs  208  are possible. For example, the drive outputs  208  can comprise receptacles or sockets that are formed as recesses into the attachment face  204 . The drive outputs  208  are configured to couple with and engage corresponding drive inputs on the medical instrument. The drive outputs  208  transfer rotational motion (or other motion depending on the embodiment) from the motors in the instrument drive mechanism  208  to the drive inputs of the medical instrument such that the motors can be used to control the medical instrument during a procedure. 
     In some embodiments, the instrument drive mechanism  200  can include additional features, such as communication module  210 . The communication module  210  can be configured to read information from a medical instrument that is docked to the instrument drive mechanism  200 . In some embodiments, the communication module  210  (or some other portion of the instrument drive mechanism  200 ) comprises one or more proximity sensors. The proximity sensors may be configured to determine when a medical instrument is in the process of being or has been docked to the instrument drive mechanism. The proximity sensors may comprise one or more magnetic proximity sensors, for example. 
       FIGS.  22 A and  22 B  illustrate isometric and end views, respectively, of an embodiment of an instrument handle  220  of a medical instrument including a plurality of drive inputs  228  configured to engage the corresponding plurality of drive outputs  208  of the instrument drive mechanism  200 . As illustrated, the instrument handle  220  can include a housing  222 . The housing  222  can include an attachment face  224  that is configured to dock to the attachment face  204  of the instrument drive mechanism  200 . The instrument handle  220  can include latching mechanisms  226  that secure the instrument handle  220  to the instrument drive mechanism  200  when docked. 
     As illustrated in  FIGS.  22 A- 22 B , the instrument handle  220  can include drive inputs  228 . The drive inputs  228  can be rotatable elements configured to be driven by the drive outputs  208  of the instrument drive mechanism  200 . In the illustrated embodiment, the drive inputs  228  are configured as receptacles or sockets that are recessed into the attachment face  224 , although other configurations for the drive inputs  228  are possible. For example, the drive inputs  228  can comprise protruding splines or gears that extend from the attachment face  224 . 
     In some embodiments, the instrument handle  220  can include additional features, such as communication module  230 , which can be configured to transmit information to communication module  210  of the instrument drive mechanism  200 . In some embodiments, the communication module  230  (or some other portion of the instrument handle  220 ) comprises one or more proximity sensors. The proximity sensors may be configured to determine when the medical instrument is in the process of being or has been docked to the instrument drive mechanism  200 . The proximity sensors may comprise one or more magnetic proximity sensors. 
       FIG.  23    illustrates a perspective view of an embodiment of an instrument drive output  208  engaging the drive input  228  during docking of the instrument handle  220  to the instrument drive mechanism  200 . As shown, the drive output  208  may comprise teeth  209  (e.g., ridges, protrusions, cutouts, indentations, etc.) that are configured to be received within corresponding grooves  229  of the drive input  229 . In the illustrated example, the teeth  209  and grooves  229  interact to transfer rotational motion. 
     In many of the examples described below, the drive output  208  is illustrated as a gear comprising teeth  209 , and the drive input  228  is configured as a socket comprising grooves  229 . However, this need not be the case in all embodiments and many other structural arrangements for transferring rotational motion between the drive output  208  and the drive input  228  are possible. For example, in some embodiments, the drive output  208  may comprise a socket, and the drive input  228  can comprise a gear configured to be received in the socket. As another example, in some embodiments, both the drive output  208  and the drive input  228  can be configured as gears configured to mesh together. For ease of description, the following examples, continue to describe and illustrate the drive output  208  as a gear and the drive input  228  as a socket with the understanding that this is done by way of illustration and is not intended to limit the disclosure to the particular illustrated structural arrangement. In other embodiments, the drive outputs  208  and drive inputs  228  can be configured to transfer other types of motion, such as linear motion. 
       FIG.  24    illustrates a view of an example where the drive output  208  is aligned with the drive input  228 . As shown, when aligned, the teeth  209  of the drive output  208  may be received within the grooves  229  of the drive input  228 . In some embodiments, because the teeth  209  are aligned within the grooves  229 , the drive input  228  does not impart any torque or force on the drive output  208 , or vice versa. This may be representative of a desired alignment between the drive input  228  and the drive output  208 . The illustrated alignment may also facilitate docking of the medical instrument to the instrument drive mechanism because, when aligned, the drive output  208  can easily be received within the drive input  228 . 
       FIGS.  25 A- 25 D  illustrate an example alignment process that can be used to align the drive output  208  with the drive input  228  during docking of the medical instrument to the instrument drive mechanism.  FIGS.  25 A- 25 C  illustrate example views of the drive output  208  and the drive input  228  at various stages during the process, and  FIG.  25 D  illustrates an example graph showing the output of a torque sensor associated with the drive output  208  during the process. 
     As shown in  FIG.  25 A , frequently, when attempting to dock the medical instrument to the instrument drive mechanism, one or more drive output  208  of the instrument drive mechanism and one or more drive input  228  of the medical instrument will not be properly aligned. For example, the teeth  209  of the drive output  208  may be misaligned with the grooves  229  of the drive input  228  as illustrated in  FIG.  25 A . When this occurs, it may be difficult to fully dock the medical instrument to the instrument drive mechanism because the misalignment may prevent the medical instrument and the instrument drive mechanism from being fully brought together. Thus, it may be desirable to bring the drive output  208  and the drive input  228  into alignment. 
     When misaligned, the drive input  228  may impart a force on the drive output  208  that creates a torque τ as shown. The torque τ may be caused by the walls of the grooves  229  contact and pressing on the walls of the teeth  209  as the medical instrument is brought toward the instrument drive mechanism. This may be particularly true in embodiments where the medical instrument includes pre-tensioned pull wires, because in such medical instruments, the drive inputs  228  may not be permitted to freely rotate. Also, in some embodiments, the motor associated with the drive output  208  may not permit the drive output  208  to freely rotate, and thus the contact between the misaligned drive output  208  and the drive input  228  can generate the torque τ as shown. A signal indicative of the torque τ can be sensed or measured by a sensor (such as a torque or force sensor) associated with the drive output  208 . In  FIG.  25 A , the torque τ is illustrated having a clockwise direction, although this need not be the case in all embodiments. For example, the torque τ can have a counterclockwise direction depending on how the drive output  208  and the drive input  228  are misaligned. 
     As shown in  FIG.  25 B , based on the torque τ, the drive output  208  can be rotated in a direction of rotation R that is the same as the direction of the torque τ so as to bring the drive output  208  into alignment with the drive input  228 . At the stage illustrated in  FIG.  25 B , the drive output  208  has been rotated in the clockwise direction. As illustrated in  FIG.  25 B , the drive output  208  is still misaligned with the drive input  228 ; however, the misalignment is lessened (when compared to  FIG.  25 A ) because of the rotation R. The rotation R can be driven by the motor associated with the drive output  208  in response to the measured torque τ as discussed throughout this application. 
     As illustrated in  FIG.  25 C , the rotation R of drive output  208  can continue until the drive output  208  is aligned with the drive input  228 . At this stage, as illustrated in  FIG.  25 C , the torque τ is no longer imparted on the drive output  208  because the drive output  208  and the drive input  228  are aligned. As shown, when aligned, the teeth  209  of the drive output  208  can be aligned with the grooves  229  of the drive input  228 . Because the teeth  209  of the drive output  208  are aligned with the grooves  229  of the drive input  228 , the drive input  228  may not impart torque τ. This may trigger the motor to stop rotating the drive output  208 . With the drive output  208  and the drive input  228  aligned, docking of the medical instrument to the instrument drive mechanism may be facilitated. 
       FIG.  25 D  illustrates an example graph of the output of the torque or force sensor associated with the drive output  208  during the docking and alignment process illustrated in  FIGS.  25 A- 25 C . In the illustrated embodiment, the graph illustrates measured torque, although this need not be the case in all embodiments. For example, the graph could be representative of measured force or torque, or an output of the sensor that is indicative of torque or force. 
     As shown in  FIG.  25 D , initially, the measured torque τ is substantially zero. This may be representative of a state in which the medical instrument is not contacting the instrument drive mechanism. In this state, nothing is contacting the drive output  208 , so the torque sensor associated with the drive output  208  does not measure any torque. As illustrated, the measured torque may begin to rise as the medical instrument is brought into contact with the instrument drive mechanism during docking because the misaligned drive output  208  may begin to contact to the drive input  228 . 
     At time t a  illustrated in  FIG.  25 D , which may be representative of the state shown in  FIG.  25 A , the torque τ has risen but is still below a threshold τ thresh . In some embodiments, while the measured torque τ remains below the threshold τ thresh , rotation of the drive output  208  is not triggered. The threshold τ thresh  may be selected to account for noise and to adjust the sensitivity of the system. 
     From time t a  the measured torque τ may continue to increase beyond the threshold τ thresh . Once the measured torque τ exceeds the threshold τ thresh , rotation R of the drive output  208  can be triggered. For example, time t b  may be indicative of the stage illustrated in  FIG.  25 B , at which, as discussed above, the drive output  208  is still misaligned with the drive input  228 , the measured torque τ is still present, and the drive output  208  is undergoing rotation R so as to align the drive output  208  with the drive input  228 . 
     As illustrated in  FIG.  25 D , from time t b  the measured torque τ continues to decrease until the measured torque τ falls below the threshold τ thresh . When the measured torque τ falls below the threshold τ thresh  the rotation R may stop because the drive output  208  and the drive input  228  are now aligned as shown in  FIG.  25 C , which may be indicative of the time t c . The time t c  can correspond to proper alignment as shown, for example, in  FIG.  25 C . 
       FIG.  26    is a block diagram illustrating an embodiment of a medical system  300  configured to align drive outputs  312  of an instrument drive mechanism  306  with drive inputs  318  of a medical instrument  314 . In some embodiments, alignment may occur automatically based on the output of torque or force sensors  308  associated with the drive outputs  312  in a manner similar to that which has been described with reference to  FIGS.  25 A- 25 D , as well as will be described in greater detail below with reference to  FIG.  27   . 
     As illustrated in  FIG.  26   , the system  300  may include one or more processors  302  and one or more computer readable medium or memories  304  in communication with the processors  302 . The memories  304  may be configured with instructions that configure the processors  302  to perform various features. For example, the memories  304  can be configured with instructions that cause the processors  302  to perform the automatic alignment and docking features described throughout the application. 
     The system  300  also includes an instrument drive mechanism  306 . Example instrument drive mechanisms have been described above, for example, with reference to  FIGS.  15 ,  16 ,  21 A and  21 B . In some embodiments, the instrument drive mechanism  306  is positioned on a distal end of a robotic arm or other instrument positioning device. The instrument drive mechanism  306  can be configured to dock with a medical instrument  314 . In the illustrated embodiment, the instrument drive mechanism  306  includes torque sensors  308 , motors  310 , and drive outputs  312 . The instrument drive mechanism  306  may also include additional features that are not illustrated in  FIG.  26    (e.g., proximity sensors, communication modules, etc.). 
     As discussed previously, the drive outputs  312  can be configured to engage with corresponding drive inputs  318  on the medical instrument  314 . The drive outputs  312  can be driven by motors  310 . The motors  310  can be configured to cause the drive outputs  312  to rotate, for example, in clockwise and counterclockwise directions. The drive outputs  312  can be configured to transfer the rotational motion of the motors  310  to the drive inputs  318  of the medical instrument  314 . As such, the drive outputs  312  can comprise any structure suitable for transferring rotational motion, including, for example, gears and sockets, among others. 
     As shown in  FIG.  26   , the instrument drive mechanism  306  can also include sensors  308 , such as the illustrated torque sensors  308 . As mentioned previously, other types of sensors, such as force sensors may also be used. The torque sensors  308  can be associated with the drive outputs  312 . For example, the torque sensors  308  may provide an output signal that is indicative of torque or force imparted on the drive outputs  312 . In some embodiments, the torque sensors  308  can comprise one or more strain gauges. The torque sensors can be positioned between the housing of the instrument drive mechanism  306  and the motors  310 . In some embodiments, the torque sensors  308  are bi-directional. That is, in some embodiments, the torque sensors  308  may be configured to measure torque in both clockwise and counter clockwise directions. The output signals of the torque sensors  308  may be indicative of the direction of the torque imparted on the drive outputs  312 . 
     As shown, the torque sensors  308  and motors  310  can be communicatively coupled to the processors  302 . This may allow, for example, the output signals of the torque sensors  308  to be used by the processors  302 , and may further allow the processors  302  to control the motors  310 . In some embodiments, the processors  302  control the motors  310  based on the output signals of the torque sensors  308  to implement the automatic alignment and docking features described herein. 
       FIG.  26    illustrates that the system  300  can also include the medical instrument  314 . Example medical instruments  314  are described above, for example, with reference to  FIGS.  1 ,  3 - 5 ,  8 ,  9 ,  16 - 18 ,  22 A, and  22 B . The medical instrument  314  can include an instrument base or handle  316  and an elongated shaft  320 . The instrument handle  316  can be configured to dock to the instrument drive mechanism  306 . The elongated shaft  320  can extend from the instrument handle  316 . In some embodiments, the elongated shaft  320  can be configured for insertion into a patient&#39;s body (e.g., laparoscopically or endoscopically) during a medical procedure. 
     The instrument handle  316  can include drive inputs  318  configured to engage with the drive outputs  312  of the instrument drive mechanism  306 . In some embodiments, the drive inputs  318  are associated with one or more pull wires  322  that are actuable to perform various functions with the medical instrument  314 . For example, in some embodiments, actuating the pull wires  322  articulates the elongated shaft  320  or operates a tool positioned at the distal end of the elongated shaft  320 . In some embodiments, the pull wires  322  are actuated by rotating the drive inputs  318 . As noted above, the drive inputs  318  may be configured to engage the drive outputs  312  such that rotational motion from the motors  310  can be transmitted from through the drive outputs  312  to the drive inputs  318  to actuate the pull wires  322 . In some embodiments, the pull wires  322  may be pre-tensioned. 
     In some embodiments, the medical instrument  314  comprises pre-tensioned pull wires. That is, in some embodiments, any rotation of the drive inputs  318  causes actuation of the pull wires. In such embodiment, inadvertent or unintentional rotation of the drive inputs  318  can be undesirable as such rotation can cause inadvertent or unintentional articulation of the medical instrument. 
     In some embodiments, the system  300  is configured to implement an alignment process for automatically aligning drive outputs  312  and drive inputs  318  to facilitate docking. 
       FIG.  27    is a flowchart illustrating an example method  400  of alignment of drive outputs of an instrument drive mechanism with drive inputs of a medical instrument. In some embodiments, the method  400  can be implemented on the system  300  of  FIG.  26   , as well as on other medical systems described herein. 
     The method  400  begins at block  402 , at which a torque signal is received from a torque sensor associated with a drive output of the instrument drive mechanism. In some embodiments, the torque signal may be indicative of a direction of the torque imparted on the drive output. The torque may, in some embodiments, be caused by misalignment between the drive output and the drive input as described above. In some embodiments, the method  400  may use a signal indicative of force, rather than torque. 
     Next, the method  400  moves to block  404 , at which a motor associated with the drive output is activated to rotate the drive output in response to the torque signal (received at block  402 ) exceeding a threshold. The threshold may be configured so as to adjust the sensitivity of the system and/or account for noise in the signal. In some embodiments, the threshold may be configured based on the medical instrument. For example, stiffer medical instruments may include a higher threshold than more flexible medical instruments. In some embodiments, threshold information is stored for each instrument (in some embodiments, on the instrument itself) and read for use in the method  400 . 
     In some embodiments, the rotation is configured to align the drive output with the drive input. In some embodiments, the drive output is rotated in the same direction as the torque imparted on the drive output. For example, if the torque is in the clockwise direction, the drive input may be rotated in the clockwise direction. In some embodiments, the drive output is configured to be rotated in a direction that is opposite the direction of the torque. 
     In some embodiments, the speed of the rotation can be proportional to the magnitude of the torque measured at block  402 . For example, the greater the torque, the greater the speed of rotation. Because the torque may be related to the degree of misalignment, the rotation may be faster when the drive outputs and drive inputs are significantly misaligned, and the rotation may slow as the drive outputs and drive inputs are rotated into alignment. In other embodiments, the speed of rotation may be constant. 
     The method  400  then moves to block  406 , at which the motor is deactivated to cause the motor to stop rotating the drive output in response to the torque signal dropping below the threshold. The torque signal dropping below the threshold may be indicative of proper alignment between the drive output and the drive input. 
     In some embodiments, the method  400  is performed during an instrument docking or instrument load state. For example, the method  400  may, in some embodiments, be performed while docking the medical instrument to the instrument drive mechanism. In some embodiments, determining whether the system is in an instrument load state can be automatic, for example, based on proximity sensors in the instrument drive mechanism and the medical instrument, or manual, based on user input. In some embodiments, once docking is completed, the system exits the instrument load state and no longer performs the method  400 . 
     In some embodiments, the method  400  may be performed for each drive output of the instrument drive mechanism, and thus may be used to align a plurality of drive outputs with a plurality of drive inputs. 
       FIGS.  28 A- 28 D  illustrate an example homing process using the drive output  208  and the drive input  228  described above. In some embodiments, the homing process is completed after the medical instrument has been docked to the instrument drive mechanism. The homing process may be used to estimate or determine the size of a gap g between the teeth  209  of the drive output  208  and the grooves  229  of the drive input  228 . The gap g may represent a clearance or tolerance between the drive output  208  and the drive input  228 . As described below, it may be desirable to compute the size of the gap g so that it can be accounted for while controlling a robotic medical instrument. 
       FIG.  28 A  illustrates the drive output  208  engaged with the drive input  228 . As shown, the teeth  209  of the drive output  208  are received within the grooves  229  of the drive input  228 . For tolerance and clearance reasons, a gap g may exist between the teeth  209  and the grooves  229 . The gap g may facilitate docking and fit between drive output  208  and the drive input  228 . As shown, the gap g can exist on one or both sides of the teeth  209 . For example, the entire gap g may exist on a first side, the entire gap g may exist on a second side, or a portion of the gap g can exist on the first side and another portion of the gap g can exist on the second side of the teeth  209 . Because of the gap g, it may be possible to rotate the drive output  208  without causing a corresponding rotation of the drive output  208 . For example, the drive output  208  must be rotating until a wall of the teeth  209  contacts a wall of the groove  229  before the drive output  208  will begin rotating. As such, it may be desirable to determine or estimate the size of the gap g so that this distance can be accounted for. The gap g may be referred to as backlash. It may be desirable to account for the backlash when switching rotational directions. For example, after being rotated in the clockwise direction, it is necessary to rotate in the counterclockwise through the distance of the gap g before counterclockwise rotation will cause actuation of the medical instrument. 
       FIG.  28 B  illustrates that, as part of the homing process that determines the size of the gap g, the drive output  208  can be rotated in a first direction to a first rotational position. In the illustrated example, the drive output  208  is rotated with rotation R in a counterclockwise direction until a torque τ is measured in the same direction as the rotation R. The torque τ can be caused by the tooth  209  contacting the groove  229 . In this manner, the process can determine the rotational position at which the tooth  209  will contact the groove  229  when rotated in the first direction. 
     As shown in  FIG.  28 C , the drive output  208  can then be rotated in a second direction to a second rotational position. In the illustrated example, the drive output  208  is then rotated with rotation R in the clockwise direction until a torque τ is measured in the same direction as the rotation R. Again, the torque τ can be caused by the tooth  209  contacting the groove  229 . In this manner, the process can determine the rotational position at which the tooth  209  will contact the groove  229  when rotated in the second direction. 
     The rotational distance between the first rotational position (shown in  FIG.  28 B ) and the second rotational position (shown in  FIG.  28 C ) can then be determined and used as the gap g. This is because the drive output  208  has been homed by locating each sidewall of the grooves  229  of the drive input  228 . The rotational distance can then be used to account for backlash in the system when changing rotational directions. 
       FIG.  28 D  illustrates an example graph of the output of a torque sensor associated with the drive output during the homing process illustrated in  FIGS.  28 A- 28 C . As before, the graph could alternatively represent force or an output signal indicative of force or torque. As shown, at time t a  (representative of the state of  FIG.  28 A ) the torque τ is substantially zero because the drive output  208  and the drive input  228  are aligned. At time t b  (representative of the state of  FIG.  28 B ) the torque τ has increased above a torque threshold +τ thresh  indicating contact with the drive output  208 . At time t c  (representative of the state of  FIG.  28 C ), the torque τ has decreased to the threshold −τ thresh  indicating contact with the drive input  228  in the opposite direction. In the graph, the positive and negative torque thresholds τ thresh  are indicative of limits in opposite rotational directions. 
       FIG.  29    is a flowchart illustrating an example homing method  500  for a medical system. The medical system can be, for example, the medical system  300  of  FIG.  26   , as well as other medical systems described herein. The homing method  500  can be used to determine or estimate a gap between a drive input and a drive output as described with reference to  FIG.  28 A , such that the gap can be accounted for during further use of the medical system. 
     The method  500  begins at block  502 , at which a motor associated with a drive output of the instrument drive mechanism is activated to rotate the drive output in a first direction until a first rotational position at which a torque signal measured by a torque sensor associated with the drive output exceeds a threshold. In some embodiments, the torque signal exceeding the threshold can be indicative of the drive output contacting the drive input, for example, as shown in  FIG.  28 B . 
     Next, the method  500  moves to block  504 , at which the motor rotates the drive output in a second direction until a second rotational position at which the torque signal measured by the torque sensor exceeds the threshold. In some embodiments, the torque signal exceeding the threshold can be indicative of the drive output contacting the drive input in the opposite direction, for example, as shown in  FIG.  28 C . 
     Finally, at block  506 , the method  500  determines the rotational distance between the first rotational position ( FIG.  28 B ) and the second rotational position ( FIG.  28 C ). The rotational distance can be representative of the gap or clearance between the drive output and the drive input. 
     In some embodiments, once the method  500  determines the gap, the gap is accounted for in future commanded motions. For example, rotation of the drive outputs is used to control the medical instrument. However, when rotation of the drive outputs changes directions, the drive output must be rotated back through the gap distance before it contacts the drive input in the opposite direction. 
       FIG.  30    illustrates an example of a robotic medical system  600  during docking of a medical instrument to an instrument drive mechanism. In the illustrated embodiment, the system  600  includes an instrument drive mechanism  602  and a robotic medical instrument  610 . The robotic medical instrument  610  includes an instrument base or handle  612  and an elongated shaft  614 . The elongated shaft  614  can be configured to articulate. In some embodiments, the elongated shaft includes one or more pull wires that are actuable to cause articulation of the elongated shaft  614 . In some embodiments, the pull wires are pre-tensioned pull wires. 
     The robotic medical instrument  610  can be configured to dock to the instrument drive mechanism  602  such that the instrument drive mechanism  602  can drive the robotic medical instrument  610 . As illustrated, the instrument drive mechanism  602  includes instrument drive outputs  604 . The instrument drive outputs  604  can be configured to engage with corresponding instrument drive inputs  616  on the base or handle  612  of the robotic medical instrument  610 . As described above, alignment between the drive outputs  604  and drive inputs  610  can facilitate docking. 
     In the illustrated example of  FIG.  30   , the instrument drive mechanism  600  includes a sensor  606 . The sensor  606  can be configured to determine when the robotic medical instrument  610  is within a threshold loading distance D of the instrument drive mechanism  602 . In some embodiments, the sensor  606  is a proximity sensor, a magnetic sensor, an RFID reader, or any other type of suitable sensor for determining when the robotic medical instrument is within the distance D of the instrument drive mechanism  602 . In some embodiments, the instrument drive mechanism includes a corresponding sensor  618  that can be read by the sensor  606  of the instrument drive mechanism  602 . For example, the sensor  618  can be a magnet or RFID tag that can be read by the sensor  606  when within the distance D. In some embodiments, the distance D is at least 20 cm, at least 15 cm, at least 10 cm, at least 5 cm, or at least 1 cm. In some embodiments, the distance D is no more than 20 cm, no more than 15 cm, no more than 10 cm, no more than 5 cm, or no more than 1 cm. 
     In the illustrated embodiment, when the robotic medical instrument  610  is brought within the distance D of the instrument drive mechanism  602 , motors of the instrument drive mechanism  602  can begin to drive oscillation of the drive outputs  604 . For example, the oscillation of the drive output can include rotation of the drive output back and forth in clockwise and counter clockwise directions (as illustrated in  FIG.  30    with arrows) through a rotational range of at least 30 degrees, at least 20 degrees, at least 15 degrees, at least 10 degrees, at least 5 degrees, at least 3 degrees, or at least 1 degree. In some embodiments, the oscillation is in a rotational range of no more than 30 degrees, no more than 20 degrees, no more than 15 degrees, no more than 10 degrees, no more than 5 degrees, no more than 3 degrees, or no more than 1 degree. 
     In some embodiments, when the instrument drive mechanism  602  is within the threshold docking distance D of the robotic medical instrument, the motors that drive the drive outputs can be placed in an admittance mode. For example, the motors can be in admittance mode while the drive outputs  604  oscillate. 
     Oscillation of the drive outputs  604  can facilitate alignment between the drive outputs and the drive inputs  616 , which can allow the medical instrument  610  to dock to the instrument drive mechanism  602 . In some embodiments, the system can determine that the robotic medical instrument has docked to the instrument drive mechanism based on an output of the sensor, and stop causing oscillation of the drive output when the robotic medical instrument has docked. 
       FIG.  31    is a flowchart illustrating an example alignment method  700  for a robotic medical system. The method  700  can begin at block  702 . At block  702 , the method  700  includes determining that a robotic medical instrument is within a threshold loading distance of an instrument drive mechanism based on an output of a sensor on the instrument drive mechanism. This can be done with a sensor as described above. At block  704 , the method  700  includes placing the motor associated with the drive input in an admittance mode. At block  706 , the method  700  includes activating a motor associated with a drive output of the instrument drive mechanism to cause the drive output to oscillate to facilitate alignment of the drive output and the corresponding drive input when the robotic medical instrument is within the threshold loading distance of the instrument drive mechanism. 
     In some embodiments, the systems and techniques for medical instrument docking described above can be considered as admittance control of the joints of the instrument drive mechanism with input force/torque coming from the misalignment between driving gears and sockets. 
     3. Implementing Systems and Terminology. 
     Implementations disclosed herein provide systems, methods and apparatus for docking medical instruments, and in some embodiments, for docking robotic medical instruments that may include one or more pre-tensioned pull wires to instrument drive mechanisms. The systems, methods, and apparatus may facilitate alignment of drive outputs on the instrument drive mechanism with drive inputs on the medical instrument. 
     It should be noted that the terms “couple,” “coupling,” “coupled” or other variations of the word couple as used herein may indicate either an indirect connection or a direct connection. For example, if a first component is “coupled” to a second component, the first component may be either indirectly connected to the second component via another component or directly connected to the second component. 
     The phrases referencing specific computer-implemented processes/functions described herein may be stored as one or more instructions on a processor-readable or computer-readable medium. The term “computer-readable medium” refers to any available medium that can be accessed by a computer or processor. By way of example, and not limitation, such a medium may comprise random access memory (RAM), read-only memory (ROM), electrically erasable programmable read-only memory (EEPROM), flash memory, compact disc read-only memory (CD-ROM) or other optical disk storage, magnetic disk storage or other magnetic storage devices, or any other medium that can be used to store desired program code in the form of instructions or data structures and that can be accessed by a computer. It should be noted that a computer-readable medium may be tangible and non-transitory. As used herein, the term “code” may refer to software, instructions, code or data that is/are executable by a computing device or processor. 
     The methods disclosed herein comprise one or more steps or actions for achieving the described method. The method steps and/or actions may be interchanged with one another without departing from the scope of the claims. In other words, unless a specific order of steps or actions is required for proper operation of the method that is being described, the order and/or use of specific steps and/or actions may be modified without departing from the scope of the claims. 
     As used herein, the term “plurality” denotes two or more. For example, a plurality of components indicates two or more components. The term “determining” encompasses a wide variety of actions and, therefore, “determining” can include calculating, computing, processing, deriving, investigating, looking up (e.g., looking up in a table, a database or another data structure), ascertaining and the like. Also, “determining” can include receiving (e.g., receiving information), accessing (e.g., accessing data in a memory) and the like. Also, “determining” can include resolving, selecting, choosing, establishing and the like. 
     The phrase “based on” does not mean “based only on,” unless expressly specified otherwise. In other words, the phrase “based on” describes both “based only on” and “based at least on.” 
     The previous description of the disclosed implementations is provided to enable any person skilled in the art to make or use the present invention. Various modifications to these implementations will be readily apparent to those skilled in the art, and the generic principles defined herein may be applied to other implementations without departing from the scope of the invention. For example, it will be appreciated that one of ordinary skill in the art will be able to employ a number corresponding alternative and equivalent structural details, such as equivalent ways of fastening, mounting, coupling, or engaging tool components, equivalent mechanisms for producing particular actuation motions, and equivalent mechanisms for delivering electrical energy. Thus, the present invention is not intended to be limited to the implementations shown herein but is to be accorded the widest scope consistent with the principles and novel features disclosed herein.