Patent Publication Number: US-2021169589-A1

Title: Image-based airway analysis and mapping

Description:
CROSS-REFERENCE TO RELATED APPLICATION 
     This application is a continuation of U.S. application Ser. No. 16/427,092, filed May 30, 2019 and titled “IMAGE-BASED AIRWAY ANALYSIS AND MAPPING,” which claims the benefit of U.S. Provisional Application No. 62/678,881, filed May 31, 2018, which is hereby incorporated by reference in its entirety. 
    
    
     TECHNICAL FIELD 
     This disclosure relates generally to systems and methods for navigation of medical instruments, and more particularly to image-based airway analysis and mapping for navigating robotically-controlled medical instruments. 
     BACKGROUND 
     Medical procedures such as endoscopy (e.g., bronchoscopy) may involve accessing and visualizing the inside of a patient&#39;s lumen (e.g., airways) for diagnostic and/or therapeutic purposes. During a procedure, a flexible tubular tool or instrument, such as an endoscope, may be inserted into the patient&#39;s body. In some instances, a second instrument can be passed through the endoscope to a tissue site identified for diagnosis and/or treatment. 
     Bronchoscopy is a medical procedure that allows a physician to examine the inside conditions of airways in a patient&#39;s lungs, such as bronchi and bronchioles. During the medical procedure, a thin, flexible tubular tool or instrument, known as a bronchoscope, may be inserted into the patient&#39;s mouth and passed down the patient&#39;s throat into his or her lung airways towards a tissue site identified for subsequent diagnosis and/or treatment. The bronchoscope can have an interior lumen (a “working channel”) providing a pathway to the tissue site, and catheters and various medical tools can be inserted through the working channel to the tissue site. 
     In certain medical procedures, surgical robotic systems may be used to control the insertion and/or manipulation of the surgical tools. Surgical robotic systems may include at least one robotic arm or other instrument positioning device including a manipulator assembly used to control the positioning of the surgical tool during the procedures. 
     SUMMARY 
     Robotically-enabled medical systems can be used to perform a variety of medical procedures, including both minimally invasive procedures, such as laparoscopic procedures, and non-invasive procedures, such as endoscopic procedures. Among endoscopic procedures, robotically-enabled medical systems can be used to perform bronchoscopy, ureteroscopy, gastroenterology, etc. During such procedures, a physician and/or computer system can navigate a medical instrument through a luminal network of a patient. The luminal network can include a plurality of branched lumens (such as in bronchial or renal networks), or a single lumen (such as a gastrointestinal tract). The robotically-enabled medical systems can include navigation systems for guiding (or assisting with the guidance of) the medical instrument through the luminal network. 
     Embodiments of this disclosure relate to systems and techniques for image-based airway analysis and mapping. Image-based airway analysis and mapping may aid navigation through the luminal network. Image-based airway analysis can include identifying, within an image captured with an imaging device on the instrument, one or more airways associated with one or more branches of a luminal network and determining branching information indicative of how the current airway in which the image is captured branches into the detected “child” airways. Image-based airway mapping can include mapping the identified airways to corresponding branches of the luminal network. These systems and techniques may be used to determine or estimate the position of an instrument within the luminal network. 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 one aspect, there is provided a method of navigating an instrument through a luminal network, the method comprising: capturing a plurality of images within the luminal network with an imaging device positioned on the instrument, the plurality of images comprising at least a first image captured at a first time and a second image captured at a second time subsequent to the first time; identifying a first airway in the first image; identifying two or more airways in the second image; determining, based on the first airway in the first image and the two or more airways in the second image, that an overlap condition is met; accessing preoperative model data indicative of an expected count of airways corresponding to a location of the instrument during the second time; and determining, based on the preoperative model data and the determination that the overlap condition is met, a mapping between the two or more airways in the second image and the airways in the preoperative model data. 
     In another aspect, there is provided a non-transitory computer readable storage medium having stored thereon instructions that, when executed, cause a processor of a device to at least: capture a plurality of images within a luminal network with an imaging device positioned on an instrument, the plurality of images comprising at least a first image captured at a first time and a second image captured at a second time subsequent to the first time; identify a first airway in the first image; identify two or more airways in the second image; determine, based on the first airway in the first image and the two or more airways in the second image, that an overlap condition is met; access preoperative model data indicative of an expected count of airways corresponding to a location of the instrument during the second time; and determine, based on the preoperative model data and the determination that the overlap condition is met, a mapping between the two or more airways in the second image and the airways in the preoperative model data. 
     In yet another aspect, there is provided a robotic surgical system for mapping one or more airways in a luminal network, the system comprising: an instrument having: an elongate body configured to be inserted into the luminal network, and an imaging device positioned on a distal portion of the elongate body; an instrument positioning device attached to the instrument, the instrument positioning device configured to move the instrument through the luminal network; at least one computer-readable memory having stored thereon executable instructions; and one or more processors in communication with the at least one computer-readable memory and configured to execute the instructions to cause the system to at least: capture a plurality of images within the luminal network with an imaging device positioned on the instrument, the plurality of images comprising at least a first image captured at a first time and a second image captured at a second time subsequent to the first time; identify a first airway in the first image; identify two or more airways in the second image; determine, based on the first airway in the first image and the two or more airways in the second image, that an overlap condition is met; access preoperative model data indicative of an expected count of airways corresponding to a location of the instrument during the second time; and determine, based on the preoperative model data and the determination that the overlap condition is met, a mapping between the two or more airways in the second image and the airways in the preoperative model data. 
    
    
     
       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 procedure(s). 
         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 bronchoscopy 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 ureteroscopy 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 exemplary instrument driver. 
         FIG. 13  illustrates an exemplary medical instrument with a paired instrument driver. 
         FIG. 14  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. 15  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. 13-14 , in accordance to an example embodiment. 
         FIG. 16  illustrates an example of an instrument navigating a luminal network. 
         FIG. 17  illustrates an example command console for a robotically-controlled surgical system. 
         FIG. 18  illustrates a distal end of an embodiment of a medical instrument. 
         FIG. 19  depicts a flowchart illustrating an example method for image-based airway analysis and mapping. 
         FIG. 20  illustrates an example image of an interior of a branch of a luminal network. 
         FIG. 21  illustrates a simplified view of a luminal network. 
         FIG. 22  illustrates two different example airway detection results. 
         FIG. 23A  illustrates an airway analysis and mapping system according to example embodiments. 
         FIG. 23B  illustrates the temporal context in which the image-based airway analysis according to example embodiments is performed. 
         FIG. 24  illustrates the spatial nature of the image-based airway analysis according to example embodiments. 
         FIG. 25  illustrates additional example relationships exhibited by detected airways in two consecutive images. 
         FIG. 26  depicts a flowchart illustrating an example method for image-based airway analysis and mapping. 
     
    
    
     DETAILED DESCRIPTION 
     I. 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 endoscopy 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 procedure. 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 the 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 ureteroscopy 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 ureteroscopy 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  11  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 bronchoscopy 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  43 , 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 be 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 ureteroscopy 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 laparoscopy 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 laparoscopy procedure. As shown, 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 laparoscopy 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. 
     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. 12  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  may be independently controlled and motorized, and the instrument driver  62  may provide multiple (e.g., four as shown in  FIGS. 13 and 14 ) 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. 13  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 the 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 the 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  71 . 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 the drive inputs  73  would transfer tension to the tendon, thereby causing the end effector to actuate in some way. In laparoscopy, 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 the 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 the 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 also exhibits more limited 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. 13 , 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 endoscopy procedure. 
       FIG. 14  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. 13 . 
     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. 
     E. 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. 15  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. 5-10 , etc. 
     As shown in  FIG. 15 , 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 computed tomography (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 model data  91  (also referred to as “preoperative model data” when generated using only preoperative CT scans). In some embodiments, the preoperative model data  91  may include data from, e.g., fluoroscopy, magnetic resonance imaging (MRI), ultrasound imaging, and/or x-rays. 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. 15  shows, a number of other input data can be used by the localization module  95 . For example, although not shown in  FIG. 15 , 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. 
     II. Navigation of Luminal Networks 
     The various robotic systems discussed above can be employed to perform a variety of medical procedures, such as endoscopic and laparoscopy procedures. During certain procedures, a medical instrument, such as a robotically-controlled medical instrument, is inserted into a patient&#39;s body. Within the patient&#39;s body, the instrument may be positioned within a luminal network of the patient. As used herein, the term “luminal network” refers to any cavity structure within the body, whether comprising a plurality of lumens or branches (e.g., a plurality of branched lumens, as in the lung or blood vessels) or a single lumen or branch (e.g., within the gastrointestinal tract). During the procedure, the instrument may be moved (e.g., navigated, guided, driven, etc.) through the luminal network to one or more areas of interest. Movement of the instrument through the system may be aided by the navigation or localization system  90  discussed above, which can provide positional information about the instrument to a physician controlling the robotic system. 
       FIG. 16  illustrates an example luminal network  130  of a patient. In the illustrated embodiment, the luminal network  130  is a bronchial network of airways  150  (i.e., lumens, branches) of the patient&#39;s lung. Although the illustrated luminal network  130  is a bronchial network of airways within the patient&#39;s lung, this disclosure is not limited to only the illustrated example. The robotic systems and methods described herein may be used to navigate any type of luminal network, such as bronchial networks, renal networks, cardiovascular networks (e.g., arteries and veins), gastrointestinal tracts, urinary tracts, etc. 
     As illustrated, the luminal network  130  comprises a plurality of airways  150  that are arranged in a branched structure. In general, the luminal network  130  comprises a three-dimensional structure. For ease of illustration,  FIG. 16  represents the luminal network  130  as a two-dimensional structure. This should not be construed to limit the present disclosure to two-dimensional luminal networks in any way. 
       FIG. 16  also illustrates an example of a medical instrument positioned within the luminal network  130 . The medical instrument is navigated through the luminal network  130  towards an area of interest (e.g., nodule  155 ) for diagnosis and/or treatment. In the illustrated example, the nodule  155  is located at the periphery of the airways  150 , although the area(s) of interest can be positioned anywhere within the luminal network  130  depending on the patient and procedure. 
     In the illustrated example, the medical instrument comprises an endoscope  115 . The endoscope  115  can include a sheath  120  and a leader  145 . In some embodiments, the sheath  120  and the leader  145  may be arranged in a telescopic manner. For example, the leader  145  may be slidably positioned inside a working channel of the sheath  120 . The sheath  120  may have a first diameter, and its distal end may not be able to be positioned through the smaller-diameter airways  150  around the nodule  155 . Accordingly, the leader  145  may be configured to extend from the working channel of the sheath  120  the remaining distance to the nodule  155 . The leader  145  may have a lumen through which instruments, for example biopsy needles, cytology brushes, and/or tissue sampling forceps, can be passed to the target tissue site of the nodule  155 . In such implementations, both the distal end of the sheath  120  and the distal end of the leader  145  can be provided with EM instrument sensors (e.g., EM instrument sensors  305  in  FIG. 18 ) for tracking their position within the airways  150 . This telescopic arrangement of the sheath  120  and the leader  145  may allow for a thinner design of the endoscope  115  and may improve a bend radius of the endoscope  115  while providing a structural support via the sheath  120 . 
     In other embodiments, the overall diameter of the endoscope  115  may be small enough to reach the periphery without the telescopic arrangement, or may be small enough to get close to the periphery (e.g., within about 2.5-3 cm) to deploy medical instruments through a non-steerable catheter. The medical instruments deployed through the endoscope  115  may be equipped with EM instrument sensors (e.g., EM instrument sensors  305  in  FIG. 18 ), and the image-based airway analysis and mapping techniques described below can be applied to such medical instruments. 
     As shown, to reach the nodule  155 , the instrument (e.g., endoscope  115 ) must be navigated or guided through the airways  150  of the luminal network. An operator (such as a physician) can control the robotic system to navigate the instrument to the nodule  155 . The operator may provide inputs for controlling the robotic system. 
       FIG. 17  illustrates an example command console  200  that can be used with some implementations of the robotic systems described herein. The operator may provide the inputs for controlling the robotic system, for example, to navigate or guide the instrument to an area of interest such as nodule  155 , via the command console  200 . The command console  200  may be embodied in a wide variety of arrangements or configurations. In the illustrated example, the command console  200  includes a console base  201 , displays  202  (e.g., monitors), and one or more control modules (e.g., keyboard  203  and joystick  204 ). A user  205  (e.g., physician or other operator) can remotely control the medical robotic system (e.g., the systems described with reference to  FIGS. 1-15 ) from an ergonomic position using the command console  200 . 
     The displays  202  may include electronic monitors (e.g., LCD displays, LED displays, touch-sensitive displays), virtual reality viewing devices (e.g., goggles or glasses), and/or other display devices. In some embodiments, one or more of the displays  202  displays position information about the instrument, for example, as determined by the localization system  90  ( FIG. 15 ). In some embodiments, one or more of the displays  202  displays a preoperative model of the patient&#39;s luminal network  130 . The positional information can be overlaid on the preoperative model. The displays  202  can also display image information received from a camera or another sensing device positioned on the instrument within the luminal network  130 . In some embodiments, a model or representation of the instrument is displayed with the preoperative model to help indicate a status of a surgical or medical procedure. 
     In some embodiments, the console base  201  includes a central processing unit (e.g., CPU or processor), a memory unit (e.g., computer-readable memory), a data bus, and associated data communication ports that are responsible for interpreting and processing signals such as camera imagery and tracking sensor data, e.g., from a medical instrument positioned within a luminal network of a patient. 
     The console base  201  may also process commands and instructions provided by the user  205  through control modules  203 ,  204 . In addition to the keyboard  203  and joystick  204  shown in  FIG. 17 , the control modules may include other devices, such as computer mice, trackpads, trackballs, control pads, controllers such as handheld remote controllers, and sensors (e.g., motion sensors or cameras) that capture hand gestures and finger gestures. A controller can include a set of user inputs (e.g., buttons, joysticks, directional pads, etc.) mapped to an operation of the instrument (e.g., articulation, driving, water irrigation, etc.). Using the control modules  203 ,  204  of the command console  200 , the user  205  may navigate an instrument through the luminal network  130 . 
       FIG. 18  illustrates a detail view of a distal end of an example medical instrument  300 . The medical instrument  300  may be representative of the endoscope  115  or steerable catheter  145  of  FIG. 16 . The medical instrument  300  may be representative of any medical instrument described throughout the disclosure, such as the endoscope  13  of  FIG. 1 , the ureteroscope  32  of  FIG. 3 , the laparoscope  59  of  FIG. 9 , etc. In  FIG. 18 , the distal end of the instrument  300  includes an imaging device  315 , illumination sources  310 , and ends of EM sensor coils  305 , which form an EM instrument sensor. The distal end further includes an opening to a working channel  320  of the instrument  300  through which surgical instruments, such as biopsy needles, cytology brushes, forceps, etc., may be inserted along the instrument shaft, allowing access to the area near the instrument tip. 
     EM coils  305  located on the distal end of the instrument  300  may be used with an EM tracking system to detect the position and orientation of the distal end of the instrument  300  while it is positioned within a luminal network. In some embodiments, the coils  305  may be angled to provide sensitivity to EM fields along different axes, giving the disclosed navigational systems the ability to measure a full 6 degrees of freedom (DoF): three positional DoF and three angular DoF. In other embodiments, only a single coil  305  may be disposed on or within the distal end with its axis oriented along the instrument shaft. Due to the rotational symmetry of such a system, it may be insensitive to roll about its axis, so only five degrees of freedom may be detected in such an implementation. Alternatively or additionally, other types of position sensors may be employed. 
     The illumination sources  310  provide light to illuminate a portion of an anatomical space. The illumination sources  310  can each be one or more light-emitting devices configured to emit light at a selected wavelength or range of wavelengths. The wavelengths can be any suitable wavelength, for example, visible spectrum light, infrared light, x-ray (e.g., for fluoroscopy), to name a few examples. In some embodiments, the illumination sources  310  can include light-emitting diodes (LEDs) located at the distal end of the instrument  300 . In some embodiments, the illumination sources  310  can include one or more fiber optic fibers extending through the length of the endoscope to transmit light through the distal end from a remote light source, for example, an x-ray generator. Where the distal end includes multiple illumination sources  310 , these can each be configured to emit the same or different wavelengths of light as one another. 
     The imaging device  315  can include any photosensitive substrate or structure configured to convert energy representing received light into electric signals, for example, a charge-coupled device (CCD) or complementary metal-oxide semiconductor (CMOS) image sensor. Some examples of the imaging device  315  can include one or more optical fibers, for example, a fiber optic bundle, configured to transmit light representing an image from the distal end  300  of the endoscope to an eyepiece and/or image sensor near the proximal end of the endoscope. The imaging device  315  can additionally include one or more lenses and/or wavelength pass or cutoff filters as required for various optical designs. The light emitted from the illumination sources  310  allows the imaging device  315  to capture images of the interior of a patient&#39;s luminal network. These images can then be transmitted as individual frames or series of successive frames (e.g., a video) to a computer system such as command console  200 . As mentioned above and as will be described in greater detail below, the images captured by the imaging device  315  (e.g., vision data  92  of  FIG. 15 ) can be utilized by the navigation or localization system  95  to determine or estimate the position of the instrument (e.g., the position of the distal tip of the instrument  300 ) within a luminal network. 
     III. Image-Based Airway Analysis and Mapping 
     Embodiments of the disclosure relate to systems and techniques for image-based airway analysis and mapping. As used herein, image-based airway analysis may refer to identifying within an image one or more airways associated with one or more branches of a luminal network and determining branching information indicative of how the current airway in which the image is captured branches into the detected “child” airways. For example, an image-based airway analysis system may capture an image of an interior of a luminal network using an imaging device positioned on an instrument within the luminal network, and the image-based airway analysis system may analyze the image to identify one or more airways shown in the image. As used herein, image-based airway mapping may refer to mapping the airways identified in the image to corresponding airways or branches of the luminal network indicated by, for example, the preoperative model data. For example, an image-based airway mapping system may be configured to identify which airways or branches of a given luminal network correspond to the airways or branches identified in the captured images. These systems and techniques may be used to determine or estimate the position of an instrument within the luminal network. In certain implementations, these systems and techniques may be used in conjunction with various other navigation and localization modalities (e.g., as described above with reference to  FIG. 15 ). 
     A. Overview of Image-Based Airway Analysis and Mapping. 
     The ability to navigate inside a luminal network may be a feature of the robotically-controlled surgical systems described herein. As used herein, navigation may refer to locating or determining the position of an instrument within a luminal network. The determined position may be used to help guide the instrument to one or more particular areas of interest within the luminal network. In some embodiments, the robotically-controlled surgical systems utilize one or more independent sensing modalities to provide intraoperative navigation for the instrument. As shown in  FIG. 15 , the independent sensing modalities may provide position data (e.g., EM data  93 ), vision data  92 , and/or robotic command and kinematics data  94 . These independent sensing modalities may include estimation modules configured to provide independent estimates of position. The independent estimates can then be combined into one navigation output, for example, using localization module  95 , which can be used by the system or displayed to the user. Image-based airway analysis and mapping may provide an independent sensing modality, based on vision data  92 , that can provide an independent estimate of position. In particular, in some instances image-based airway analysis and mapping provides a combination of a sensing modality and a state/position estimation module that estimates which lumen or branch of a luminal network an imaging device of the instrument is located based on one or more images captured by the imaging device. In some embodiments, the estimate provided by image-based airway analysis and mapping may be used alone or with other position estimates to determine a final position estimate that can be used by the system or displayed to the user. In some embodiments, the image-based airway analysis and mapping systems and methods described herein may base its estimate on prior position estimates determined using a plurality sensing modalities. 
       FIG. 19  illustrates an example method  400  for image-based airway analysis and mapping. The method  400  may be implemented in various robotically-controlled surgical systems as described herein. The method  400  may include two steps or blocks: detecting airways in an image (block  402 ) and mapping the detected airways to corresponding airways (e.g., indicated by the preoperative model data) of the luminal network (block  404 ). 
     At block  402 , the method  400  detects one or more airways within an image. As noted above, during a medical procedure, an instrument may be positioned within a luminal network (see  FIG. 16 ). As shown in  FIG. 18 , the instrument may include an imaging device  315  (such as a camera) positioned thereon. The imaging device  315  may capture images of the interior of the luminal network. For example, at a particular instant, the imaging device  315  may capture an image of the interior of the particular airway of the luminal network in which the instrument is currently positioned. At block  402 , the method  400  can analyze the image to detect one or more airways within the image. For example, an airway detected within the image may be a set of pixels that satisfy an airway detection condition (e.g., having a pixel intensity greater than a threshold value). The detected airway may be the current airway in which the image is captured by the imaging device  315  and/or one or more child airways (e.g., subsequent branches of the luminal network) of the current airway. Block  402  may involve image analysis that processes an image to determine the number and location of the airways shown in the image. In certain implementations, if the image is determined to contain one or more airways, various features of the airways may also be determined. Such features may include determining a shape or contour of the detected airways and/or determining a centroid of the detected airways. 
     At block  404 , the method  400  maps the one or more detected airways to specific airways of the luminal network. At block  404 , the method  400  determines which airways of the luminal network branches into which other subsequent airways of the luminal network. For example, based on certain preoperative model data (e.g., CT data), the system may be aware of the airways that are expected to be captured in a given image (e.g., based on the current location of the imaging device  315 ). Upon detecting one or more airways in the image at block  402 , the method  400  may map the detected airways to the expected airways based on the preoperative model data. 
     By mapping the airways detected in the camera image to corresponding expected airways in the luminal network, the method  400  may provide an estimate of position for the instrument. For example, using the method  400 , the system or the instrument can identify which airways the instrument “sees” and use this information to estimate, within the luminal network, the airway in which the instrument is currently located and the airway that the instrument is about to enter. 
     B. Image-Based Airway Analysis. 
     Image-based airway analysis may include analyzing an image captured by the imaging device  315  of an instrument positioned within a luminal network to detect one or more airways in the image.  FIG. 20  provides an example image  500  of an interior of a branch of a luminal network. In the illustrated example, the image  500  is an interior image of an airway of a lung, although the image  500  may be representative of any type of luminal network. Two subsequent airways  502  are shown in the image  500 . The airways  502  are connected to the current airway from which the image is captured. 
     Image-based airway analysis can include a method whereby a computer system can recognize the airways  502  computationally. In some cases, the image  500  includes two classes of pixels: (1) pixels representing walls of the luminal network (e.g., tissue), and (2) pixels representing airways (e.g., airway openings). According to certain embodiments, the image-based airway analysis can systematically detect these two classes of pixels to identify and detect airways within an image. For example, the airways  502  may be detected by classifying the pixels into these two classes based on the pixel intensity. Image analysis and detection methods based on pixel intensity are described in greater detail in U.S. patent application Ser. No. 15/783,903, the contents of which are herein incorporated in its entirety. 
     C. Image-Based Airway Mapping 
     Image-based airway mapping techniques described herein may be used to determine which branches of the luminal network are associated with the detected branches or airways. That is, image-based airway mapping can determine which subsequent branches of the luminal network are connected to the current branch from which the image is captured. By mapping the detected airways to branches of the luminal network, the position of the instrument within the luminal network can be determined. Further, an estimate or prediction of which branch the instrument will be moved into can also be obtained. 
     In some embodiments, detected airways can be mapped to branches of the luminal network by comparing features of the detected airways to features of the branches of the luminal network. The features of the detected airways may be determined through image analysis as described above. The features of the branches of the luminal network can be determined from a model of the luminal network, such as a preoperative model of the luminal network. Further, in certain embodiments, mapping detected airways to branches of the luminal network can be based on a current position estimate of the instrument within the luminal network. The current position estimate can be determined based on various sensing modalities as described above with reference to  FIG. 15 . Mapping detected airways to branches of the luminal network based on a current position estimate can improve the efficiency, speed, and/or accuracy of the mapping process. For example, given a current position estimate, features of the detected airways can be compared to features of expected subsequent branches. This may minimize the computational load required to perform the mapping and improve mapping speed. 
       FIG. 21  illustrates a simplified representation of a luminal network  1000 . The luminal network  1000  comprises a plurality of branches (e.g., lumens, segments, airways, etc.)  1002 ,  1004 ,  1006 ,  1008 ,  1010 ,  1012 ,  1014 ,  1016 . The luminal network  1000  also comprises bifurcations  1020 ,  1022  and trifurcation  1024  connecting various branches to each other. In the example of  FIG. 21 , the branches  1004 ,  1006  are in the same generation, and the branches  1008 ,  1010 ,  1012 ,  1014 ,  1016  are in the same generation. In some embodiments, the luminal network  1000  may represent a portion of a bronchial network of a lung, and the branches may represent airways. Although many example embodiments of the present disclosure are described with reference to airways in a bronchial network, the embodiments are not limited as such and may be extended to other types of branches in other types of luminal networks. 
     The luminal network  1000  may be represented by a model. In some embodiments, the model is determined preoperatively. For example, preoperative model data  91  (i.e., information about the preoperative model) may be stored and made available to the navigation and localization system  90  ( FIG. 15 ). In other embodiments, at least a portion of the model is determined intraoperatively. As will be described below as an example, image-based airway mapping can be configured to map the detected branches to the branches of the luminal network  1000  generated based on the preoperative model data  91 . 
     D. Potential Challenges with Image-Based Airway Detection 
     In some cases, the images captured by a bronchoscopic camera may contain airways from different generations. In such cases, the number of airways detected by the image-based airway detection methods described herein may be incorrect. For example,  FIG. 22  shows image  2200 ( a ) (left) and image  2200 ( b ) (right) captured in the branch  1002  of the luminal network  1000  of  FIG. 21 . In the example of  FIG. 22 , airway projections have been added to the images  2200 ( a ),  2200 ( b ) to indicate the number and locations of the branches expected to be seen from the current camera location. 
     The image-based airway detection method performed on the image  2200 ( a ) has resulted in four detected airways as shown in the image  2200 ( a ). Such a result may cause the system to determine that the current airway branches into the four detected branches. However, as indicated by the hierarchical structure of  FIG. 21 , such a determination would be incorrect. The preoperative model data (e.g., hierarchical structure of the luminal network  1000  illustrated in  FIG. 21 ) indicates (correctly, and in a manner consistent with the preoperative model data) that the branch  1002  from which the image  2200 ( a ) is captured is expected to branch into two branches (i.e. branches  1004  and  1006 ), and not four branches as detected in the image  2200 ( a ). While the image  2200 ( a ) clearly shows four airways, three of the airways pictured at the bottom right corner of the image  2200 ( a ) are “grandchildren” (i.e. branches  1012 ,  1014 ,  1016 ) of the current branch  1002  that branched out from the branch  1006  that is immediately subsequent to the current branch  1002  (i.e. “child” of the current branch  1002 ). 
     Thus, in some embodiments, by utilizing the preoperative model data indicative of the number (i.e. count and/or location) of airways to be present in a given image, the airway analysis and mapping systems and methods of the present disclosure can detect the correct number of airways, as illustrated in the image  2200 ( b ). 
     E. Airway Analysis 
       FIG. 23A  illustrates an example airway analysis and mapping system  2300 A. As shown, the airway analysis and mapping system  2300 A includes an airway tracking module  2300 A- 1 , an airway association module  2300 A- 2 , and an airway merging module  2300 A- 3 . The airway analysis and mapping system  2300 A receives as input (i) image data (e.g., image captured using an imaging device) from an image data store  2310  ( ii ) model data (e.g., preoperative model data such as fluoroscopy data, MRI data, ultrasound imaging data, x-ray data, and the like) from a preoperative model data store  2320 , (iii) sensor data (e.g., EM data, vision data, robot data, shape sensing fiber data, and the like) from a sensor data store  2330  and outputs airway data (e.g., location, size, and center of identified or merged airways, mapping between identified or merged airways and preoperative model data, and the like) to the airway data store  2340 . The airway tracking module  2300 A- 1  identifies the airway(s) in each image in the image data. The airway association module  2300 A- 2  associates the airway(s)s in current image with the airway(s) in prior images. The airway merging module  2300 A- 3  determines whether two or more airways should be merged based on their relationship, for example, using the sensor data and the preoperative model data. The process of identifying, associating, and merging airways according to various embodiments is described in greater detail below with reference to  FIGS. 23B, 24, and 25 . 
       FIG. 23B  illustrates the temporal context in which the image-based airway analysis according to example embodiments is performed. For simplicity, one or more steps are described as being performed by a system (e.g., the airway analysis and mapping system  2300 A). 
     As shown, a series of images (i.e., images t 0 , t 1 , . . . ) are captured by an imaging device on a medical instrument navigating the luminal network of a patient, and images captured at different times (e.g., t 0  and t 1 ) undergo airway tracking, airway association, and airway merging. At a high level, this process of performing airway tracking, airway association, and airway merging analyzes a stream of images captured by the imaging device to compare locations of currently detected airways with estimated locations of airways detected in prior images and then determines a relationship between the airways detected in the current and prior images to determine whether the airways should be merged. The stream of images, or data derived therefrom, such as airway location information, may be stored by the system to perform the analysis. Temporal airway tracking, airway association, and airway merging are now described in greater detail. 
       FIG. 24  illustrates the spatial nature of the image-based airway analysis according to example embodiments. As shown, the airways in the previous and current images can exhibit a variety of different types of spatial relationship (e.g., one-to-one, one-to-many, many-to-one, zero-to-one, and one-to-zero). These examples are described in greater detail below in connection with Airway Association. 
     E.1. Temporal Airway Tracking 
     At a high level, image-based temporal tracking involves estimating the status (e.g., locations and sizes) of the airways in a current image relative to the status of the airways in a previous image. As shown in  FIG. 23B , the airway tracking process receives as input a current image at t 1  and airway information derived from a prior image, say prior image at t 0 . Based on the input, the system can determine an expected location of the prior airway relative to the current image and determine the current locations of the airways detected in the current image. 
     This process of identifying current locations of airways and expected locations of past airways is shown in  FIG. 25 . For example, in the first row, at time t 0  locations of airways A and B are identified, as represented in solid boxes. At time t 1  the temporal airway tracking receives as input the detected locations of A and B and may optionally estimate an updated location for these airways based on, for example, movement of the scope using, as way of example and not limitation, optical flow techniques. Examples of optical flow techniques may include motion detection, object segmentation calculations, luminance, motion compensated encoding, stereo disparity measurement, etc. The estimated locations of prior airways at time t 1  are shown in dashed boxes. The temporal airway tracking also analyzes the current image to detect locations of airways detectable in the current image at time t 1 . The current locations of the detected airways at the image at time t 1  is shown in solid boxes.  FIG. 25  is described in greater detail below in connection with Airway Association. 
     Accordingly, the airway tracking process determines, for a current time, the estimated locations of prior airways relative to the current image and the locations of airways currently detected in the image data for the current time. 
     E.2. Airway Association Based on Temporal and Spatial Analysis 
     In general, Airway Association, as executed by the system, may create a relationship between the airways detected in prior images and the airways detected in the current images. Airway Association creates these relationships based on the locations of the prior airways and the locations of the detected airways as may be determined by the airway tracking. A relationship may represent cases where a prior airway is now detected as two separate airways. Such situations that may cause an airway to be depicted as two different airways include, but not be limited to: detecting airways visible through another airway (e.g., descendent airways); and detecting a transition where an airway initially appears as a single airway but then become apparent that the single airway is actually multiple airways located in close proximity with each other. Further, in some cases, an airway that is not originally part of a prior image may become visible and the Airway Association may take actions to avoid relating that new airway with prior airways. 
       FIG. 24  illustrates examples of the type of relationship that can be exhibited by the airways in the previous and current images. As shown in  FIG. 24 , example relationships may include a one-to-one (A→A) association and a one-to-many (B→C,D) association illustrated in  2400 ( a ); a one-to-one (E→E) association and a many-to-one (F,G→H) association illustrated in  2400 ( b ); a zero-to-one (none→J) and a one-to-one (I→I) association illustrated in  2400 ( c ); and a one-to-zero (L→none) and a one-to-one (K→K) association illustrated in  2400 ( d ). The solid rectangles are bounding boxes encapsulating the detected airways in the current image (e.g., image t 1 ), and the dashed rectangles are bounding boxes encapsulating the detected airways in the previous image (e.g., image t 0 ). Although rectangles and/or bounding boxes are used in some embodiments, such embodiments are not limited as such and may be extended to embodiments using any polygons or other shapes. The associations may be stored by the system as a series of records where the airways are given unique identifiers and may include data that links the unique identifiers for the airways that are associated together. 
     The system may determine a correspondence between the airways detected in the previous image and the airways detected in the current image by comparing the overlap between the rectangles (or more broadly, the location and shape of the airways) illustrated in  FIG. 24 . In some embodiments, one or more of the following overlap ratio values (or any combination thereof) may be used to determine whether a given airway corresponds to another airway: 
     
       
         
           
             
               
                 
                   
                     
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     where ∩ and ∪ denote the intersection and union operators, respectively, between two rectangles b 1  and b 2 . The area (e.g., in pixels) of a rectangle or other bounding shape (which may be calculated by counting the pixels inside the rectangle) is denoted as Λ(⋅). min(p, q) and max(p, q) return the smaller value and larger values from p and q, respectively. 
     In some embodiments, an association between two rectangles (e.g., one corresponding to one or more airways detected in the previous image, and the other corresponding to one or more airways detected in the current image) is established if the following condition is satisfied: 
         O ( b   1   ,b   2 )&gt;τ  (4)
 
     where τ is a pre-defined threshold and O(b 1 , b 2 ) can be one of the three overlap ratio values (O 1 , O 2  and O 3 ). The three overlap ratio values are examples, and other overlap ratio values may be used instead of or in additional to these overlap ratio values. Although rectangles are used in the example of  FIG. 24 , in some embodiments, any geometric shapes (e.g., polygons or other shapes) may be used to determine the overlap between the airways. In such embodiments, the overlap between one set of one or more geometric shapes corresponding to one or more airways detected in the current picture and another set of one or more geometric shapes corresponding to one or more airways detected in the previous picture may be calculated. In some embodiments, the geometric shapes used for determining the overlap fully encapsulate the detected airways. In other examples, the geometric shapes do not fully encapsulate the detected airways and partially overlap with the airways. In the earlier example in which the identity of the airways to be merged is known, the system may skip part or all of the geometrical overlap analysis illustrated in  FIG. 24 . 
     Although the above has been described as creating associations that are one level deep (e.g., one association between two or more airways), it is to be appreciated that other embodiments may create chains that are greater than one level deep. For example, where airway X is associated with airways Y and Z, subsequent images may detect airways within Y, labelled Y′ and Y″, that meet the overlap threshold. In those cases, the system may then create a relationship between Y and Y′,Y″, such as an association chain that includes X→Y→Y′,Y″. 
     E.3. Adjusting the Overlap Threshold 
       FIG. 25  illustrates three examples in which incorrect associations may be determined due to an incorrect setting of the overlap ratio threshold. For example, the relationship shown in images  2500 ( a ) should be two one-to-one associations (e.g., A→A and B→B). However, the overlap illustrated in the fourth column of images  2500 ( a ) may cause airway B of the current image to be associated with airway A of the previous image (or airways A,B to be associated with airways A,B of the previous image). In such a case, the overlap threshold value may be adjusted so that the overlap illustrated in the fourth column of images  2500 ( a ) does not satisfy the overlap condition. Similarly images  2500 ( b ) and  2500 ( c ) illustrate other examples in which incorrect associations may be determined and how the overlap threshold value can be adjusted to prevent such associations (e.g., adjusted such that the overlap illustrated in the fourth column does not satisfy the overlap threshold). 
     In some embodiments, the overlap ratio threshold can be a design-time parameter configured by the designers of the system. However, in other embodiments, the system may track and record surgical data to track the failure rate of different overlap threshold values. Such systems may utilize such surgical data to train the system on the use of different overlap threshold values and update the system with an updated overlap threshold value that may lead to fewer failure rates. Furthermore, multiple systems may share the surgical data to increase the surgical data available for such training and selection of overlap threshold values. 
     E.4. Airway Merging Based on Temporal and Spatial Analysis 
     In Airway Merging, the system may merge two or more current airways based on the determined airway association(s) and data from preoperative model data. To determine whether to merge two or more airways in the current image, the system may determine the current location of the instrument and then determine the number of airways expected at the location from the preoperative model. It is to be appreciated that the system can utilize any number of approaches for determining a location of the instrument. As way of example and not limitation, such approaches may include the sensor fusion system described above, which may include one or more of the following sensor types: EM, vision, robot data, shape sensing fiber, and the like. 
     The preoperative model data may be stored in a form that allows for retrieval of expected airways for a given location. Such data may be generated before the procedure, where expected airways are indexed by the location of the instrument with respect to the preoperative model. As used here, location may be a positional location with or without orientation, a segment with or without an insertion depth within the segment, or any other representation of location. 
     Once the system determines that a set of airways in the current image are to be merged, the system may determine the new airway center of the merged airway. The new airway centers can then be used in the image based airway mapping methods described above. 
     In the example of merging two airways having a single parent airway, the airway centers of the two airways, respectively, can be denoted as {x 1 , y 1 } and {x 2 , y 2 }. According to one approach, the airway center of the merged airway may be calculated as a center of the respective center locations of the airways detected in the current image (e.g., geometric shapes representative of the airways in the current image). For example, such a value may be calculated as follows: 
     
       
         
           
             
               
                 
                   
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     In another example, the airway center of the merged airway may be calculated as a weighted center of the respective center locations of the airways detected in the current image (e.g., geometric shapes representative of the airways in the current image). For example, such a value may be calculated as follows: 
     
       
         
           
             
               
                 
                   
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                   ) 
                 
               
             
           
         
       
     
     where Λ 1  and Λ 2  are the areas (e.g., in pixels) of the two airways that are being merged, respectively. 
     In yet another example, the airway center of the merged airway can be calculated as a center of a bounding polygon that encapsulates the airways detected in the current image (e.g., geometric shapes representative of the airways in the current image). For example, if the coordinates of the left-top corner and right-bottom corner of the rectangle that encapsulates the first one of the two airways are denoted as {x 1   LT , y 1   LT } and {x 1   RB , y 1   RB }, and the coordinates of the left-top corner and right-bottom corner of the rectangle that encapsulates the second one of the two airways are denoted as {x 2   LT , y 2   LT } and {x 2   RB , y 2   RB }, the corners {x LT , y LT } and {x RB , y RB } of the encapsulation rectangle can be derived as follows: 
         x   LT =min( x   1   LT   ,x   2   LT )  (7)
 
         y   LT =min( y   1   LT   ,y   2   LT )  (8)
 
         x   RB =max( x   1   RB   ,x   2   RB )  (9)
 
         y   RB =max( y   1   RB   ,y   2   RB )  (10)
 
     Using these values, the airway center of the merged airway can be calculated as the center of the encapsulation rectangle, which is obtained as follows: 
     
       
         
           
             
               
                 
                   
                     { 
                     
                       x 
                       , 
                       y 
                     
                     } 
                   
                   = 
                   
                     { 
                     
                       
                         
                           
                             x 
                             
                               L 
                                
                               T 
                             
                           
                           + 
                           
                             x 
                             
                               R 
                                
                               B 
                             
                           
                         
                         2 
                       
                       , 
                       
                         
                           
                             y 
                             
                               L 
                                
                               T 
                             
                           
                           + 
                           
                             y 
                             
                               R 
                                
                               B 
                             
                           
                         
                         2 
                       
                     
                     } 
                   
                 
               
               
                 
                   ( 
                   11 
                   ) 
                 
               
             
           
         
       
     
     For example, the calculated merged center may be different from any other center location of the airways detected in the current image. As shown in the image  2200 ( b ) of  FIG. 22 , a graphical representation of the merged center of the merged airway may be output on a display of the system instead of the centers of the airways that were merged into the merged airway. In some cases, the merged center may be output on the display along with the centers of the airways that were merged. Although the example techniques of calculating the airway center of the merged airways are described above, other techniques of calculating the airway center representative of the merged airways can be used. 
     F. Example Image-Based Airway Analysis and Mapping Methods and Systems 
       FIG. 26  illustrates an example method  2600  for implementing the image-based airway analysis and mapping as described above. The method  2600  can be implemented in various of the robotically-controlled systems described throughout this disclosure. The method  2600  can be implemented with a robotic system including an instrument having an elongate body configured to be inserted into a luminal network. An imaging device can be positioned on the elongate body (e.g., on a distal end of the elongate body). The instrument can be attached to an instrument positioning device (e.g., a robotic arm) configured to move the instrument through the luminal network. A system employing the method  2600  can include a processor configured with instructions that cause a processor to execute the method  2600 . The method  2600  is provided by way of example only and the image-based airway analysis and mapping can be implemented using different steps than those shown in  FIG. 26 . For simplicity, the steps illustrated in  FIG. 26  are described as being performed by a system (e.g., one of the systems described herein or a system configured to perform one or more of the techniques described here). 
     At block  2602 , the system for mapping one or more airways in a luminal network captures a plurality of images within the luminal network with an imaging device positioned on an instrument. The plurality of images may comprise at least two images, where one of the images (e.g., current image, or second image) is captured at a time subsequent to the other image (e.g., previous image, or first image). The time at which the first image is captured may be referred to as a first time, and the time at which the second image is captured may be referred to as a second time. 
     At block  2604 , the system identifies one or more airways in the first image. In some embodiments, the system identifies a single airway in the first image. In other embodiments, the system identifies multiple airways in the first image. The system may utilize any of the airway identification or detection techniques described herein (e.g., pixel intensity analysis) or other techniques. For example, the identified airways may include one or more polygons or other geometrical shapes whose pixels satisfy the pixel intensity threshold specified by the airway detection method. In some embodiments, a point location such as a centroid is determined and associated with the detected airway. 
     At block  2606 , the system the system identifies two or more airways in the second image. In some embodiments, the system identifies a single airway in the second image. In other embodiments, the system identifies multiple airways in the second image. The system may identify the one or more airways in the second image in a manner similar to that utilized at block  2604 . 
     At block  2608 , the system determines, based on the first airway in the first image and the two or more airways in the second image, that an overlap condition is met. The determination that the overlap condition is met may involve, for example: determining a degree of spatial overlap between a first set of one or more geometric shapes representative of the first airway in the first image and a second set of one or more geometric shapes representative of the two or more airways in the second image; and determining the degree of spatial overlap meets or exceeds a defined overlap threshold value, parameter, or indicia. It is to be appreciated that blocks  2602 - 2606  may involve one or more features described with respect to Airway Tracking and Airway Association. That is, the system may track the location and sizes of airways in a current image as well as the expected locations and sizes of airways previously detected in prior images. When an overlap condition is met, the system may create an association with airways in a prior image and one or more images in a current image. Other associations, as explained above, may be one-to-one or many-to-one. 
     At block  2610 , the system accesses preoperative model data indicative of an expected count of airways corresponding to a location of the instrument during the second time. For example, although not illustrated in  FIG. 26 , the system may access a position state estimate for the instrument positioned within the luminal network. The position state estimate can include an identification of which branch the instrument is currently positioned (e.g., in the hierarchical structure of luminal network  1000  of  FIG. 21 ). Based on the position state estimate and the preoperative model data (e.g., CT images), the system may determine the expected count of airways corresponding to the location of the instrument during the second time (i.e. at the time the second image is captured). The position state estimate can be determined, for example, by the navigation and localization system  90  of  FIG. 15 . The position state estimate can be determined based on various and/or multiple position sensing modalities and information, such as preoperative model data  91 , vision data  92 , EM data  93  (or other position sensing data), and/or robotic command and kinematics data  94 . 
     At block  2612 , the system determines, based on the preoperative model data and the determination that the overlap condition is met, a mapping between the two or more airways in the second image and the airways in the preoperative model data. At this block, the system may determine the mapping between airways in the second image and the airways in the preoperative model data using Airway Merging (see section E.4). That is, according to some embodiments, the system may use the data derived from blocks  2602 - 2606  (Airway Tracking and Airway Association) and a count of the expected number of airways for the current location within the luminal network, as may be determined by preoperative model data, to determine whether or not to merge airways detected in the second image. The system may then map the merged or non-merged to airways in the preoperative model. Mapping airways to preoperative model data is further described in U.S. patent application Ser. No. 15/783,903, filed on Oct. 13, 2017, the entirety of which is incorporated herein by reference and appended hereto as Appendix A. 
     As just discussed, as part of block  2612 , the system may determine the mapping between the two or more airways in the second image and the airways in the preoperative model data based on the preoperative model by accessing the preoperative model data indicative of an expected count of airways corresponding to a location of the instrument during the second time. Accessing the preoperative model data to determine expected airway counts is now explained in greater detail. Although not illustrated in  FIG. 26 , the preoperative model data may include data structures that allow the system to retrieve the number of airways expected for a given location. Further, the system may access a position state estimate for the instrument positioned within the luminal network. The position state estimate can include an identification of which branch the instrument is currently positioned (e.g., in the hierarchical structure of luminal network  1000  of  FIG. 21 ). Based on the position state estimate and the preoperative model data (e.g., data derived from CT images, in one embodiment), the system may determine the expected count of airways corresponding to the location of the instrument during the second time (i.e. at the time the second image is captured) by accessing the aforementioned data structures. The position state estimate can be determined, for example, by the navigation and localization system  90  of  FIG. 15 . The position state estimate can be determined based on various and/or multiple position sensing modalities and information, such as preoperative model data  91 , vision data  92 , EM data  93  (or other position sensing data), and/or robotic command and kinematics data  94 . 
     As further examples, the preoperative model data may indicate that the system is expected to detect branches  1004 ,  1006  of the luminal network  1000 . If the system has detected two airways at block  2606 , the system may determine that merging is not needed based on the count of the two or more airways detected in the second image being equal to the expected count of airways indicated by the preoperative model data. In such a case, the system may map the two detected airways to the branches  1004 ,  1006 , respectively (e.g., based on the orientation of the image and/or the two airways) shown in  FIG. 21 . In the example of  FIG. 26 , based on the determination that the count of the two or more airways identified in the second image is equal to the expected count of airways indicated by the preoperative model data, the system, at block  2612 , may determine the mapping such that each one of the two or more airways identified in the second image is mapped to a different one of the airways in the preoperative model data. 
     In another example, as illustrated in  FIG. 22 , the preoperative model data may indicate that the system is expected to detect branches  1004 ,  1006  of the luminal network  1000 , but the system may have detected four airways at block  2606  (e.g., branches  1004 ,  1012 ,  1014 ,  1016 ). In such a case, the system may merge the four airways into two airways (e.g., by merging the detected airways corresponding to the branches  1012 ,  1014 ,  1016  into a single airway), and map the merged airway to the branch  1006 , and the unmerged airway to the branch  1004 . In the example of  FIG. 26 , based on the determination that the count of the two or more airways identified in the second image is different than the expected count of airways indicated by the preoperative model data, the system, at block  2612 , may determine the mapping such that at least two of the two or more airways identified in the second image is mapped to a single airway in the preoperative model data. In some embodiments, mapping comprises storing the association between the two or more airways in a database. For example, the system may store an indication that a given airway identified in the image branches into two or more airways indicated by the preoperative model data. 
     As discussed above, the system may confirm, based on the mapping between the two or more airways in the second image and the airways in the preoperative model data, a segment of the luminal network that the instrument is currently located. In some embodiments, the system may adjust, based on the mapping between the two or more airways in the second image and the airways in the preoperative model data, a confidence value of a position state estimate based on other data. For example, this other data may include EM data, robotic data, optical shape sensor data, and inertial measurement unit (IMU) data, any other input data described herein (e.g., input data  91 - 94  of  FIG. 15 ), or any combination thereof. Additionally or alternatively, the system may predict, based on the mapping between the two or more airways in the second image and the airways in the preoperative model data, a segment of the luminal network that the instrument will be entering. 
     In one embodiment of block  2608 , upon determining that a combination of airways in the current image overlaps with a combination of airways in the previous image by more than a threshold amount (or equal to the threshold amount), the system may merge the combination of airways in the current image into one or more airways such that the number of airways in the current image after the merger matches the number of airways in the combination of airways in the previous image. For example, the system may compare an overlap ratio value (e.g., any of the overlap ratio values in Equations (1)-(3) above) to a threshold overlap value to determine whether an association between the two combinations of airways exists. 
     As discussed above, the system may also determine the merged center of the merged airway. For example, the system may calculate a merged center location of the combination of airways in the current image (e.g., the set of geometric shapes representative of the combination of airways in the current image), where the merged center location is different than any of respective center locations of the airways detected in the current image (e.g., the geometric shapes in the set that are representative of the combination of airways in the current image). 
     In the case that the system determines that multiple pairings of combinations of airways satisfy the overlap condition (e.g., A→B having 60% overlap and A→C having 25% overlap), the system may determine the pairing of combinations of airways that has a greater overlap to be in association (e.g., A→B). In some embodiments, the determination of whether an overlap condition is satisfied is not one of degree (e.g., overlap ratio being greater than or equal to a threshold overlap ratio), and is instead a binary determination (e.g., whether the mid-point of three or more segments of a rectangle encapsulating the combination of airways in the current image is within a rectangle encapsulating the combination of airways in the parent image). 
     In some embodiments, the determination of whether the overlap condition is met may include determining a bounding polygon (e.g., rectangle or other shapes) that encapsulates the combination of airways in the previous image (e.g., the set of geometric shapes representative of the combination of airways in the previous image), determining a bounding polygon that encapsulates the combination of airways in the current image (e.g., the set of geometric shapes representative of the combination of airways in the current image), and determining the degree of spatial overlap based on an overlap between the two bounding polygons. 
     The image-based airway analysis and mapping techniques described herein compensate the Vision Branch Prediction (VBP) approach or other image-based branch prediction approaches. VBP may not able to perform correct airway mapping in some cases due to the visibility of airways that are from different generations in a given image (e.g., as illustrated in image  2200 ( a ) of  FIG. 22 ). The image-based airway analysis and mapping techniques described herein can determine or confirm the hierarchical structure of the airways in a luminal network and determine airway centers that correspond to the same generation. This helps establish correct airway mappings, as illustrated in image  2200 ( b ) of  FIG. 22 ). 
     G. Recursive Distance Searching 
     In some embodiments, upon determining that two or more airways in the current image are to be merged, the system can merge the airways using recursive distance searching. In doing so, the system may assume that an airway is closer to the airways from its same generation than other generations. For example, this assumption holds true in the example of  FIGS. 21 and 22 , where the airways in the third generation (e.g., branches  1012 ,  1014 ,  1016 , illustrated in the bottom right corner in  FIG. 22 ) are all closer to each other than the airway in the second generation (e.g., branch  1004 , illustrated in the top left corner in  FIG. 22 ). 
     In the recursive distance searching may involve a set P={p i } i=1   n  which represents a set of n airway centers detected in the current image. Each airway center may be denoted as p i ={x i , y i }. Then, the system may compute the following value: 
     
       
         
           
             
               
                 
                   
                     { 
                     
                       
                         p 
                         i 
                       
                       , 
                       
                           
                       
                        
                       
                         p 
                         j 
                       
                     
                     } 
                   
                   = 
                   
                     
                       
                         arg 
                          
                         
                             
                         
                          
                         min 
                       
                       
                         
                           
                             p 
                             i 
                           
                           , 
                           
                             
                               p 
                               j 
                             
                             ∈ 
                             P 
                           
                         
                         
                           i 
                           &lt; 
                           j 
                         
                       
                     
                      
                     
                         
                     
                      
                     
                        
                       
                         
                           p 
                           i 
                         
                         - 
                         
                           p 
                           j 
                         
                       
                        
                     
                   
                 
               
               
                 
                   ( 
                   12 
                   ) 
                 
               
             
           
         
       
     
     where ∥⋅∥ denotes the L2 norm operator. The above equation finds the pair of centers that have the closest distance to each other among the airways centers in the set P, and the system may assume that these two airways are from the same generation. The system then merges the two airways (e.g., obtains the airway center of the merged airway), for example, based on Equations (5)-(11). The system then removes p i  and p j  from P and add p k  into P and repeats this process (e.g., computation, merger, removal, and addition) until only one airway (or a desired number of airways) remains in P. 
     IV. Implementing Systems and Terminology 
     Implementations disclosed herein provide systems, methods and apparatus for image-based airway analysis and mapping for navigation robotically-controlled medical instruments. Various implementations described herein provide for improved navigation of luminal networks. 
     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 position estimation and robotic motion actuation 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.