Patent Publication Number: US-2023137726-A1

Title: Systems, Methods and Devices for Forming Respiratory-Gated Point Cloud for Four Dimensional Soft Tissue Navigation

Description:
FIELD OF INVENTION 
     The present invention generally relates to devices and methods associated with a medical procedure, and, in one embodiment, to medical devices for use in and methods associated with the respiratory system. 
     BACKGROUND 
     Image guided surgery (IGS), also known as image guided intervention (IGI), enhances a physician&#39;s ability to locate instruments within a patient&#39;s anatomy during a medical procedure. IGS can include 2-dimensional (2D), 3-dimensional (3D), and 4-dimensional (4D) applications. The fourth dimension of IGS can include multiple parameters either individually or together such as time, motion, electrical signals, pressure, airflow, blood flow, respiration, heartbeat, and other patient measured parameters. 
     Existing imaging modalities can capture the movement of dynamic anatomy. Such modalities include electrocardiogram (ECG)-gated or respiratory-gated magnetic resonance imaging (MRI) devices, ECG-gated or respiratory-gated computer tomography (CT) devices, standard computed tomography (CT), 3D Fluoroscopic images (Angio-suites), and cinematography (CINE) fluoroscopy and ultrasound. Multiple image datasets can be acquired at different times, cycles of patient signals, or physical states of the patient. The dynamic imaging modalities can capture the movement of anatomy over a periodic cycle of that movement by sampling the anatomy at several instants during its characteristic movement and then creating a set of image frames or volumes. 
     Although significant improvements have been made in these fields, a need remains for improved medical devices and procedures for visualizing, accessing and manipulating a targeted anatomical tissue. 
     SUMMARY OF THE INVENTION 
     Among the various aspects of the present invention may be noted devices for use in and methods associated with medical procedures; such devices and methods, for example, may include devices and methods that enhance a physician&#39;s ability to locate instruments within anatomy during a medical procedure, such as image guided surgery (IGS) or image guided intervention (IGI) and such devices and methods may further include devices and methods that facilitate accessing and manipulating a targeted anatomical tissue. 
     Briefly, therefore, one aspect of the present invention is a method for modifying or deforming a segmented image dataset for a region of a respiratory system of a patient to the corresponding anatomy of a patient&#39;s respiratory system. The method comprises (i) forming a respiratory-gated point cloud of data that demarcates anatomical features in a region of a patient&#39;s respiratory system at one or more discrete phases within a respiration cycle of a patient, (ii) density filtering the respiratory-gated point cloud, (iii) classifying the density filtered respiratory-gated point cloud according to anatomical points of reference in a segmented image dataset for the region of the patient&#39;s respiratory system, and (iv) modifying the segmented image dataset to correspond to the classified anatomical points of reference in the density filtered respiratory-gated point cloud. 
     Another aspect of the present invention is a method of preparing a segmented image dataset to match the anatomy of a patient&#39;s respiratory system. The method comprises forming a respiratory-gated point cloud of data that demarcates anatomical features in a region of a patient&#39;s respiratory system at one or more discrete phases within a respiration cycle of a patient. The method further comprises density filtering the respiratory-gated point cloud, classifying the density filtered respiratory-gated point cloud according to anatomical points of reference in a segmented image dataset for the region of the patient&#39;s respiratory system, registering the classified respiratory-gated point cloud to the segmented image dataset, comparing the registered respiratory-gated point cloud to a segmented image dataset to determine the weighting of points comprised by the classified respiratory-gated point cloud, distinguishing regions of greater weighting from regions of lesser weighting and modifying the segmented image dataset to correspond to the classified respiratory-gated point cloud. 
     A further aspect of the present invention is a method for simulating the movement of a patient&#39;s respiratory system during respiration. The simulation method comprises (i) forming a respiratory-gated point cloud of data that demarcates anatomical features in a region of a patient&#39;s respiratory system at one or more discrete phases within a respiration cycle of a patient, (ii) density filtering the respiratory-gated point cloud, (iii) classifying the density filtered respiratory-gated point cloud according to anatomical points of reference in a segmented image dataset for the region of the patient&#39;s respiratory system, (iv) creating a cine loop comprising a plurality of modified segmented image datasets through multiple modifications of the segmented image dataset to correspond to a plurality of classified anatomical points of reference in the respiratory-gated point cloud over the respiration cycle, and (v) displaying the cine loop comprising the plurality of modified segmented image datasets over the patient&#39;s respiration cycle. 
     A still further aspect of the present invention is a surgical catheter for use in medical procedures. The surgical catheter comprises an elongate flexible shaft having a longitudinal axis, a proximal end portion, a distal end portion, and a handle attached to the proximal end portion. The elongate flexible shaft further comprises an outer wall extending from the proximal end portion to the distal end portion. The surgical catheter further comprises a biopsy device at the distal end portion, and an actuation wire extending from the proximal end portion to the distal end portion to operate the biopsy device. Additionally, a steering mechanism is connected to the steering actuator wherein the distal end portion may be moved relative to the proximal end portion by manipulating the steering actuator. 
     A still further aspect of the present invention is an apparatus comprising a steerable catheter comprising a biopsy device for accessing or manipulating tissue. 
     A yet further aspect of the present invention is a surgical catheter for navigated surgery, the surgical catheter comprises an elongate flexible shaft having a longitudinal axis, a proximal end portion, a distal end portion, a side exit in the distal end portion, and a handle attached to the proximal end portion. The elongate flexible shaft further comprises an outer wall extending from the proximal end portion to the distal end portion, and an electromagnetic localization element at the distal end portion. A medical instrument housed within the elongate flexible shaft that is extendable along a path from a position within the outer wall and through the side exit to an extended position outside the outer wall, the medical instrument being disposed at an angle of at least 10 degrees relative to the longitudinal axis at the side exit when in the extended position. The position of the medical instrument along the path can be calibrated to the location of the electromagnetic localization element and displayed by a surgical instrument navigation system. 
     A further aspect of the present invention is a method of guiding a surgical instrument to a region of interest in a patient. The method comprises displaying an image of the region of the patient, inserting a flexible lumen into the region of the patient, inserting a surgical catheter comprising an electromagnetic localization element into the lumen, navigating the surgical catheter to the region of interest, detecting a location and orientation of the electromagnetic localization element, displaying, in real-time, a virtual representation of the surgical catheter and the medical instrument superimposed on the image based upon the location and orientation of the electromagnetic localization element, and performing a medical procedure at the region of interest. 
     A further aspect of the present invention is a method of placing a localization element in an organ of a patient for use in a medical procedure. The method comprises attaching a first localization element to tissue in a region of the organ of a patient using an endolumenal device. The attached localization element may be separate from the endolumenal device and is registered to a segmented image dataset. The body of the patient may then be modified such that the body does not match the segmented image dataset, and the position of the first localization element is identified from outside the patient&#39;s organ using a second localization element to facilitate a medical procedure. 
     Other objects and features will be in part apparent and in part pointed out hereinafter. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The details of the present invention, both as to its construction and operation can best be understood with reference to the accompanying drawings, in which like numerals refer to like parts, and in which: 
         FIG.  1    is a schematic illustration of an exemplary surgical instrument navigation system according to an embodiment of the present invention; 
         FIG.  2    is a flowchart that depicts a technique for simulating a virtual volumetric image of a body cavity from a point of view of a surgical instrument positioned within the patient according to an embodiment of the present invention; 
         FIG.  3 A  is an illustration showing an initially collected respiratory-gated point cloud and  FIG.  3 B  is an illustration showing a respiratory-gated point cloud registered to a patient&#39;s respiratory system according to an embodiment of the present invention; 
         FIG.  4    is an exemplary display from the surgical instrument navigation system according to an embodiment of the present invention; 
         FIG.  5    is a flowchart that depicts a technique for synchronizing the display of an indicia or graphical representation of the surgical instrument with the cardiac or respiration cycle of the patient according to an embodiment of the present invention; 
         FIG.  6    is a flowchart that depicts a technique for generating four-dimensional image data that is synchronized with the patient according to an embodiment of the present invention; 
         FIG.  7    is a front view of a patient during the generation of a respiratory-gated point cloud in the respiratory system of a patient using a catheter and a top panel illustrating that the respiratory-gated point cloud may be taken over the entire respiratory cycle of the patient according to an embodiment of the present invention; 
         FIG.  8    is a flow chart depicting the deformation of a segmented image dataset to a respiratory-gated point cloud according to an embodiment of the present invention; 
         FIG.  9    depicts an exemplary real-time respiration compensation algorithm according to an embodiment of the present invention; 
         FIG.  10    is a flow chart depicting the registration of a respiratory-gated point cloud to a segmented image dataset and the subsequent deformation of a segmented image dataset to the respiratory-gated point cloud according to an embodiment of the present invention; 
         FIG.  11 A  illustrates a generated image of an anterior to posterior (A-P) view of a region (or tissue) of interest of a patient and  FIG.  11 B  illustrates a generated image of a lateral view of a region (or tissue) of interest of a patient according to an embodiment of the present invention; 
         FIG.  12    is a perspective view of a generated image of a region (or tissue) of interest of a patient according to an embodiment of the present invention; 
         FIGS.  13 A and  13 B  show an alternative method of generating a 4D dataset for 4D thoracic registration using surgical instrument navigation system according to an embodiment of the present invention; 
         FIG.  14    shows an apparatus and method for respiratory 4D data acquisition and navigation according to an embodiment of the present invention; 
         FIG.  15 A  is a side perspective view of the implanting of a first localization element and  FIG.  15 B  is a side perspective view of locating the first localization element with a second localization element according to an embodiment of the present invention; 
         FIGS.  16  and  16 A  show a side perspective view and a cutaway view of a steerable catheter according to an embodiment of the present invention; 
         FIG.  17 A  shows a side perspective view of a steerable catheter and associated possible biopsy devices including a forceps device ( FIG.  17 B ), an auger device ( FIG.  17 E ), a boring bit device ( FIG.  17 C ), a brush device ( FIG.  17 D ), an aspiration needle device ( FIG.  17 F ), and a side exiting tip component ( FIG.  17 G ) according to various embodiment of the present invention; 
         FIGS.  18 A and  18 B  are a side views of a steerable catheter deflected by actuating the steering actuator according to an embodiment of the present invention; 
         FIGS.  19  and  19 A  are a top cutaway view and a cross-section view of a navigated steerable catheter wherein the steerable shaft portion comprises spline rings according to an embodiment of the present invention; 
         FIGS.  20 A,  20 B, and  20 C  show a side, top, and bottom view of the distal end portion of a steerable catheter wherein the biopsy device comprises an angled or directional pattern visible via fluoroscopic imaging according to an embodiment of the present invention; 
         FIGS.  21 A,  21 B, and  21 C  show a side, top, and bottom view of the distal end portion of a steerable catheter wherein the biopsy device comprises markers visible via fluoroscopic imaging according to an embodiment of the present invention; 
         FIGS.  22  and  22 A  show a side view of the distal end portion of a steerable catheter wherein the biopsy device comprises an echogenic pattern of partially spherical indentations visible via ultrasonic imaging according to an embodiment of the present invention; 
         FIGS.  23  and  23 A  show a side view of the distal end portion of a steerable catheter wherein the biopsy device comprises an echogenic pattern that is visible via ultrasonic imaging according to an embodiment of the present invention; 
         FIG.  24    is a side cutaway view of the distal end portion of a steerable catheter wherein the biopsy device comprises an actuatable sensor-equipped forceps device according to an embodiment of the present invention; 
         FIGS.  25 A and  25 B  are side cutaway views of the distal end portion of a steerable catheter wherein the biopsy device comprises a navigated auger device according to an embodiment of the present invention; 
         FIGS.  26 A and  26 B  are side cutaway views of the distal end portion of a steerable catheter wherein the biopsy device comprises a non-navigated auger device according to an embodiment of the present invention; 
         FIG.  27    is a side view of the distal end portion of a steerable catheter wherein the biopsy device comprises an auger device having wherein the tissue collection region comprises a viewing window according to an embodiment of the present invention; 
         FIGS.  28 A and  28 B  are side cutaway views of the distal end portion of a steerable catheter wherein the biopsy device comprises a navigated boring bit device according to an embodiment of the present invention; 
         FIG.  29    is a side perspective cutaway view of the distal end portion of a steerable catheter wherein the biopsy device comprises a boring bit device according to an embodiment of the present invention; 
         FIGS.  30 A and  30 B  are side cutaway views of the distal end portion of a steerable catheter wherein the biopsy device comprises a non-navigated boring bit according to an embodiment of the present invention; 
         FIGS.  31 A and  31 B  are side cutaway views of the distal end portion of a steerable catheter wherein the biopsy device comprises a navigated boring bit device wherein the actuation wire is hollow and to which a vacuum pressure is applied to assist in the removal of tissue according to an embodiment of the present invention; 
         FIG.  32    is a side perspective cutaway view of the distal end portion of a steerable catheter wherein the biopsy device comprises a boring bit device wherein the actuation wire is hollow and to which a vacuum pressure is applied to assist in the removal of tissue according to an embodiment of the present invention; 
         FIG.  33    is a side cutaway view of the distal end portion of a steerable catheter wherein the biopsy device comprises an aspiration needle according to an embodiment of the present invention; 
         FIGS.  34 A and  34 B  show a side view and a side perspective cutaway view of the distal end portion of a steerable catheter wherein the biopsy device comprises a brush device according to an embodiment of the present invention; 
         FIG.  35    is a front perspective view of the surgical catheter with a side exiting medical instrument according to an embodiment of the present invention; 
         FIG.  36    is a side view illustrating the calibration of path of the medical instrument as it extends out the side exit of the surgical catheter according to an embodiment of the present invention; 
         FIG.  37    is a side cutaway view of the surgical catheter wherein the medical instrument may comprise possible devices including a forceps device ( FIG.  37 A ), a boring bit device ( FIG.  37 B ), a brush device ( FIG.  37 C ), and an auger device ( FIG.  37 D ) according to various embodiment of the present invention; 
         FIG.  38    is a side cutaway view of the surgical catheter with a medical instrument extended through the side exit, wherein the medical instrument is an aspiration needle, and a localization element is at the distal end portion of an elongate flexible shaft according to an embodiment of the present invention; 
         FIG.  39    is a side cutaway view of the surgical catheter with a medical instrument extended through the side exit and a localization element is at the tip of the side exiting tip component according to an embodiment of the present invention; 
         FIG.  40    is a side cutaway view of the surgical catheter wherein the medical instrument comprises a shape memory alloy extended out of the side exit according to an embodiment of the present invention; 
         FIGS.  41 A- 41 D  are side views of the medical instrument in the extended position disposed at various angles relative to the longitudinal axis of an elongate flexible shaft at a side exit according to an embodiment of the present invention; 
         FIG.  41 E  is a side view of the medical instrument in the extended position disposed at an angle relative to the longitudinal axis of an elongate flexible shaft at a side exit wherein an arc is introduced into the elongate flexible shaft according to an embodiment of the present invention; 
         FIGS.  42 A,  42 B, and  42 C  are a side, top, and bottom view of the surgical catheter comprising an angled or directional pattern visible via fluoroscopic imaging according to an embodiment of the present invention; 
         FIGS.  43 A,  43 B, and  43 C  are a side, top, and bottom view of the surgical catheter comprising markers visible via fluoroscopic imaging according to an embodiment of the present invention; 
         FIGS.  44 A,  44 B, and  44 C  are a side, top, and bottom view of the surgical catheter comprising rings visible via fluoroscopic imaging according to an embodiment of the present invention; 
         FIGS.  45  and  45 A  are a side view, and detailed partially cut-away view of the surgical catheter comprising an echogenic pattern visible via ultrasonic imaging according to an embodiment of the present invention; 
         FIGS.  46  and  46 A  are a side view, and detailed partially cut-away view of the surgical catheter comprising an echogenic pattern of partially spherical indentations visible via ultrasonic imaging according to an embodiment of the present invention; 
         FIG.  47    is a side cutaway view of the surgical catheter comprising an echogenic pattern visible via ultrasonic imaging that is on the medical instrument according to an embodiment of the present invention; 
         FIG.  48    is a side cutaway view of the surgical catheter with a medical instrument extended through the side exit and a localization element in the distal end portion of the elongate flexible shaft according to an embodiment of the present invention; 
         FIGS.  49 A,  49 B, and  49 C  show a side, top, and bottom view of the surgical catheter comprising an angled or directional pattern visible via fluoroscopic imaging according to an embodiment of the present invention. 
         FIGS.  50 A and  50 B  are side views of a port offset device according to an embodiment of the present invention; 
         FIGS.  51 A and  51 B  are side views of a port offset device according to an embodiment of the present invention; 
         FIGS.  52 A,  52 B,  52 C, and  52 D  are perspective views of affixing localization elements to existing surgical instruments according to an embodiment of the present invention; 
     
    
    
     DETAILED DESCRIPTION 
     Referring now to  FIG.  1   , a surgical instrument navigation system  10  in accordance with one embodiment of the present invention is operable to visually simulate a virtual volumetric scene within the body of a patient, such as an internal body cavity, from a point of view of a surgical instrument  12  residing in the cavity of a patient  13 . The surgical instrument navigation system  10  comprises a surgical instrument  12 , a processor  16  having a display  18 , and a tracking subsystem  20 . The surgical instrument navigation system  10  may further include (or is accompanied by) an imaging device  14  that is operable to provide image data to the system. 
     Imaging device  14  can be used to capture images or data of patient  13 . Imaging device  14  can be, for example, a computed tomography (CT) device (e.g., respiratory-gated CT device, ECG-gated CT device), a magnetic resonance imaging (MRI) device (e.g., respiratory-gated MRI device, ECG-gated MRI device), an X-ray device, or any other suitable medical imaging device. In one embodiment, imaging device  14  is a computed tomography—positron emission tomography device that produces a fused computed tomography—positron emission tomography image dataset. Imaging device  14  is in communication with processor  16  and can send, transfer, copy and/or provide image data taken (captured) of patient  13  to processor  16 . 
     Processor  16  includes a processor-readable medium storing code representing instructions to cause processor  16  to perform a process. Processor  16  may be, for example, a commercially available personal computer, or a less complex computing or processing device that is dedicated to performing one or more specific tasks. For example, processor  16  may be a terminal dedicated to providing an interactive graphical user interface (GUI). Alternatively, processor  16  may be a commercially available microprocessor, an application-specific integrated circuit (ASIC) or a combination of ASICs, which are designed to achieve one or more specific functions, or enable one or more specific devices or applications. In yet another embodiment, processor  16  may be an analog or digital circuit, or a combination of multiple circuits. 
     Processor  16  preferably includes a memory component (not shown) comprising one or more types of memory devices. For example, the memory component may comprise a read only memory (ROM) device and/or a random access memory (RAM) device. The memory component may also comprise other types of memory devices that may be suitable for storing data in a form retrievable by processor  16 . For example, the memory component may comprise electronically programmable read only memory (EPROM), erasable electronically programmable read only memory (EEPROM), flash memory, as well as other suitable forms of memory. The memory component may also comprise a non-transitory processor-readable medium. Processor  16  may also include a variety of other components, such as for example, coprocessors, graphic processors, etc., depending upon the desired functionality of the code. Processor  16  can store data in or retrieve data from the memory component. 
     Processor  16  may also comprise components to communicate with devices external to processor  16  by way of an input/output (I/O) component (not shown). According to one or more embodiments of the invention, the I/O component can include a variety of suitable communication interfaces. For example, the I/O component can include wired connections, such as standard serial ports, parallel ports, universal serial bus (USB) ports, S-video ports, local area network (LAN) ports, and small computer system interface (SCSI) ports. Additionally, the I/O component may include, for example, wireless connections, such as infrared ports, optical ports, Bluetooth® wireless ports, wireless LAN ports, or the like. 
     In one embodiment, processor  16  is connected to a network (not shown), which may be any form of interconnecting network including an intranet, such as a local or wide area network, or an extranet, such as the World Wide Web or the Internet. The network can be physically implemented on a wireless or wired network, on leased or dedicated lines, including a virtual private network (VPN). 
     In one embodiment, processor  16  can receive image data from imaging device  14  and generate a segmented image dataset using various segmentation techniques, such as Hounsfield unit thresholding, convolution, connected component, or other combinatory image processing and segmentation techniques. For example, in one embodiment processor  16  can determine a distance and direction between the position of any two data points within a respiratory-gated point cloud (as described in greater detail elsewhere herein) during multiple instants in time, and store the image data, as well as the position and distance data, within the memory component. Multiple images can be produced providing a visual image at multiple instants in time through the path of motion of the patient&#39;s body. 
     Surgical instrument  12  may be any medical device used in a medical procedure. In one embodiment, surgical instrument  12  comprises a relatively flexible catheter that may be guided to the region or tissue of interest. Thus, for example, surgical instrument  12  may comprise or be used to implant one or more surgical devices such as a guide wire, a pointer probe, a stent, a seed, an implant, or an endoscope. It is also envisioned that the surgical instruments may encompass medical devices which are used for exploratory purposes, testing purposes or other types of medical procedures. Additionally or alternatively, surgical instrument  12  may incorporate one or more localization elements  24  that are detectable by tracking subsystem  20 . As illustrated in  FIG.  10   , surgical instrument  12  is connected by wire to tracking subsystem  20 ; in alternative embodiments, surgical instrument  12  may be wirelessly connected to tracking subsystem  20 . 
     Imaging device  14  may be used to capture volumetric scan data (see box  32  of  FIG.  2   ) representative of an internal region of interest within patient  13 . The scan data, preferably three-dimensional data, may be obtained prior to and/or during surgery on patient  13  and stored in the memory component associated with processor  16 . It should be understood that volumetric scan data may be acquired using various known medical imaging devices  14 , including but not limited to a magnetic resonance imaging (MRI) device, a computed tomography (CT) imaging device, a positron emission tomography (PET) imaging device, a 2D or 3D fluoroscopic imaging device, and 2D, 3D or 4D ultrasound imaging devices. In the case of a two-dimensional ultrasound imaging device or other two-dimensional image acquisition device, a series of two-dimensional data sets may be acquired and then assembled into volumetric data as is well known in the art using a two-dimensional to three-dimensional conversion. 
     Dynamic reference frame  19  may be attached to patient  13  proximate to the region (tissue) of interest within the patient  13 . For ease of illustration, dynamic reference frame  19  is attached to the forehead of patient  13  in  FIG.  1   ; in an actual medical procedure, dynamic reference frame  19  may be located in a cavity, vessel or otherwise within patient  13 . In one embodiment, dynamic reference frame  19  includes localization elements detectable by the tracking subsystem  20  to enable dynamic reference frame  19  to function as a point of reference for tracking subsystem  20  during the procedure as further described below. 
     Tracking subsystem  20  is also configured to track localization elements  24  associated with surgical instrument  12 . In general, tracking subsystem  20  may comprise any tracking system typically employed in image guided surgery, including but not limited to an electromagnetic tracking system. An example of a suitable electromagnetic tracking subsystem is the AURORA electromagnetic tracking system, commercially available from Northern Digital Inc. in Waterloo, Ontario Canada. In one embodiment, tracking subsystem  20  is an electromagnetic tracking system, typically comprising an electromagnetic field generator  22  that emits a series of electromagnetic fields designed to engulf patient  13 , and localization elements  24  coupled to surgical instrument  12  could be coils that would receive an induced voltage that could be monitored and translated into a coordinate position of localization elements  24 . In certain embodiments, localization element  24  may be electrically coupled to twisted pair conductors to provide electromagnetic shielding of the conductors. This shielding prevents voltage induction along the conductors when exposed to the magnetic flux produced by the electromagnetic field generator. The twisted pair conductors extend from the localization element through surgical instrument  12 . 
       FIG.  2    illustrates a flowchart of a technique for simulating a virtual volumetric scene of a body cavity from a point of view of a surgical instrument positioned within the patient. Volumetric scan data captured by imaging device  14  (see box  32 ) may be registered to patient  13  (see box  34 ) using dynamic reference frame  19 . This registration process is sometimes referred to as registering image space to patient space. Often, the volumetric scan data captured by imaging device  14  is also registered to other image datasets, typically an image dataset acquired at an earlier point time or an atlas. Registration of the image space to patient space is accomplished through knowledge of the coordinate vectors of at least three non-collinear points in the image space and the patient space.  FIG.  3 A , for example, illustrates an initially generated point cloud superimposed on a segmented image dataset of a patient&#39;s respiratory system and  FIG.  3 B  illustrates a point cloud registered to a segmented image dataset of a patient&#39;s respiratory system. 
     Registration of image space to patient space for image guided surgery (see box  34  of  FIG.  2   ) can be completed by different known techniques. Registration can be performed in multiple ways: point registration, pathway registration, 2D/3D image registration, etc. Such registration may be performed using 4D-gating information to track the patient&#39;s motion such as respiration and/or heartbeat. For example, point-to-point registration may be accomplished by identifying points in an image space and then touching the same points in patient space. These points are generally anatomical landmarks that are easily identifiable on the patient. By way of further example, surface registration involves the user&#39;s generation of a surface in patient space by either selecting multiple points or scanning, and then accepting the best fit to that surface in image space by iteratively calculating with the processor until a surface match is identified. By way of further example, repeat fixation devices entail the user repeatedly removing and replacing a device (i.e., dynamic reference frame, etc.) in known relation to the patient or image fiducials of the patient. By way of further example, automatic registration is accomplished by first attaching the dynamic reference frame to the patient prior to acquiring image data. It is envisioned that other known registration procedures are also within the scope of the present invention, such as that disclosed in U.S. Pat. No. 6,470,207, which is hereby incorporated by reference in its entirety. Once registration is complete the system can determine potential regions of the image dataset that may not match the patient&#39;s real-time anatomy. After image registration (see box  34  of  FIG.  2   ) the image data may be rendered (see box  36  of  FIG.  2   ) as a volumetric perspective image and/or a surface rendered image of the region of interest based on the scan data using rendering techniques well known in the art. 
     During surgery, surgical instrument  12  is directed by the physician or other healthcare professional to the region (or tissue) of interest within patient  13 . Tracking subsystem  20  preferably employs electromagnetic sensing to capture position data (see box  37  of  FIG.  2   ) indicative of the location and/or orientation of surgical instrument  12  within patient  13 . Tracking subsystem  20  may be defined as an electromagnetic field generator  22  and one or more localization elements  24  (e.g., electromagnetic sensors) may be integrated into the items of interest, such as the surgical instrument  12 . In one embodiment, electromagnetic field generator  22  may be comprised of three or more field generators (transmitters) mounted at known locations on a plane surface and localization elements (receivers)  24  are further defined as a single coil of wire. The positioning of the field generators (transmitter) and the localization elements (receivers) may also be reversed, such that the generators are associated with surgical instrument  12  and the receivers are positioned elsewhere. Although not limited thereto, electromagnetic field generator  22  may be affixed to an underneath side of the operating table that supports the patient. 
     In certain embodiments, localization element  24  comprises a six (6) degree of freedom (6DOF) electromagnetic sensor. In other embodiments, localization element  24  comprises a five (5) degree of freedom (5DOF) electromagnetic sensor. In other embodiments, localization element  24  comprises other localization devices such as radiopaque markers that are visible via fluoroscopic imaging and echogenic patterns that are visible via ultrasonic imaging. In yet other embodiments, localization elements  24  can be, for example, infrared light emitting diodes, and/or optical passive reflective markers. Localization elements  24  can also be, or be integrated with, one or more fiber optic localization (FDL) devices. In other embodiments surgical instrument  12  is non-navigated, such that it does not include any localization elements. 
     In operation, the field generators of localization device  22  generate magnetic fields which are detected by localization element  24 . By measuring the magnetic field generated by each field generator at localization element  24 , the location and orientation of localization element  24  may be computed, thereby determining position data for localization element  24  associated with surgical instrument  12 . Although not limited thereto, exemplary electromagnetic tracking subsystems are further described in U.S. Pat. Nos. 5,913,820; 5,592,939; and 6,374,134 which are incorporated herein by reference in their entirety. In addition, it is envisioned that other types of position tracking devices are also within the scope of the present invention. For instance, tracking subsystem  20  may comprise a non-line-of-sight device based on sonic emissions or radio frequency emissions. In another instance, a rigid surgical instrument, such as a rigid endoscope may be tracked using a line-of-sight optical-based tracking subsystem (i.e., LED&#39;s, passive markers, reflective markers, etc.). 
     Position data for localization element  24 , such as location and/or orientation data from the tracking subsystem  20  is in turn relayed to the processor  16 . Processor  16  is adapted to receive position/orientation data (see box  37  of  FIG.  2   ) from tracking subsystem  20  and the volumetric perspective and/or surface image data may be further manipulated (see box  38  of  FIG.  2   ) based on the position/orientation data for surgical instrument  12  received from tracking subsystem  20 . Specifically, the volumetric perspective or surface rendered image is rendered from a point of view which relates to position of the surgical instrument  12 . For instance, at least one localization element  24  may be positioned at the distal end of surgical instrument  12 , such that the image is rendered from a leading point on the surgical instrument. In this way, surgical instrument navigation system  10  of the present invention is able, for example, to visually simulate a virtual volumetric scene of an internal cavity from the point of view of surgical instrument  12  residing in the cavity without the use of an endoscope. It is readily understood that tracking two or more localization elements  24  which are embedded in surgical instrument  12  enables orientation of surgical instrument  12  to be determined by the system  10 . 
     As surgical instrument  12  is moved by the physician or other healthcare professional within the region of interest, its position and orientation may be tracked and reported on a real-time basis by tracking subsystem  20 . Referring again to  FIG.  2   , the volumetric perspective image may then be updated by manipulating (see box  38 ) the rendered image data (see box  36 ) based on the position of surgical instrument  12 . The manipulated volumetric perspective image (see box  38 ) is displayed  40  as a primary image on a display device  18  associated with the processor  16 . The display  18  is preferably located such that it can be easily viewed by the physician or other healthcare professional during the medical procedure. In one embodiment, the display  18  may be further defined as a heads-up display or any other appropriate display. The image may also be stored by processor  16  for later playback, should this be desired. 
     It is envisioned that the primary of the region of interest may be supplemented by other secondary images. For instance, known image processing techniques may be employed to generate various multi-planar images of the region of interest. Alternatively, images may be generated from different view points (see box  39 ) as specified by a physician or other healthcare professional, including views from outside of the vessel or cavity or views that enable the user to see through the walls of the vessel using different shading or opacity. In another instance, the location data of the surgical instrument may be saved and played back in a movie format. It is envisioned that these various secondary images may be displayed simultaneously with or in place of the primary perspective image. 
     In addition, surgical instrument  12  may be used to generate real-time maps corresponding to an internal path traveled by the surgical instrument or an external boundary of an internal cavity. Real-time maps may be generated by continuously recording the position of the instrument&#39;s localized tip and its full extent. A real-time map may be generated by the outermost extent of the instrument&#39;s position and minimum extrapolated curvature as is known in the art. The map may be continuously updated as the instrument is moved within the patient, thereby creating a path or a volume representing the internal boundary of the cavity. It is envisioned that the map may be displayed in a wire frame form, as a shaded surface or other three-dimensional computer display modality independent from or superimposed on the volumetric perspective image of the region of interest. It is further envisioned that the map may include data collected from a localization element embedded into the surgical instrument, such as pressure data, temperature data or electro-physiological data. In this case, the map may be coded with a color or some other visual indicia to represent the collected data. 
       FIG.  4    illustrates another type of secondary image  28  which may be displayed in conjunction with the primary perspective image  30 . In this instance, primary perspective image  30  is an interior view of an air passage within patient  13 . Secondary image  28  is an exterior view of the air passage which includes an indicia or graphical representation  29  that corresponds to the location of surgical instrument  12  within the air passage. In  FIG.  4   , indicia  29  is shown as a crosshairs. It is envisioned that other indicia may be used to signify the location of the surgical instrument in the secondary image. As further described below, secondary image  28  may be constructed by superimposing indicia  29  of surgical instrument  12  onto the manipulated image data  38 . 
     The displayed indicia  29  of surgical instrument  12  tracks the movement of surgical instrument  12  as it is moved by the physician or other healthcare professional within patient  13 . In certain instances, the cardiac or respiration cycle of the patient may cause surgical instrument  12  to flutter or jitter within the patient. For instance, a surgical instrument  12  positioned in or near a chamber of the heart will move in relation to the patient&#39;s heart beat. In this instance, the indicia of the surgical instrument  12  will likewise flutter or jitter on the displayed image (see box  40  of  FIG.  2   ). It is envisioned that other anatomical functions which may affect the position of the surgical instrument  12  within the patient are also within the scope of the present invention. Rather than display indicia  29  of surgical instrument  12  on a real-time basis, the display of indicia  29  of surgical instrument  12  is periodically updated based on a timing signal from timing signal generator  26 . In one exemplary embodiment, the timing signal generator  26  is electrically connected to tracking subsystem  20 . 
     As shown by the flowchart of  FIG.  5   , another embodiment may be a technique for synchronizing the display of an indicia or graphical representation of surgical instrument  12  with cardiac or respiration cycle of the patient in order to reduce flutter. The display of an indicia of surgical instrument  12  may be synchronized with an anatomical function, such as the cardiac or respiration cycle of the patient. As described above, imaging device  14  may be used to capture (see box  32  of  FIG.  5   ) volumetric scan data representative of an internal region of interest within a given patient. An may then be rendered (see box  36  of  FIG.  5   ) from the volumetric scan data by processor  16 . A timing signal generator  26  (not shown) may be operable to generate and transmit a timing signal (see box  46  of  FIG.  5   ) that correlates to at least one of (or both) the cardiac cycle or the respiration cycle of patient  13 . For a patient having a consistent rhythmic cycle, the timing signal might be in the form of a periodic clock signal. Alternatively, the timing signal may be derived from an electrocardiogram signal from the patient  13 . One skilled in the art will readily recognize other techniques for deriving a timing signal that correlate to at least one of the cardiac or respiration cycle or other anatomical cycle of the patient. The acquisition of position data (see box  37  of  FIG.  5   ) for surgical instrument  12  may then be synchronized to the timing signal. 
     Tracking subsystem  20  is, in turn, operable to report position data (see box  37  of  FIG.  5   ) for surgical instrument  12  in response to a generated timing signal (see box  46  of  FIG.  5   ) received from timing signal generator  26 . The position of indicia  29  of surgical instrument  12  may then be updated and superimposed (see box  50  of  FIG.  5   ) on the display of the image data (see box  40  of  FIG.  5   ). It is readily understood that other techniques for synchronizing the display of indicia  29  of surgical instrument  12  based on the timing signal are within the scope of the present invention, thereby eliminating any flutter or jitter which may appear on the displayed image (see box  40  of  FIG.  5   ). It is also envisioned that a path (or projected path) of surgical instrument  12  may also be illustrated on displayed image data (see box  40  of  FIG.  5   ). 
     In another aspect of the present invention, surgical instrument navigation system  10  may be further adapted to display four-dimensional image data for a region of interest as shown in the flowchart of  FIG.  6   . In this case, imaging device  14  is operable to capture 4D volumetric scan data (see box  62 ) for an internal region of interest over a period of time, such that the region of interest includes motion that is caused by either the cardiac cycle or the respiration cycle of patient  13 . A volumetric perspective image of the region may be rendered (see box  64 ) from the captured 4D volumetric scan data (see box  62 ) by processor  16  as described above. The four-dimensional image data may be further supplemented with other patient data, such as temperature or blood pressure, using a color code or some other visual indicia. 
     The display of the volumetric perspective image may be synchronized (see box  66 ) in real-time with the cardiac or respiration cycle of patient  13  by adapting processor  16  to receive a generated timing signal (see box  46 ) from timing signal generator  26 . As described above, the timing signal generator  26  is operable to generate and transmit a timing signal that correlates to either the cardiac cycle or the respiration cycle of patient  13 . In this way, the 4D volumetric perspective image may be synchronized (see box  66 ) with the cardiac or respiration cycle of patient  13 . The synchronized image is then displayed (see box  68 ) on the display  18  of the system. The four-dimensional synchronized image may be either (or both of) the primary image rendered from the point of view of the surgical instrument or the secondary image depicting the indicia of the position of surgical instrument  12  within patient  13 . It is readily understood that the synchronization process is also applicable to two-dimensional image data acquire over time. 
     To enhance visualization and refine accuracy of the displayed image data, the surgical navigation system can use prior knowledge such as a segmented vessel or airway structure to compensate for error in the tracking subsystem or for inaccuracies caused by an anatomical shift occurring since acquisition of scan data. For instance, it is known that surgical instrument  12  being localized is located within a given vessel or airway and, therefore may be displayed within the vessel or airway. Statistical methods can be used to determine the most likely location; within the vessel or airway with respect to the reported location and then compensate so the display accurately represents surgical instrument  12  within the center of the vessel or airway. The center of the vessel or airway can be found by segmenting the vessels or airways from the three-dimensional datasets and using commonly known imaging techniques to define the centerline of the vessel or airway tree. Statistical methods may also be used to determine if surgical instrument  12  has potentially punctured the vessel or airway. This can be done by determining the reported location is too far from the centerline or the trajectory of the path traveled is greater than a certain angle (worse case 90 degrees) with respect to the vessel or airway. Reporting this type of trajectory (error) may be desired by the physicians or other healthcare professionals. The tracking along the center of the vessel or airway may also be further refined by correcting for motion of the respiratory or cardiac cycle, as described above. While navigating along the vessel or airway tree, prior knowledge about the last known location can be used to aid in determining the new location. Surgical instrument  12  or other navigated device follows a pre-defined vessel or airway tree and therefore cannot jump from one branch to the other without traveling along a path that would be allowed. The orientation of surgical instrument  12  or other navigated device can also be used to select the most likely pathway that is being traversed. The orientation information can be used to increase the probability or weight for selected location or to exclude potential pathways and therefore enhance system accuracy. 
     Surgical instrument navigation system  10  of the present invention may also incorporate atlas maps. It is envisioned that three-dimensional or four-dimensional atlas maps may be registered with patient specific scan data or generic anatomical models. Atlas maps may contain kinematic information (e.g., heart models) that can be synchronized with four-dimensional image data, thereby supplementing the real-time information. In addition, the kinematic information may be combined with localization information from several instruments to provide a complete four-dimensional model of organ motion. The atlas maps may also be used to localize bones or soft tissue which can assist in determining placement and location of implants. 
     In general, a consistent feature between lung scans is the existence of an airway tree within the lung tissue, consisting of multiple branches and carinas. The branches and carinas, however, move as a consequence of a patient&#39;s respiration. To provide more accurate navigation of an instrument through the airway tree of a patient, a set of data points may be collected from a patient pathway (e.g., an airway) and a model of points may be calculated to match the image dataset. In one embodiment, each discrete segment of the image dataset and its corresponding information are matched to the collected points, creating a “point cloud” of information. Then, the data points that create the outer region or shell of the point cloud are determined, followed by correlation or matching of the outer points to the patient&#39;s 3D image data sets. 
     A respiratory-gated point cloud comprises a plurality of data points corresponding to the internal volume of a patient&#39;s respiratory system measured by a localization element during the respiration cycle of a patient. Each data point of the respiratory-gated point cloud comprises three dimensional data (x, y, and z location) in reference to a 3D coordinate system. In this embodiment, each data point of the respiratory-gated point cloud may be gated to the respiration cycle of the patient. The respiratory-gated point cloud also comprises a fourth dimension representing the phase (inspiration, expiration, and, if desired, points in between) of the respiration cycle of the patient at which point the individual data point was generated. The phase information may be provided by a patient tracker that real-time tracks the patient&#39;s respiratory cycle. In certain embodiments, the generation of the individual data points in the point cloud may occur on a time-gated basis triggered by a physiological signal of the patient&#39;s respiration cycle. In other embodiments, a respiratory-gated point cloud can be collected at inspiration and another respiratory-gated point cloud collected at expiration. These two respiratory-gated point clouds can then be matched to an image dataset to assist registration. Alternatively, a single respiratory-gated point cloud can be collected including data points from both inspiration and expiration and matched to an image dataset. 
     Referring now to  FIG.  7   , a respiratory-gated point cloud can be collected in one embodiment using a surgical instrument navigation system  10  (not shown) comprising catheter  612  having localization element  624  at the distal end thereof. More specifically, a physician or other healthcare professional moves catheter  612  through a plurality of locations  614  within the branches of a patient&#39;s respiratory system  602 , including trachea  608 , right main bronchus (RMB)  604 , and left main bronchus (LMB)  606  over a full respiration cycle of patient  613  to form respiratory-gated point cloud corresponding to position/orientation data of localization element  624 . According to one particular embodiment, a respiratory signal is used to gate the localization information. Additionally or alternatively, the respiratory signal can be derived, for example, using a device that records the resistance between two locations on the patient; such a method is similar to a variable potentiometer in that the resistance of the patient changes between two fixed points as the patient inhales and exhales. Thus, the resistance can be measured to create a respiratory signal. When a signal indicating a particular phase of the respiration cycle is received, the processor begins acquiring valid position/orientation data regarding the localization element(s)  624  in catheter  612  through a plurality of locations  614  within the branches of a patient&#39;s respiratory system  602 , thereby generating respiratory-gated point cloud. Once the respiration cycle moves outside of that phase, a stop signal halts the point cloud data collection. In this way, it is not necessary to track the motion of the patient&#39;s anatomy if the respiratory motion is the only motion occurring. 
     Density filtering of the generated respiratory-gated point clouds can reduce the number of duplicate data points generated which can significantly decrease the processing time. Depending on the desired strength of filtering, a duplicate data point in the respiratory-gated point is defined as having identical three dimensional coordinates (x, y, and z) to another data point in the respiratory-gated point cloud wherein both points were generated in the same respiratory phase or a duplicate data point in the respiratory-gated point is defined as having three dimensional coordinates x1, y1, and z1 within a certain distance to another data point in the respiratory-gated point cloud having three dimensional coordinates x2, y2, and z2 wherein both points were generated in the same respiratory phase. This duplicated data point, and any additional duplicate data points can be eliminated, leaving only one data point for each three dimensional coordinate and corresponding respiratory phase. In another embodiment, additional density filtering can be done by eliminating duplicate data points without reference to a given respiratory phase. This would eliminate duplicate data points from the respiratory-gated point cloud that were generated throughout multiple phases. By eliminating the duplicate data points, a processor need not perform subsequent calculations of unnecessary data points. 
     Additionally, in certain embodiments, the generated point cloud may be compared to the segmented image data to determine the strength or weighting of each point collected in the point cloud. Calculating the strength or weighting of discrete points in the point cloud can enhance registration accuracy. By way of example, collecting a single string of points that are only 1 mm wide to represent an airway that is 5-6 mm wide as determined in the image model would be an insufficient point cloud. Feedback can be provided to the user such as color coding or some other visual indicia to identify the strength of the point cloud. 
     In one exemplary embodiment, a physician or other healthcare professional captures a respiratory-gated point cloud and the captured cloud is density filtered as previously described to form a density-filtered point cloud comprising unclassified point cloud data points. The density-filtered point cloud may then be classified using a first k-means algorithm which performs orientation classification resulting in the data points in the respiratory-gated point cloud being classified into the trachea, the right main bronchus and the left main bronchus. A second k-means algorithm is performed to further classify the data points in the respiratory-gated point cloud into control points. The respiratory-gated point cloud may then be registered to a pre-existing image dataset and the data points of the respiratory-gated point cloud are weighted. Each data point in the respiratory-gated point cloud may then be displayed to the user with a color code or some other visual indicia corresponding to the calculated weight for each data point in the respiratory-gated point cloud. In certain embodiments, feedback may be provided to the physician or other healthcare professional indicating that additional respiratory-gated point cloud data points may be collected in locations having lesser weighting. This method may then be repeated until a desired weighting is achieved across the respiratory-gated point cloud. 
     Image datasets may not perfectly match if the image data was acquired at a different phase in the respiration cycle (e.g., full inspiration, partial inspiration, full expiration, etc.) or if the patient&#39;s anatomy has been changed due to positioning on the table, weight gain/loss, skin shift, delivery of drugs, etc. In such embodiments, an image dataset taken at a first time point can be modified or deformed to better correspond to the respiratory-gated point cloud generated during the medical procedure (i.e., a second and subsequent time point). Additionally, a sequence of motion of the respiratory-gated point cloud can be generated over the complete procedure or significant period of time. The distance, range, acceleration, and speed between one or more selected pairs of respiratory-gated data points within the point cloud generated by the localization element  624  (see  FIG.  7   ) can be determined and various algorithms can be used to analyze and compare the distance between selected data points at given instants in time. 
     Referring now to  FIG.  8   , a method for modifying or deforming a segmented image dataset for a region of a respiratory system of a patient to the corresponding anatomy of a patient&#39;s respiratory system in one embodiment comprises forming (see box  700 ) a respiratory-gated point cloud of data that demarcates anatomical features in a region of a patient&#39;s respiratory system at one or more discrete phases within a respiration cycle of a patient. The respiratory-gated point cloud is then density filtered (see box  702 ). The density filtered point cloud is then classified (see box  703 ) according to anatomical points of reference in a segmented image dataset for the region of the patient&#39;s respiratory system (as described above), and a segmented image dataset for the region of the respiratory system is modified (or deformed) (see box  704 ) using a deformation vector field to correspond to the classified anatomical points of reference in the density filtered respiratory-gated point cloud. In certain embodiments, the phases at which the respiratory-gated point cloud is formed include inspiration, expiration and phases in between. 
     A deformation vector field can be calculated between a first set of points in the respiratory-gated point cloud that correspond to inspiration and a second set of points in the respiratory-gated point cloud that correspond to expiration. This deformation vector field may then be used to modify or deform a pre-existing or pre-acquired segmented image dataset, taken from a first time interval, to correspond to the correlated anatomical points of reference in the respiratory-gated point cloud, taken during a second time interval. In certain embodiments, the segmented image dataset to be modified is from a first discrete phase of the patient&#39;s respiration cycle and the respiratory-gated point cloud is from a second and different discrete phase of the patient&#39;s respiration cycle. Accordingly, a pre-existing or pre-acquired segmented image dataset can be from an inspiration phase and it can be modified or deformed to the expiration phase using the deformation vector field calculated from the respiratory-gated point cloud. Thus a segmented image dataset need not require an image for each phase of the patient&#39;s respiration cycle. 
     A deformation vector field can be calculated between data points in the respiratory-gated point cloud that correspond to different phases of the patient&#39;s respiratory cycle. The image dataset from a first time interval may then be modified or deformed by the deformation vector field to match the anatomy of the patient during the second time interval. This modification or deformation process can be done continuously during the medical procedure, producing simulated real-time, intra-procedural images illustrating the orientation and shape of the targeted anatomy as a catheter, sheath, needle, forceps, guidewire, fiducial delivery devices, therapy device (ablation modeling, drug diffusion modeling, etc.), or similar structure(s) is/are navigated to the targeted anatomy. Thus, during the medical procedure, the physician or other healthcare professional can view selected modified or deformed image(s) of the targeted anatomy that correspond to and simulate real-time movement of the anatomy. In addition, during a medical procedure being performed during the second time interval, such as navigating a catheter or other instrument or component thereof to a targeted anatomy, the location(s) of a localization element (e.g., an electromagnetic coil sensor) coupled to the catheter during the second time interval can be superimposed on an image of a catheter. The superimposed image(s) of the catheter can then be superimposed on the modified or deformed image(s) from the first time interval, providing simulated real-time images of the catheter location relative to the targeted anatomy. This process and other related methods are described in U.S. Pat. No. 7,398,116, the entire disclosure of which is incorporated herein by reference. 
     The deformation vector field may be calculated between a first set of points in the respiratory-gated point cloud that correspond to a first respiration phase and a second set of points in the respiratory-gated point cloud that correspond to a second respiration phase. Typically, the first respiration phase is inspiration and the second respiration phase is expiration. Additionally, the two phases can be reversed wherein the first phase is expiration and the second phase is inspiration. For example, the deformation vector field can be applied to modify or deform an image dataset of 3D fluoroscopic images or CT images in order to compensate for different patient orientations, patient position, respiration, deformation induced by the catheter or other instrument, and/or other changes or perturbations that occur due to therapy delivery or resection or ablation of tissue. 
     In some embodiments, for example, real-time respiration compensation can be determined by applying an inspiration-to-expiration deformation vector field. In combination with the respiratory signal, for example, the surgical instrument location can be calculated using the deformation vector field. A real-time surgical instrument tip correction vector can be applied to a 3D localized instrument tip. The real-time correction vector is computed by scaling an inspiration-to-expiration deformation vector (found from the inspiration-to-expiration deformation vector field) based on the respiratory-gated point cloud. This correction vector can then be applied to the 3D localized surgical instrument tip. This can further optimize accuracy during navigation. 
     An example of an algorithm for real-time respiration compensation can be found in  FIG.  9   . In accordance with this algorithm, for each 3D localized point  :
         (a) find v i  such that scalar d is minimized;   (b) compute c, wherein:       

     
       
      
       c=−v 
       i 
       t  
      
         
         
           
             and (c) compute  ′, wherein: 
           
         
       
    
         ′+ + c  
 
     Thus,  ′ is a respiration compensated version of  . 
     Although  FIG.  9    and the above discussion generally relate to real-time respiration motion, it will be understood that these calculations and determinations may also be applied to real-time heartbeat and/or vessel motion compensation, or any other motion of a dynamic body (e.g., the patient&#39;s body, an organ, or tissue thereof) as described herein. In one embodiment, for example, the deformation vector field is calculated based upon inspiration and expiration. In another embodiment, for example, the deformation vector field is calculated based upon heartbeat. In yet another embodiment, for example, the deformation vector field is based upon vessel motion. In these and other embodiments, it is also possible to extend these calculations and determinations to develop multiple deformation vector fields across multiple patient datasets, by acquiring the multiple datasets over the course of, for example, a single heartbeat cycle or a single respiration cycle. 
     Deformation of 2D images can also be calculated based upon therapeutic change of tissue, changes in Hounsfield units for images, patient motion compensation during the imaging sequence, therapy monitoring, and temperature monitoring with fluoroscopic imaging, among other things. One potential issue with conventional therapy delivery, for instance, is monitoring the therapy for temperature or tissue changes. In accordance with the methods described herein, this monitoring can be carried out using intermittent fluoroscopic imaging, where the images are compensated between acquisition times to show very small changes in image density, which can represent temperature changes or tissue changes as a result of the therapy and/or navigation. 
     Another method to modify/deform the image dataset and match to the patient is to segment the airway from the image dataset and skeletonize it to find the central airway tree. The physician or other healthcare professional can then modify/deform the image dataset by identifying points within the image space and patient space that match such as the main carina and/or collect multiple branch information that defines branches and carina points between branches. These points can be used to modify or deform the image dataset. Deformation of a complete 3D volume would be time consuming so methods to create deformation matrices for regions may be preferred. 
     In general, the embodiments described herein have applicability in “Inspiration to Expiration”-type CT scan fusion. According to various methods, the user navigates on the expiration CT scan to aid accuracy, while using the inspiration scan to aid airway segmentation. In one embodiment, for example, a user could complete planning and pathway segmentation on an inspiration scan of the patient. Preferably, a deformation vector field is created between at least two datasets. The deformation vector field may then be applied to the segmented vessels and/or airways and the user&#39;s planned path and target. In these and other embodiments, the deformation vector field can also be applied to multiple datasets or in a progressive way to create a moving underlying dataset that matches the patient&#39;s respiratory or cardiac motion. In other embodiments, using a respiratory-gated point cloud, a deformation vector field is calculated between a first set of points in the respiratory-gated point cloud that correspond to inspiration and a second set of points in the respiratory-gated point cloud that correspond to expiration. This deformation vector field may then used to modify or deform a pre-existing or pre-acquired segmented image dataset to correspond to the correlated anatomical points of reference in the respiratory-gated point cloud. 
     In accordance with various embodiments, “Inspiration to Expiration” CT fusion using the lung lobe centroid and vector change to modify an airway model may be used to translate and scale each airway based on the lung lobe change between scans. The lung is constructed of multiple lobes and these lobes are commonly analyzed for volume, shape, and translation change. Each lobe changes in a very different way during the patient&#39;s respiration cycle. Using this information to scale and translate the airways that are located in each lobe, it is possible to adapt for airway movement. This scaled airway model can then be linked to the 4D tracking of the patient as described herein. In accordance with various embodiments using a respiratory-gated point cloud, this technique may be used to translate and scale each airway based on the lung lobe change between respiration phases. The lung is constructed of multiple lobes and these lobes are commonly analyzed for volume, shape, and translation change. Each lobe changes in a very different way during the patient&#39;s respiration cycle. Using the respiratory-gated point cloud information to scale and translate the airways that are located in each lobe, it is possible to adapt for airway movement. This scaled airway model can then be linked to the 4D tracking of the patient as described herein. 
     In general, it may also be preferable to reduce the level of radiation that patients are exposed to before or during a procedure (or pre-procedural analysis) as described herein. One method of reducing radiation during the acquisition of a 3D fluoroscopic dataset (or other dataset described herein), for example, is to use a deformation vector field between data points in a respiratory-gated point cloud to reduce the actual number of 2D images that need to be acquired to create the 3D dataset. In one particular embodiment, the deformation field is used to calculate the deformation between images in the acquisition sequence to produce 2D images between the acquired slices, and these new slices can be used to calculate the 3D fluoroscopic dataset. For example, if 180 2D image slices were previously required, e.g., an image(s) taken every 2 degrees of a 360 degree acquisition sequence, in accordance with some embodiments 90 2D images can be acquired over a 360 degree acquisition sequence and the data from the images that would have ordinarily been acquired between each slice can be calculated and imported into the 3D reconstruction algorithm. Thus, the radiation is effectively reduced by 50%. 
     In another embodiment, illustrated by  FIG.  10   , a process of registration and deformation may assist the navigation of a surgical instrument. One method of preparing a segmented image dataset to match the anatomy of a patient&#39;s respiratory system comprises the steps of (i) forming (see box  700 ) a respiratory-gated point cloud of data that demarcates anatomical features in a region of a patient&#39;s respiratory system at one or more discrete phases within a respiration cycle of a patient, (ii) density filtering (see box  702 ) the respiratory-gated point cloud, (iii) classifying (see box  703 ) the density filtered respiratory-gated point cloud according to anatomical points of reference in a segmented image dataset for the region of the patient&#39;s respiratory system, (iii) registering (see box  800 ) the classified respiratory-gated point cloud to the segmented image dataset, (iv) comparing (see box  802 ) the registered respiratory-gated point cloud to a segmented image dataset to determine the weighting of points comprised by the classified respiratory-gated point cloud, (v) distinguishing (see box  804 ) regions of greater weighting from regions of lesser weighting and optionally increasing the data set comprised by the registered respiratory-gated point cloud for regions of lesser weighting, and (vi) modifying or deforming (see box  704 ) the segmented image dataset to correspond to the classified respiratory-gated point cloud. In alternative embodiments, the user may optionally perform a loop  806  and generate additional data points in the respiratory-gated point cloud to increase the weighting of certain points in the respiratory-gated point cloud. In certain embodiments, the phases at which the respiratory-gated point cloud is formed include inspiration, expiration and phases in between. 
     In addition to modifying or deforming the segmented image dataset, in one embodiment of the present invention the movement of a patient&#39;s respiratory system in the patient&#39;s respiration cycle over the patient&#39;s entire respiration cycle may be simulated in a method comprising (i) forming (see box  700  of  FIG.  10   ) a respiratory-gated point cloud of data that demarcates anatomical features in a region of a patient&#39;s respiratory system at one or more discrete phases within a respiration cycle of a patient, (ii) density filtering (see box  702  of  FIG.  10   ) the respiratory-gated point cloud, (iii) classifying (see box  703  of  FIG.  10   ) the density filtered respiratory-gated point cloud according to anatomical points of reference in a segmented image dataset for the region of the patient&#39;s respiratory system, (iv) creating a cine loop comprising a plurality of modified segmented image datasets through multiple modifications of the segmented image dataset to correspond to a plurality of classified anatomical points of reference in the respiratory-gated point cloud over the respiration cycle, and (v) displaying the cine loop comprising the plurality of modified segmented image datasets over the patient&#39;s respiration cycle. In certain embodiments, the phases at which the respiratory-gated point cloud is formed include inspiration, expiration and phases in between. In certain embodiments, the plurality of modified segmented image datasets may be created by modifying a segmented image dataset according to the deformation vector field. In yet other embodiments, this simulated movement of the patient&#39;s respiratory system can be synchronized with the patient&#39;s respiration cycle. Accordingly, the gating information from the respiratory-gated point cloud is matched to a real-time gating signal corresponding to the patient&#39;s respiration cycle. The physician can then observe the modified or deformed image during the medical procedure on a targeted portion of the patient&#39;s body. Thus, during the medical procedure, the above simulation process can be continuously executed such that multiple modified images are displayed and modified images corresponding to real-time positions of the patient&#39;s body can be viewed. In certain embodiments, the plurality of modified segmented image datasets comprises 2 or more segmented image datasets. In other embodiments, the plurality of modified segmented image datasets comprises 3 or more segmented image datasets. In yet other embodiments, the plurality of modified segmented image datasets comprises 4 or more segmented image datasets. In certain embodiments, the creation and display of the cine loop comprising the plurality of modified segmented image datasets can be over the patient&#39;s entire respiratory cycle. 
     In another aspect, the system involves generating a respiratory-gated point cloud of a dynamic anatomy using implanted localization elements. In general, one or more (and typically multiple, e.g., 2, 3, 4, or more) localization elements may be placed in the organ and tracked continuously and registered to a discrete section of the organ. In this embodiment, the localization elements may have a pigtail or anchoring mechanism that allows it to be attached to an internal organ or along a vessel. Using image processing techniques, voxels from an image dataset, or set of voxels from an image dataset; multiple 3D data sets of the organ can be used to create discrete sections of the organ (i.e., in a grid-like pattern). For each section, a deformation vector field analysis can be performed between the phases of the organ and/or based upon the motion of the organ tracked by localization elements attached to or adjacent to a wall of the organ such that the motion of the organ is translated to the sensors. Each section will then have unique signature or deformation vector field, which can be matched to the tracked motion of the localization element(s) attached to the organ. For example, the wall localization element motion will match the space-time signature of the device. Preferably, a deformation vector field is created between at least two datasets. The deformation vector field may then be applied to the segmented vessels and/or airways and the user&#39;s planned path and target. 
     Another technique for maximizing registration accuracy is a centroid finding algorithm that can be used for refining point locations in a local area. Often, a user will want to select a vessel bifurcation. The vessel bifurcation will be seen as a bright white location on the CT and US images. An algorithm can be used to help the user select the center location for these locations. Once a user selects a point on the image, the local algorithm can be employed to find similar white voxels that are connected and, for that shape in the 3D space, refine the point to the centroid or any other point (such as, for example, the most anterior or most posterior point). 
     Skeletonization of the segmented image dataset can help refine the respiratory-gated point cloud. It may be difficult to capture a respiratory-gated point cloud that would match a patient image dataset due to the inability to physically touch the airway wall in many orientations. Therefore the system can use the calculated centerlines between the dataset and the respiratory-gated point cloud to refine accuracy. Various methods of skeletonization are well known in the art and can be applied to the image datasets of certain embodiments of the present invention. 
     In an alternative embodiment, registering the classified respiratory-gated point cloud to the segmented image dataset comprises registering the classified respiratory-gated point cloud representing at least one branch of the patient&#39;s respiratory system to corresponding anatomical points of reference in the registered segmented image data set representing the branch(es) of the patient&#39;s respiratory system. In certain embodiments, the classified respiratory-gated point cloud sections corresponding to the trachea, the right main bronchus (RMB), and the left main bronchus (LMB) are registered to a plurality of branches of the patient&#39;s respiratory system, wherein the plurality of branches comprise the trachea, the right main bronchus (RMB), and the left main bronchus (LMB). Rotational shifts may be found through lumen data collection. Matching the trachea, RMB, and LMB in patient space and image space will provide rotational registration refinement. While the lung is commonly defined as one organ, in certain embodiments separate registrations between the right and left lung or even different lobes of the lung can provide additional refinement. Carina touch points can be used to perform translational shifts to the registration between patient space and image space. 
     In one embodiment a lung atlas can be used to develop patient specific airway trees, lung regions, lobes, lymph nodes, vessels, and other structures. These structures can be key to things such as correctly staging lung cancer. Correctly identifying the spread of cancer to lymph nodes can determine the best course of patient treatment. Recording the sampled locations to determine a consistent staging methodology and correctly identifying the region of the lung is key. A lung atlas can also be used to automatically select registration points within a patient such as the Main Carina or other branch points that can be touched by the user to register a dataset to the patient space. Using a lung atlas with an airway tree segmented, a patient specific airway tree can be determined by deforming the lung atlas to the patient&#39;s dataset to produce a patient specific airway tree. This can be used for a navigation pathway map, initialization points for other image processing steps, or to produce an error metric for multiple algorithms. Accordingly, in certain embodiments, a lung atlas can be modified or deformed according to the respiratory-gated point cloud. 
     In another embodiment, 3D image datasets of an organ (e.g., the heart or lung(s)) are segmented to determine a center line of the pathway, such that a string of points, shape or diameter of the pathway can be determined. Patient image information can be matched to the localization information in order to match 3D image space to actual patient space. Thus, an airway shape may be provided along with discrete segments providing shape, orientation, and location information. 
     In yet another embodiment, 3D image datasets of an organ (e.g., the heart or lung(s)) are segmented to determine a wall, inner surface, or effective inner surface of the pathway, such that a shape or diameter of the pathway can be determined. An effective inner surface may be the representation of an airway that can be tracked based upon the instrumentation used to collect points. An instrument dragged through or passed through and airway may be limited to its ability to track exactly along the surface of the airway and is generally a fixed distance from the wall (i.e., a 5 mm diameter airway may only be tracked in a 3 mm diameter space as there is a 1 mm offset of the sensor from the instrument or device it is inserted to the outer wall). Patient image information may be matched to the localization information in order to match 3D image space to actual patient space. Thus, an airway shape is provided along with discrete segments providing shape, orientation, and location information. 
     In one embodiment, the tracking of therapy delivery such as energy, material, device, or drug is described. Delivery of a therapy for COPD, asthma, lung cancer and other lung diseases needs tracking of the delivery location and/or pattern. This can be done over treatment sessions (i.e., Bronchial Thermoplasty) or have a dynamically changing dose or energy (RF, cryo, microwave, steam, radiation, or drugs) based on location and trajectory of the delivery device. Using the tracking location and trajectory to modify the dose or energy real-time is described. The power of an ablation device can be changed as the device is directed at the target or can be turned off if outside a defined region. For delivery of therapy that is delivered over multiple sessions, the recorded locations of treated areas can be merged together for each session to give the patient a complete treatment. The treatments can also be modeled before delivery to determine a more effective delivery pattern, dose, or energy. 
     In another embodiment, a catheter used in the forming of the respiratory-gated point cloud can be integrated with one or more fiber optic localization (FDL) devices and/or techniques. In this way, the localization element (such as an electromagnetic (EM) sensor) provides the 3D spatial orientation of the device, while the FDL provides shape sensing of the airway, vessel, pathway, organ, environment and surroundings. Conventional FDL techniques can be employed. In various embodiments, for example, the FDL device can be used to create localization information for the complete pathway or to refine the localization accuracy in a particular segment of the pathway. By either using 3D localization information, shape, or both detected by the FDL device, the system can use a weighted algorithm between multiple localization devices to determine the location and orientation of the instrument in the patient. The FDL device can also be used as or in conjunction with the PTD to track the patient&#39;s motion such as respiration or heartbeat. 
     In other embodiments, surgical instrument  12  (see  FIG.  1   ) may be a bronchoscope that can capture a video view. This embodiment may comprise, a guidewire or other navigated instrument with one to one rotation to continuously align a virtual display view to be consistent with the actual bronchoscopic video view. A similar technique can be used with OCT, IVUS, or EBUS devices to orient the virtual view to the image captured by the OCT, IVUS, or EBUS devices. 
     Still other embodiments involve using video input of the bronchoscope to adjust the virtual “fly-through” view to be consistent with the user&#39;s normal perspective. For example, conventional video processing and matching techniques can be used to align the real-time video and the virtual image. 
     Still other embodiments involve using bronchoscopic video to provide angular information at a current location to provide targeting or directional cues to the user. Angular information can be derived from the location of patient anatomy in the image and the relative size of each within the image. Using information extracted from the video captured by the bronchoscope, the system can determine the direction of the display. This can be done using, for example, translation, rotation, or a combination of both. By comparing the real-time image captured to the modified image constructed from the respiratory-gated point cloud, the system can use this information to align the modified image and/or enhance the system accuracy. 
     In yet another embodiment, a high-speed three-dimensional imaging device, such as an optical coherence tomography (OCT) device, can be tracked. In accordance with conventional methods, such a device can only view 1-2 mm below the surface. With a localization element (e.g., electromagnetic sensor) attached in accordance with the systems and methods described herein, multiple 3D volumes of data can be collected and a larger 3D volume of collected data can be constructed. Knowing the 3D location and orientation of the multiple 3D volumes will allow the user to view a more robust image of, for example, pre-cancerous changes in the esophagus or colon. This data can also be correlated to pre-acquired or intra-procedurally acquired CT, fluoroscopic, ultrasound, or 3D fluoroscopic images to provide additional information. 
     Among several potential enhancements that could be provided by a surgical instrument navigation system as described herein is that a user could overlay the planned pathway information on to the actual/real-time video image of the scope or imaging device (such as ultrasound based device). Additionally, the system and apparatus could provide a visual cue on the real-time video image showing the correct direction or pathway to take. 
     According to another particular embodiment, 3D location information may be used to extend the segmented airway model. The 3D airway can be extended as the instrument is passed along the airway by using this location information as an additional parameter to segment the airway from the CT data. Using an iterative segmentation process, for instance, the 3D location information of the instrument can be used to provide seed points, manual extension, or an additional variable of likelihood of a segmented vessel or airway existing in the 3D image volume. These added airways can be displayed in a different format or color (for example) or some other visual indicia to indicate to the user that they are extending the segmented airway using instrument location information. 
     The multi-dimensional imaging modalities described herein may also be coupled with digitally reconstructed radiography (DRR) techniques. In accordance with a fluoroscopic image acquisition, for example, radiation passes through a physical media to create a projection image on a radiation-sensitive film or an electronic image intensifier. Given a 3D or 4D dataset as described herein, for example, a simulated image can be generated in conjunction with DRR methodologies. DRR is generally known in the art, and is described, for example, by Lemieux et al. (Med. Phys. 21(11), November 1994, pp. 1749-60). 
     When a DRR image is created, a fluoroscopic image is formed by computationally projecting volume elements, or voxels, of the 3D or 4D dataset onto one or more selected image planes. Using a 3D or 4D dataset of a given patient as described herein, for example, it is possible to generate a DRR image that is similar in appearance to a corresponding patient image. This similarity can be due, at least in part, to similar intrinsic imaging parameters (e.g., projective transformations, distortion corrections, etc.) and extrinsic imaging parameters (e.g., orientation, view direction, etc.). The intrinsic imaging parameters can be derived, for instance, from the calibration of the equipment. 
     Referring now to  FIGS.  11 A and  11 B , in one embodiment of the present invention, the generated DRR image simulates bi-planar fluoroscopy wherein an image of a region (or tissue) of interest  1602  near the ribs  1208  of a patient  13  can be displayed for two planes of a 3D or 4D image dataset. In certain embodiments, the two image planes of the simulated bi-planar fluoroscopy are oriented 90 degrees apart, however it is understood that other angles are contemplated. One image view that may be displayed is the anterior-to-posterior (A-P) plane ( FIG.  11 A ) and another image view that may be displayed is the lateral plane ( FIG.  11 B ). The display of these two image views provides another method to see the up-and-down (and other directional) movement of the surgical instrument  12  (not shown). This simulated bi-planar fluoroscopy further provides the ability to see how the surgical instrument  12  moves in an image(s), which translates to improved movement of surgical instrument  12  in a patient  13 . Additional information can be simultaneously integrated with the simulated bi-planar fluoroscopy (in A-P and lateral views) using minP (minimum intensity projection or maxP (maximum intensity projection) volume, including one or more of: (i) the segmented airway  1601 , (ii) the region (or tissue) of interest  1602 , (iii) a real-time or simulated real-time rendering of the trajectory and location  1606  of surgical instrument  12 , (iv) and the historical pathway  1204  of the surgical instrument  12 . Displaying the historical pathway  1204  of surgical instrument  12  can assist the navigation of surgical instrument  12  in areas or situations in which there may be incomplete segmentation of the images of the patient&#39;s respiratory system. In another embodiment, a physician or other healthcare professional may be able to zoom in or out or pan through the simulated bi-planar fluoroscopy images. 
     According to another embodiment of the present invention,  FIG.  12    depicts a CT minP/maxP volume reading where precise navigation of a surgical instrument  12  (not shown) having a localization element  24  (e.g., using an electromagnetic sensor) (not shown) near a region(s) (or tissue) of interest is carried out with incomplete segmentation results. This embodiment may provide the physician or other healthcare professional with a view or image  1600  using minP (minimum intensity projection) or maxP (maximum intensity projection) volume renderings to simultaneously integrate one or more of the segmented airway  1601 , the region(s) (or tissue) of interest  1602 , and a visually distinct representation of previously traversed paths that are “bad” (i.e., incorrect)  1603 . Additionally, this embodiment may also simultaneously integrate the distance and angle  1604  to the region(s) (or tissue) of interest  1602  (e.g., a target lesion or tumor) using a vector fit to the last 1 cm (or so) of travel (in addition to, or in place of, instantaneous orientation provided by a 5DOF localization element as described herein) and may incorporate user provided “way points” to create a final-approach tube  1605  to the region(s) (or tissue) of interest  1602 . As described herein, the image  1600  may also provide a real-time or simulated real-time rendering the trajectory and location  1606  of surgical instrument  12  (e.g., the tip component as shown with a virtual extension  1607  to the region(s) (or tissue) of interest). 
     In another embodiment, an alternative method of generating a 4D dataset for 4D thoracic registration using surgical instrument navigation system  10  is illustrated by  FIGS.  13 A and  13 B . In general, the 4D dataset may be acquired through respiratory gating or tracheal temporal registration. In accordance with the methods described herein, for example, acceleration of N data collectors (e.g., magnetic or MEMS accelerometers, for instance) are measured to register the thorax in time and space, using the general formula: data T thorax =F(t). As shown in  FIGS.  13 A and  13 B , the various sensors  1701  and tracheal sensor  1702  provide data as described herein, as does sternum sensor  1703  (e.g., x, y, and z dynamic tracking). The position and trajectory of a device (e.g., biopsy device or other device or medical instrument described herein) is further capable of being tracked as described herein. 
       FIG.  14    shows another embodiment of an apparatus and method for respiratory 4D data acquisition and navigation. As shown in the upper box, a respiratory problem or issue is scanned (e.g., by a CT and/or MR scanner) and signal S from the tracking subsystem is provide to the CT/IR unit (lower box). The 4D registration based on the motion of the fiducial and tracker units (which could be, e.g., electromagnetic sensors, MEMS devices, combinations thereof, and the like) is provided to the user (shown as an interventional radiologist (IR)) on computer C. The system is capable of displaying the current position of the device tip in the image data shown to the IR, using the fiducial or tracker locations in the scan coupled with the real-time motion information provided by the device tip (e.g., which can include a sensor as described herein), thus providing registration. 
     Other embodiments include, for example, using an electromagnetic sensor as an LC or energy transmission device. This stored energy could be used to actuate a sampling device such as forceps or power a diagnostic sensor. 
     In various aspects and embodiments described herein, one can use the knowledge of the path traveled by the surgical instrument and segmented airway or vessel from the acquired image (e.g., CT) to limit the possibilities of where the surgical instrument is located in the patient. The techniques described herein, therefore, can be valuable to improve virtual displays for users. Fly through, fly-above, or image displays related to segmented paths are commonly dependent upon relative closeness to the segmented path. For a breathing patient, for example, or a patient with a moving vessel related to heartbeat, the path traveled information can be used to determine where in the 4D patient motion cycle the system is located within the patient. By comparing the 3D location, the patient&#39;s tracked or physiological signal is used to determine 4D patient motion cycle, and with the instrument&#39;s traveled path, one can determine the optical location relative to a segmented airway or vessel and use this information to provide the virtual display. 
     The surgical instrument navigation system of certain embodiments of the present invention may also incorporate atlas maps. It is envisioned that three-dimensional or four-dimensional atlas maps may be registered with patient specific scan data, respiratory-gated point clouds, or generic anatomical models. Atlas maps may contain kinematic information (e.g., heart and lung models) that can be synchronized with four-dimensional image data, thereby supplementing the real-time information. In addition, the kinematic information may be combined with localization information from several instruments to provide a complete four-dimensional model of organ motion. The atlas maps may also be used to localize bones or soft tissue which can assist in determining placement and location of implants. 
     As noted herein, a variety of instruments and devices can be used in conjunction with the systems and methods described herein. 
     As a result of or in the course of certain surgical procedures, a patient&#39;s physical state may be changed relative to an acquired image dataset. Incisions, insufflations, and deflation of the lung and re-positioning of the patient are just some of the procedures that may cause a change in the patient&#39;s physical state. Such changes in physical state may make it more difficult to find a lesion or point in an organ of the patient. For example, in a lung wedge resection the thoracic surgeon is palpating the lung to find the lesion to resect; if this lesion is 1-2 cm under the surface it can be very difficult to find. 
     In one embodiment, a first localization element is placed at a location or region of interest (e.g., a tumor) within an organ of a patient and a second localization element is used to identify the location of the first localization element from outside the organ in which the first localization element has been positioned. Preferably, the first localization element is attached or otherwise connected to tissue or situated such that its position relative to the location or region of interest remains fixed. In some embodiments, for example, the first localization element can be sutured in place, and/or or may have barbs, hooks, flexed spring shape (bowed) and/or wires, or other suitable connection techniques, to hold it substantially in place. 
     Referring now to  FIG.  15 A , in one embodiment first localization element  904  is attached to tissue in a region of the organ  900  of the patient. First localization element  904  may be placed, for example, percutaneously, endobronchially, or via the vasculature. As illustrated, first localization element may be wireless, however in other embodiments first localization element may be wired. In one embodiment, first localization element  904  is placed using an endolumenal device  902 . In percutaneous (or other) methods, the leads of the first localization element may exit the patient and the device removed during or after a procedure (e.g., during resection of a tumor). 
     In one embodiment, first localization element  904  is positioned in the organ and may be registered to a segmented image dataset prior to any procedural resection or incision has occurred. Otherwise, pre-procedural images may not match the patient&#39;s anatomy (e.g., once an incision is made, the patient is insufflated for a VATS procedure, or the patient is otherwise re-positioned). 
     After the first localization element  904  is positioned in an organ and registered, as shown in  FIG.  15 B , the patient may then be manipulated in a manner that would potentially induce a physical change that would cause the patient&#39;s anatomy to not match a pre-procedure acquired segmented image dataset. A second localization element  908  (e.g., a pointer probe) may then be used to identify the location of the first localization element  904  from outside the patient&#39;s organ  900 . Typically, second localization element  908  is placed near patient&#39;s organ  900  or other area of interest, e.g., via an incision or through a working port of a VATS procedure or otherwise in a position to locate first localization element  904 . 
     Although the second localization element  908  will be outside the organ into which first localization element  904  is placed, it need not be outside the body of the patient. In certain embodiments of the present invention, second localization element  908  can be inserted into the patient through a surgical portal. In other embodiments, second localization element  908  will be outside the body of the patient. Optionally, and as illustrated in  FIG.  15   , in one embodiment a third localization element  906  may be used to locate first localization element  904  and second localization element  908  relative to third localization element  906 , wherein the third localization element  906  may comprise a 3D localizing device (e.g., an electromagnetic field generator) with a 3D coordinate system. In another embodiment, third localization element  906  may be used to locate second localization element  908  relative to third localization element  906 . 
     As illustrated in  FIG.  15   , in one embodiment, the organ to which first localization element  904  is attached is a lung. In other embodiments, however, first localization element  904  may be attached in another organ such as a kidney or the liver. 
     In certain embodiments, the first, second and (optional) third localization elements may all be elements of a tracking subsystem  20  (see  FIG.  1   ). If tracking subsystem  20  is an electromagnetic tracking system, the third localization element would typically comprise an electromagnetic field generator (transmitter) that emits a series of electromagnetic fields designed to engulf the patient, and the first and second localization elements could be coils that would receive (receivers) an induced voltage that could be monitored and translated into a coordinate position. However, the positioning of the electromagnetic field generator (transmitter), and the first and second localization elements (receivers) may also be reversed, such that the first localization element is a generator and the second and third localization elements are receivers or the second localization element is a generator and the first and third localization elements are receivers. Thus in certain embodiments, first localization element  904  may be a receiver, while in other embodiments, first localization element  904  may be a receiver. In certain embodiments, second localization element  908  may be a receiver, while in other embodiments, second localization element  908  may be a receiver. In certain embodiments, third localization element  906  may be a receiver, while in other embodiments, third localization element  906  may be a receiver. 
     In one embodiment of the present invention, surgical instrument  12  (see  FIG.  1   ) comprises a surgical catheter that is steerable (referred herein to as “steerable catheter”) to gain access to, manipulate, remove or otherwise treat tissue within the body including, for example, heart or lung tissue. Generally, steerable catheters can be remotely manipulated via a steering actuator. In a typical medical procedure, the steering actuator is located outside of the patient&#39;s body and is manipulated in order to steer the steerable catheter to a desired location within the body. 
     In accordance with one embodiment of the present invention and referring now to  FIG.  16   , steerable catheter  200  comprises actuating handle  216  and elongate flexible shaft  230 . Elongate flexible shaft  230  has proximal end portion  232 , distal end portion  234 , central longitudinal axis  207  extending from proximal end portion  232  to distal end portion  234 , and outer wall  236  comprising a biocompatible material extending from proximal end portion  232  to distal end portion  234 . In certain embodiments, the biocompatible material is a biocompatible polymer. 
     In certain embodiments, elongate flexible shaft comprises a flexible shaft portion  202  at its proximal end portion  232  and a steerable shaft portion  203  at its distal end portion  234 . In other embodiments, elongate flexible shaft  230  comprises flexible shaft portion  202  at its distal end portion  234  and a steerable shaft portion at its proximal end portion  232 . Flexible shaft portion  202  has a first stiffness and steerable shaft portion  203  has a second stiffness that is less than the first stiffness. Stated differently, flexible shaft portion  202  may be comprised of a more rigid material which has a first stiffness, while steerable shaft portion  203  may be comprised of a softer material having a second stiffness. In certain embodiments, flexible shaft portion  202  is formed from a relatively high-durometer material and steerable shaft portion  203  is formed from a less stiff, lower-durometer material than the flexible shaft portion. Additionally, flexible shaft portion  202  may be reinforced with a molded-in braided reinforcement material. In one alternative embodiment, flexible shaft portion  202  comprises a spring having a first coil diameter and steerable shaft portion  203  comprises a spring having a second coil diameter. The first coil diameter may be greater than the second coil diameter and, accordingly, the first coil diameter of the flexible shaft portion has a greater stiffness than the second coil diameter of the steerable shaft portion. In one embodiment, elongate flexible shaft  230 , including flexible shaft portion  202  and steerable shaft portion  203 , are preferably formed from a biocompatible material such as Pebax™, manufactured by Arkema. 
     Biopsy device  220  is at distal end portion  234  of elongate flexible shaft  230  and, in certain embodiments, may be used to access or manipulate tissue. In one embodiment, biopsy device  220  is operated by actuation wire  212  (see  FIG.  16 A ) which is housed within actuation channel  209  extending through elongate flexible shaft  230 . Actuation wire  212  has a proximal end (not shown) attached to handle  216  and a distal end (not shown) attached to biopsy device  220 . As illustrated in  FIG.  17 A  and as described in greater detail elsewhere herein, a variety of biopsy devices  220  can be used with the steerable catheter, including, but not limited to, for example, a forceps device  17 B, an auger device  17 E, a boring bit device  17 C, an aspiration needle device  17 F, or a brush device  17 D. In one embodiment, biopsy device  220  is comprised by a side exiting tip component  17 G comprising a forceps device, and auger device, a boring bit device, a brush device, or an aspiration needle device as described in greater detail elsewhere herein. 
     Referring again to  FIG.  16   , steerable catheter  200  further includes a steering mechanism comprising steering actuator  218  (proximate actuating handle  216 ) and at least one pull wire  210  (see  FIG.  16 A ) housed in elongate flexible shaft  230  and attached to steering actuator  218 . In certain embodiments, manipulation of steering actuator  218  applies a tension to pull wire(s)  210  and effects a deflection of steerable shaft portion  203  (located at or near the distal end portion of elongate flexible shaft  230 ) relative to flexible shaft portion  202 . In certain embodiments, pull wire  210  extends the entire length of elongate flexible shaft  230 . In other embodiments, pull wire  210  may extend only into proximal end portion  232  of elongate flexible shaft  230 . In yet other embodiments, pull wire  210  may extend only into distal end portion  234  of elongate flexible shaft  230 . In certain embodiments, pull wire  210  is operably connected at its proximal end to steering actuator  218  and anchored at its distal end to biopsy device  220  mounted on distal end portion  234  of elongate flexible shaft  230 . Thus, pull wire  210  passes through the flexible shaft portion and the steerable shaft portion of the elongate flexible shaft. The material for pull wire  210  may be any suitable material usable with a catheter, such as stainless steel wire. 
     Referring now to  FIG.  18 A , distal end portion  234  may be deflected relative to proximal end portion  232  such that an arc β of at least 20 degrees may be introduced into elongate flexible shaft  230  by manipulation of steering actuator  218 . As shown in  FIGS.  18 A and  18 B , biopsy device is shown as an aspiration needle device  1100  (described in greater detail elsewhere herein). In other embodiments, as described in greater detail elsewhere herein, biopsy device  220  may comprise any of a range of other biopsy devices such as an auger device, a boring bit device, a brush device, a side exiting tip component, etc. In one embodiment, an arc of at least about 30 degrees (i.e.,  13  is at least 30 degrees) may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 40 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 45 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 60 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 70 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 80 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 90 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 100 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 110 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 120 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 130 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 140 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 150 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 160 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of at least about 170 degrees may be introduced into elongate flexible shaft  230 . By way of further example, an arc of about 180 degrees may be introduced into elongate flexible shaft  230 . 
     As illustrated in  FIG.  18 B , in one embodiment, manipulation of steering actuator  218  introduces an arc β of at least 180 degrees into elongate flexible shaft  230 . Distal end portion  234  may be moved such that a distance of no more than 1.5 inch separates two regions of elongate flexible shaft  230  located at opposing ends of a chord X connecting to two points separated by at least 180 degrees on the arc. In certain embodiments, a distance of no more than 1 inch separates two regions of elongate flexible shaft  230  located at opposing ends of chord X. In certain embodiments, a distance of no more than 0.75 inches separates two regions of elongate flexible shaft  230  located at opposing ends of chord X. In certain embodiments, a distance of no more than 0.5 inches separates two regions of elongate flexible shaft  230  located at opposing ends of chord X. In certain embodiments, a distance of no more than 0.25 inches separates two regions of elongate flexible shaft  230  located at opposing ends of chord X. In other embodiments, manipulation of steering actuator  218  introduces an arc β of at least 120 degrees into elongate flexible shaft  230 . Distal end portion  234  may be moved such that a distance of no more than 1.5 inch separates two regions of elongate flexible shaft  230  located at opposing ends of a chord X connecting to two points separated by at least 120 degrees on the arc. In certain embodiments, a distance of no more than 1 inch separates two regions of elongate flexible shaft  230  located at opposing ends of chord X. In certain embodiments, a distance of no more than 0.75 inches separates two regions of elongate flexible shaft  230  located at opposing ends of chord X. In certain embodiments, a distance of no more than 0.5 inches separates two regions of elongate flexible shaft  230  located at opposing ends of chord X. In certain embodiments, a distance of no more than 0.25 inches separates two regions of elongate flexible shaft  230  located at opposing ends of chord X. 
     In another embodiment, elongate flexible shaft  230  of steerable catheter  200  houses more than one pull wire  210  attached to steering actuator  218 . The use of multiple pull wires may be preferred in some embodiments over steerable catheters having a single pull wire. A steerable catheter having only one pull wire  210  attached to steering actuator  218  will typically bend in only one direction, commonly referred to as uni-directional steering. A steerable catheter capable of only uni-directional steering could be rotated, such that any point surrounding the distal end of the elongate flexible shaft may be reached by bending the catheter tip and rotating the catheter. Two or more pull wires (e.g., two, three, four, or even more) attached to steering actuator  218 , however, could provide multi-directional steering thereby permitting the elongate flexible shaft to be deflected in two or more directions. 
     In one embodiment, elongate flexible shaft  230  comprises one or more lumens extending from proximal end portion  232  to distal end portion  234  of elongate flexible shaft  234  that may be used to deliver a medical device or therapy to a surgical site (e.g., fluids, biopsy devices, drugs, radioactive seeds, combinations thereof, or the like). In other embodiments, the lumen(s) may house additional structures such as electrical wires or optical fibers connected to biopsy device  220  on distal end portion  234  of elongate flexible shaft  230 . In other embodiments, a vacuum pressure may be applied to the lumen(s) to assist removal of tissue or fluid. In certain embodiments, the lumen may be a working channel in which a biopsy device such as an aspiration needle is housed and operated, wherein the aspiration needle is described in greater detail elsewhere herein (see  FIG.  33   ). 
     Referring now to  FIG.  19   , in another embodiment elongate flexible shaft  230  of steerable catheter  200  comprises articulated spline  204  containing a plurality of spline rings  206 . Spline rings  206  are affixed in series to at least one hollow spline guide  208  and extend in the direction of longitudinal central axis  207 . Articulated spline  204  may be covered in a casing  214  comprising a biocompatible material. In other embodiments, articulated spline  204  is at distal end portion  234  of elongate flexible shaft  230 . In yet other embodiments, articulated spline  204  is at proximal end portion  232  of elongate flexible shaft  230 . In yet other embodiments, steerable shaft portion  203  comprises articulated spline  204 . 
     In one embodiment, as illustrated in  FIG.  19   , steerable catheter  200  further comprises forceps device  300  as the biopsy device  220 . In other embodiments, as described in greater detail elsewhere herein, biopsy device  220  may comprise any of a range of other biopsy devices such as an auger device, a boring bit device, a brush device, a side exiting tip component, etc. Forceps device  300  comprises forceps housing  301 , first and second forceps jaws  302 , localization element  24  and localization element lead wire  103 , wherein the first and second forceps jaws  302  are operably connected to actuation wire  212 . The physician or other healthcare professional actuates forceps device  300  by manipulating handle  216  causing first and second forceps jaws  302  to pivot relative to one another, thereby closing first and second forceps jaws  302  thereby removing tissue. In certain embodiments, forceps device  300  may also comprise a tissue collection region where the removed tissue can be collected. In other embodiments, forceps device  300  can be equipped with, or used in conjunction with, a vacuum pressure (suction) may be used to pull the removed tissue into tissue collection region. In yet other embodiments, tissue collection region of forceps device  300  may have a viewing window through which the removed tissue can be inspected from outside forceps device  300  (see  FIG.  27   ). In other embodiments, localization element  24  may be attached to actuation wire  212  such that movement of actuation wire  212  as handle  215  is manipulated causes coordinated movement of localization element  24  thereby providing an indication that forceps device  300  is being operated. A number of mechanically operated forceps devices are known in the prior art and can be adapted to operably connect to the actuation wire  212  of the steerable catheter  200 . As described in greater detail elsewhere herein, biopsy device  220  may comprise any of a range of other biopsy devices such as an auger device, a boring bit device, an aspiration needle device, a brush device, a side exiting tip component, etc. 
     Referring now to  FIG.  19 A , hollow spline guides  208  are affixed to opposing inner surfaces of spline rings  206 . Pull wires  210  are housed in hollow spline guides  208  with one pull wire housed within each hollow spline guide  208 . The hollow spline guides  208  can be made of, for example, stainless steel or other metal, or from a hard polymeric material, such as polyimide or PTFE, or from a polymer lined metal tube, such as a Teflon lined stainless steel tube. Each hollow spline guide  208  may be made of a type of tube commonly used to fabricate hypodermic needles, e.g., a stainless steel tube having an outside diameter of about 0.050 inches or less, and more preferably about 0.018 inches or less. This tubing is sometimes referred to as “hypotube.” By way of example, the guide tube may be a 26 gauge stainless steel hypodermic tube, with a nominal outside diameter of 0.0183 inches and a nominal wall thickness of 0.004 inches. The hollow spline guides  208  provide and exhibit high strength and resiliency that resists compression. In one embodiment, by way of example, hollow spline guides  208  are affixed to spline rings  206  by a laser weld. In another embodiment, by way of further example, hollow spline guides  208  are affixed to spline rings  206  by an epoxy. In another embodiment, by way of further example, hollow spline guides  208  are affixed to the spline rings  206  by solder. In another embodiment, by way of further example, hollow spline guides  208  are affixed to spline rings  206  by a brazed joint. 
     Typically, the outer diameter of elongate flexible shaft  230  of steerable catheter  200  is less than 5 mm. By way of example, in certain embodiments, the outer diameter of elongate flexible shaft  230  of steerable catheter  200  is less than 1 mm. By way of further example, in certain embodiments, the outer diameter of elongate flexible shaft  230  of steerable catheter  200  is less than 2 mm. By way of further example, in certain embodiments, the outer diameter of elongate flexible shaft  230  of steerable catheter  200  is less than 3 mm. By way of further example, in certain embodiments, the outer diameter of elongate flexible shaft  230  of steerable catheter  200  is less than 4 mm. By way of further example, in certain embodiments, the outer diameter of elongate flexible shaft  230  of steerable catheter  200  is less than 5 mm. 
     While in certain embodiments the steerable catheter  200  is non-navigated, other embodiments of the steerable catheter  200  are navigated. In certain embodiments in which steerable catheter  200  is navigated, a localization element  24  is positioned in elongate flexible shaft  230  or biopsy device  220 , preferably at or near the distal end thereof. In certain embodiments, localization element  24  may comprise electromagnetic sensors. However, in other embodiments the steerable catheter  200  may be navigated wherein elongate flexible shaft  230  or biopsy device  220  may further comprise radiopaque markers visible via fluoroscopic imaging, or echogenic materials or patterns that increase visibility of the tip component under an ultrasonic beam. In yet other embodiments the steerable catheter  200  may be navigated wherein distal end portion  234  of elongate flexible shaft  230  or distal end of biopsy device  220  may further comprise radiopaque markers visible via fluoroscopic imaging, or echogenic materials or patterns that increase visibility of the tip component under an ultrasonic beam. In one embodiment, localization element  24  comprises a six (6) degree of freedom (6DOF) electromagnetic sensor. In another embodiment the localization element comprises a five (5) degree of freedom (5DOF) electromagnetic sensor. Using the localization element, the user can have the location of the biopsy device  220  is defined on the navigation screen. 
     In one embodiment, localization element  24  may be attached to actuation wire  212 . Movement of actuation wire  212  as handle  216  is manipulated causes coordinated movement of localization element  24  thereby providing an indication that biopsy device  220  is being operated. In accordance with other embodiments, for example, a localization element as described herein (e.g., an electromagnetic (EM) sensor) is affixed (preferably permanently affixed, but may also be removable) to a biopsy device or medical instrument so that both the biopsy device or medical instrument (or component thereof) and the localization element move together, such that they can be imaged and viewed. In one embodiment, for example, biopsy device  220  is an aspiration needle and the needle tip and the sensor move together. In another embodiment, for example, biopsy device  220  is a brush, forceps, or forceps tissue capture mechanism and these components and the localization element move together. In these and other embodiments, handle  216  may be coupled with localization element  24 , thus allowing movement tracking. These various embodiments allow the biopsy device or medical instrument (and components thereof) to be tracked using the localization element, improving overall accuracy and reliability. 
     Referring now to  FIGS.  20 A,  20 B and  20 C , in one embodiment biopsy device  220  further comprises an angled or directionally arranged radiopaque marker pattern  115  that is visible via fluoroscopic imaging. The radiopaque marker pattern  115  may be made of stainless steel, tantalum, platinum, gold, barium, bismuth, tungsten, iridium, or rhenium, alloys thereof, or of other radiopaque materials known in the art. The radiopaque marker pattern  115  allows for tracking of the location and orientation of the biopsy device  220 . Based upon the orientation of the radiopaque marker pattern  115  on the biopsy device  220  with respect to the incident fluoroscopic beam, a distinct image is visible on a fluoroscope. As the biopsy device  220  is navigated and rotated into position at the patient target, the orientation of the radiopaque marker pattern  115  with respect to the incident fluoroscopic beam will be altered resulting in a corresponding change to the fluoroscopic image, thereby allowing the user to know the location and orientation of the biopsy device  220 . Accordingly, the user can then operate the biopsy device  220  at the desired patient target. In other embodiments, radiopaque marker pattern  115  may be at distal end portion  234  of elongate flexible shaft  230 . In this embodiment, biopsy device  220  may comprise any of the biopsy devices described elsewhere herein (see, e.g.,  FIGS.  17 A- 17 G ). 
     Referring now to  FIGS.  21 A,  21 B, and  21 C , in one embodiment biopsy device  220  further comprises generally circular radiopaque markers  116  placed around biopsy device  220 , with 3 radiopaque markers on one side of biopsy device  220  and 1 radiopaque marker on the opposite side of biopsy device  220 . By way of example, in certain embodiments, 4 radiopaque markers are placed on one side of biopsy device  220  and 2 radiopaque markers are placed on the opposite side of biopsy device  220 . By way of further example, in certain embodiments, 5 radiopaque markers are placed on one side of biopsy device  220  and 3 radiopaque markers are placed on the opposite side of biopsy device  220 . In other embodiments, circular radiopaque markers  116  may be at distal end portion  234  of elongate flexible shaft  230 . In this embodiment, biopsy device  220  may comprise any of the biopsy devices described elsewhere herein (see, e.g.,  FIGS.  17 A- 17 G ). 
     Referring now to  FIGS.  22  and  23   , in one embodiment biopsy device  220  further comprises an echogenic pattern that may be viewed via ultrasonic imaging. Several approaches of enhancing the ultrasonic signature of medical instruments through modification of the instrument surface reflectivity are known in the prior art and can be applied to embodiments of the present invention. In one embodiment, an echogenic pattern can be positioned around the side wall of biopsy device  220 , such that the echogenic pattern fully encompasses the exterior circumference of biopsy device  220 . In other embodiments, an echogenic pattern may be at distal end portion  234  of elongate flexible shaft  230 . In this embodiment, biopsy device  220  may comprise any of the biopsy devices described elsewhere herein (see, e.g.,  FIGS.  17 A- 17 G ). 
     Referring now to  FIGS.  22  and  22 A , the echogenic pattern comprises a plurality of partially spherical indentations  114  on the exterior surface of biopsy device  220 , such that the radius of the partially spherical indentations is less than the wavelength of the incident ultrasonic beam. The plurality of partially spherical indentations  114  cause constructive interference of the ultrasonic beam to affect an amplification of the reflecting beam along the line of the incident beam; such amplification may occur at any incident ultrasonic beam angle. In this embodiment, biopsy device  220  may comprise any of the biopsy devices described elsewhere herein (see, e.g.,  FIGS.  17 A- 17 G ). 
     Referring now to  FIGS.  23  and  23 A , the echogenic pattern comprises a plurality of grooves  113  cut into the exterior surface of biopsy device  220  that increase the reflective coefficient of biopsy device  220 . The plurality of grooves  113  may cause constructive interference of the ultrasonic beam to affect an amplification of the reflecting beam along the line of the incident beam. In this embodiment, biopsy device  220  may comprise any of the biopsy devices described elsewhere herein (see, e.g.,  FIGS.  17 A- 17 G ). 
     In certain embodiments, as discussed herein, localization element  24  may be positioned at or near the distal end of biopsy device  220 . Alternatively, in other embodiments, localization element  24  is positioned at or near the proximal end of biopsy device  220 . In yet other embodiments, multiple localization elements  24  (e.g., 5DOF or 6DOF electromagnetic sensors) and/or radiopaque markers, echogenic patterns, etc. may be positioned at or near the proximal end of biopsy device  220 . Alternatively, in other embodiments, multiple localization elements  24  (e.g., 5DOF or 6DOF electromagnetic sensors) and/or radiopaque markers, echogenic patterns, etc. may be positioned at or near the distal end of the biopsy device  220 . In yet other embodiments, multiple localization elements  24  (e.g., 5DOF or 6DOF electromagnetic sensors) and/or radiopaque markers, echogenic patterns, etc. may be positioned at or near the proximal and distal ends of the biopsy device  220 . In another embodiment of the present invention, biopsy device  220  contains no localization element  24 . Alternatively, localization element  24  is positioned at or near distal end portion  234  of elongate flexible shaft  230 . By positioning localization element  24  at or near distal end portion  234  of elongate flexible shaft  230 , in certain embodiments, the biopsy device  220  could be made smaller or at a lesser cost. In this embodiment, biopsy device  220  may comprise any of the biopsy devices described elsewhere herein (see, e.g.,  FIGS.  17 A- 17 G ). 
     In yet other embodiments, forceps device  300  (see  FIG.  17 B ) may be visible via fluoroscopic imaging wherein an angled or directionally arranged radiopaque marker pattern  115  is at or near the proximal end and/or the distal end of forceps device  300  (see  FIGS.  20 A,  20 B, and  20 C ). In yet other embodiments, forceps device  300  may be visible via fluoroscopic imaging wherein a radiopaque marker pattern  115  comprising generally circular radiopaque markers  116  is placed around forceps device  300  (see  FIGS.  21 A,  21 B, and  21 C ). In yet other embodiments, forceps device  300  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of grooves  113  is in forceps device  300  (see  FIG.  23   ). In yet other embodiments, forceps device  300  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of partially spherical indentations  114  is in forceps device  300  (see  FIG.  22   ). 
     Referring now to  FIG.  24   , in an alternative embodiment, steerable catheter  200  comprises an alternative forceps device  300  as the biopsy device  220 . Instead of a mechanical forceps device actuated by an actuation wire (see  FIG.  19   ), first and second forceps jaws  302  are operated by a solenoid coil  1601 . Solenoid coil  1601  is housed within in forceps housing  301  and when the solenoid is in an “active” mode, it is activated by energy stored in capacitor  1603  thereby actuating the first and second forceps jaws  302  via armature  1604 . In a “passive” mode solenoid coil  1601  may act as a localization element  24  (e.g., an electromagnetic or other sensor). In other embodiments, other biopsy devices as described elsewhere herein (see, e.g.,  FIGS.  17 A- 17 G ), may be actuated or operated in a similar manner. 
     Referring now to  FIGS.  25 A and  25 B , in an alternative embodiment, steerable catheter  200  comprises an auger device  400  as the biopsy device  220 . Auger device  400  may be positioned proximate to the region (or tissue) of interest and is adapted to remove tissue from the respiratory system of a patient. In certain embodiments, auger device  400  may comprise an auger bit housing  401 , and an auger bit  402  within the auger bit housing  401 . Auger bit  402  has a base and a tip, and a tissue collection region  406  at the base of the auger bit  402 , wherein the auger bit  402  may be operably connected to the actuation wire  212 . Auger bit  402  may be helical in shape. Auger bit housing  401  has a closed proximal end attached to distal end portion  234  of elongate flexible shaft  230  and an open distal end. The proximal end of auger bit housing  401  has a hole through which the actuation wire extends toward the open distal end. In certain embodiments, auger bit housing  401  and auger bit  402  can be made of, for example, stainless steel or other metal, plastic, for example PVC, or from a hard polymeric material. In one particular embodiment, the auger bit  402  has a constant diameter from the base to the tip. In another embodiment, the diameter of auger bit  402  decreases from the base to the tip. In this particular embodiment, as illustrated in  FIG.  25 B , auger bit  402  is extendable out the open distal end of auger bit housing  401  and rotatable by manipulation of the actuation wire  212  at handle  216  (not shown). Auger device  400  may be navigated via the inclusion of a localization element  24  with a sensor lead  103  extending to proximal end portion  232  of elongate flexible shaft  230 . In other embodiments, localization element  24  may be attached to actuation wire  212  such that movement of actuation wire  212  as handle  216  is manipulated causes coordinated movement of localization element  24  thereby providing an indication that auger device  400  is being operated. In other embodiments, localization element  24  may be attached to auger bit  402 . Once the target tissue of a patient&#39;s respiratory system is reached by steerable catheter  200 , the physician or other healthcare professional actuates auger device  400  by manipulating handle  216  which actuates actuating wire  212  thereby causing auger bit  402  to extend and rotate, removing tissue from the patient. Rotation of auger bit  402  draws the removed tissue into the auger bit housing  401  and into tissue collection region  406 . In other embodiments, a vacuum pressure may be used to pull the removed tissue into tissue collection region  406 . In yet other embodiments as illustrated by  FIGS.  26 A and  26 B , auger device  400  may have no localization element. 
     As shown in  FIG.  27   , in another embodiment of auger device  400 , tissue collection region  406  of auger device  400  has a viewing window  408 . Viewing window  408  allows for inspection, e.g., via bronchoscope or other viewing or sensing device such as described herein while the steerable catheter  200  is still in the patient&#39;s body, of when the tissue collection region  406  is full or a sufficient sample size has been collected. In other embodiments, the removed tissue can be viewed through viewing window  408  after the steerable catheter  200  has been removed from the patient&#39;s body or it can be viewed by a bronchoscope inserted into the patient&#39;s body. 
     In yet other embodiments, auger device  400  may be visible via fluoroscopic imaging wherein an angled or directionally arranged radiopaque marker pattern  115  is at or near the proximal end and/or the distal end of auger device  400  (see  FIGS.  20 A,  20 B, and  20 C ). In yet other embodiments, auger device  400  may be visible via fluoroscopic imaging wherein a radiopaque marker pattern  115  comprising generally circular radiopaque markers  116  is placed around auger device  400  (see  FIGS.  21 A,  21 B, and  21 C ). In yet other embodiments, auger device  400  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of grooves  113  is in auger device  400  (see  FIG.  23   ). In yet other embodiments, auger device  400  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of partially spherical indentations  114  is in auger device  400  (see  FIG.  22   ). 
     Referring now to  FIGS.  28 A and  28 B , in an alternative embodiment, steerable catheter  200  comprises a boring bit device  500  as the biopsy device  220 . Boring bit device  500  may be positioned proximate to the region (or tissue) of interest and is adapted to remove tissue from the respiratory system of a patient. Additionally, in certain embodiments, elongate flexible shaft  200  further comprises a vacuum channel  506 . In certain embodiments, boring bit device  500  may comprise a boring bit housing  501  and a boring bit  502  within boring bit housing  501 . Boring bit  502  may comprise a hollow cylinder having a closed proximal end and an open distal end having a plurality of cutting teeth around the circumference of the cylinder, wherein boring bit  502  may be operably connected to actuation wire  212 . Boring bit housing  501  and boring bit  502  can be made of, for example, stainless steel or other metal, plastic, for example PVC, or from a hard polymeric material. Boring bit device  500  may be navigated via the inclusion of an attached localization element  24  with a sensor lead  103  extending to the proximal end portion  232  of elongate flexible shaft  230 . In other embodiments, localization element  24  may be attached to actuation wire  212  such that movement of actuation wire  212  as handle  216  is manipulated causes coordinated movement of localization element  24  thereby providing an indication that boring bit device  500  is being operated. In other embodiments, localization element  24  may be attached to boring bit  502 . In this particular embodiment, as illustrated in  FIG.  28 B , boring bit  502  is extendable out the open distal end of boring bit housing  501  and rotatable by manipulation of the actuation wire  212  at handle  216  (not shown). Once the target tissue of a patient&#39;s respiratory system is reached by steerable catheter  200 , the physician or other healthcare professional actuates boring bit device  500  by manipulating handle  216  which actuates actuating wire  212  thereby causing boring bit  502  to extend and rotate, removing tissue from the patient. In certain embodiments, boring bit device  500  may also comprise a tissue collection region where the removed tissue can be collected. In yet other embodiments, tissue collection region of boring bit device  500  may have a viewing window through which the removed tissue can be inspected from outside boring bit device  500  (see  FIG.  27   ). In certain embodiments, boring bit device  500  may have no localization element as illustrated in  FIGS.  30 A and  30 B . 
       FIG.  29    illustrates another embodiment where, boring bit housing  501  may have at least one opening  510  in the proximal end attached to distal end portion  234  of elongate flexible shaft  230  and an open distal end through which the boring bit  502  is extended. Additionally, in this embodiment, the proximal end of boring bit  502  may have at least one opening  510 . The proximal end of boring bit housing  501  has a hole through which the actuation wire  212  extends toward the open distal end. In this particular embodiment, boring bit  502  is extendable out the open distal end of the boring bit housing  501  and rotatable by manipulation of the actuation wire  212  at handle  216  (not shown). Once the target tissue of a patient&#39;s respiratory system is reached by the steerable catheter  200 , the physician or other healthcare professional actuates boring bit device  500  by manipulating handle  216  which actuates actuating wire  212  thereby causing boring bit  502  to extend and rotate, removing tissue from the patient. Additionally, a vacuum pressure may be applied at proximal end portion  232  of elongate flexible shaft  230  wherein this pressure acts on the vacuum channel  506 , the at least one opening  510  in the proximal end of boring bit housing  501 , and the at least one opening  510  in the proximal end of boring bit  502  to aid in the removal of the patient&#39;s tissue. In other embodiments, wherein boring bit device  500  may further comprise a tissue collection region, the applied vacuum pressure may be used to pull the removed tissue into tissue collection region. 
     In another embodiment, as illustrated by  FIGS.  31 A and  31 B , boring bit housing  501  has closed proximate end attached to the distal end portion  234  of elongate flexible shaft  230  and an open distal end through which boring bit  502  is extended. The proximal end of boring bit housing  501  has a hole through which the actuation wire  504  extends toward the open distal end. Additionally, in this embodiment, actuation wire  504  is hollow. In this particular embodiment, as illustrated in  FIG.  32   , boring bit  502  is extendable out the open distal end of boring bit housing  501  and rotatable by manipulation of hollow actuation wire  504  at handle  216 . Once the target tissue of a patient&#39;s respiratory system is reached by steerable catheter  200 , the physician or other healthcare professional actuates the boring bit device  500  by manipulating handle  216  which actuates hollow actuating wire  504  thereby causing boring bit  502  to extend and rotate, removing tissue from the patient. Additionally, a vacuum pressure may be applied at proximal end portion  232  of elongate flexible shaft  230  wherein this pressure acts on hollow actuation wire  504  to aid in the removal of the patient&#39;s tissue. 
     In yet other embodiments, boring bit device  500  may be visible via fluoroscopic imaging wherein an angled or directionally arranged radiopaque marker pattern  115  is at or near the proximal end and/or the distal end of boring bit device  500  (see  FIGS.  20 A,  20 B, and  20 C ). In yet other embodiments, boring bit device  500  may be visible via fluoroscopic imaging a radiopaque marker pattern  115  comprising generally circular radiopaque markers  116  is placed around boring bit device  500  (see  FIGS.  21 A,  21 B, and  21 C ). In yet other embodiments, boring bit device  500  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of grooves  113  is in boring bit device  500  (see  FIG.  23   ). In yet other embodiments, boring bit device  500  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of partially spherical indentations  114  is in boring bit device  500  (see  FIG.  22   ). 
     Referring now to  FIG.  33   , in an alternative embodiment, steerable catheter  200  comprises an aspiration needle device  1100  as the biopsy device  220 . Aspiration needle device  1100  may be positioned proximate to the region (or tissue) of interest and is adapted to remove tissue from the respiratory system of a patient. In certain embodiments, aspiration needle device  1100  may comprise an aspiration needle housing  1101  and an aspiration needle  1102  within aspiration needle housing  1101 . Aspiration needle device  1100  may be navigated via the inclusion of an attached localization element  24  with a sensor lead  103  extending to proximal end portion  232  of elongate flexible shaft  230 . In other embodiments, localization element  24  may be attached to hollow actuation wire  504  such that movement of hollow actuation wire  504  as handle  216  is manipulated causes coordinated movement of localization element  24  thereby providing an indication that aspiration needle device  1100  is being operated. In other embodiments, localization element  24  may be attached to aspiration needle  1102 . In certain embodiments, aspiration needle device  1100  may have no localization element. In certain embodiments, aspiration needle  1102  may be between 18 and 22 ga. Aspiration needle housing  1101  and aspiration needle  1102  can be made of, for example, nitinol, stainless steel or other metal, plastic, for example PVC, or from a hard polymeric material. In certain embodiments, aspiration needle  1102  may be a flexible needle. In other embodiments, aspiration needle  1102  may be a relatively rigid (non-flexible) needle. In yet other embodiments, aspiration needle  1102  may comprise a shape memory alloy, as described in greater detail elsewhere herein. There are a number of mechanically operated aspiration needle devices that are known in the prior art and can be adapted to operably connect to a hollow actuation wire of the steerable catheter  200 . In additional embodiments, the aspiration needle device comprises a single biopsy device that is attached at the proximal end portion  232  of elongate flexible shaft  230  and extends to the distal end portion  234  of elongate flexible shaft  232 . Aspiration needle device  1100  may be navigated via the inclusion of an attached localization element  24  with a sensor lead  103  extending to proximal end portion  232  of elongate flexible shaft  230 . Once the target tissue of a patient&#39;s respiratory system is reached by steerable catheter  200 , the physician or other healthcare professional actuates aspiration needle device  1100  by manipulating handle  216  which actuates the actuating wire  504  thereby causing aspiration needle  1102  to extend and pierce tissue in the patient. Additionally, a vacuum pressure may be applied at proximal end portion  232  of elongate flexible shaft  230  wherein this pressure acts on hollow actuation wire  504  to aid in the removal of the patient&#39;s tissue. In another embodiments, aspiration needle device  1100  comprises a single biopsy device that is attached at proximal end portion  232  of elongate flexible shaft  230  and extends to distal end portion  234  of elongate flexible shaft  230 , the physician or other healthcare professional actuates aspiration needle device  1100  by manipulating handle  216  which causes aspiration needle  502  to extend and pierce tissue from the patient. Additionally, a vacuum pressure may be applied at proximal end portion  232  of elongate flexible shaft  230  wherein this pressure acts on aspiration needle  1102  to aid in the removal of the patient&#39;s tissue. In certain embodiments, aspiration needle device  1100  may also comprise a tissue collection region where the removed tissue can be collected. In other embodiments, the applied vacuum pressure may be used to pull the removed tissue into tissue collection region. In yet other embodiments, tissue collection region of aspiration needle device  1100  may have a viewing window through which the removed tissue can be inspected from outside aspiration needle device  1100  (see  FIG.  27   ). 
     In yet other embodiments, aspiration needle device  1100  may be visible via fluoroscopic imaging wherein an angled or directionally arranged radiopaque marker pattern  115  is at or near the proximal end and/or the distal end of aspiration needle device  1100  (see  FIGS.  20 A,  20 B, and  20 C ). In yet other embodiments, aspiration needle device  1100  may be visible via fluoroscopic imaging wherein a radiopaque marker pattern  115  comprising generally circular radiopaque markers  116  is placed around aspiration needle device  1100  (see  FIGS.  21 A,  21 B, and  21 C ). In yet other embodiments, aspiration needle device  1100  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of grooves  113  is in aspiration needle device  1100  (see  FIG.  23   ). In yet other embodiments, aspiration needle device  1100  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of partially spherical indentations  114  is in aspiration needle device  1100  (see  FIG.  22   ). 
     Referring now to  FIGS.  34 A and  34 B , in an alternative embodiment, steerable catheter  200  comprises a brush device  1000  as the biopsy device  220 . Brush device  1000  may be positioned proximate to the region (or tissue) of interest and is adapted to remove tissue from the respiratory system of a patient. In certain embodiments, brush device  1000  may comprise a brush housing  1001  and a brush  1002  wherein brush  1002  comprises a plurality of bristles affixed to an actuation wire  212 . Brush housing  1001  may have a closed proximal end attached to the distal end portion  234  of elongate flexible shaft  230  and an open distal end. Additionally brush housing  1001  may have an internal wall  1003  with an aperture  1004  having a diameter less than that of the diameter of brush  1002 . The proximal end of brush housing  1001  has a hole through which the actuation wire  212  extends toward the open distal end. Brush housing  1001  can be made of, for example, stainless steel or other metal, plastic, for example PVC, or from a hard polymeric material. Brush  1002  is extendable out the open distal end of brush housing  1001  and rotatable by manipulation of the actuation wire  212  at handle  216 . Brush device  1000  may be navigated via the inclusion of an attached localization element  24  with a sensor lead  103  extending to proximal end portion  232  of elongate flexible shaft  230 . In other embodiments, localization element  24  may be attached to actuation wire  212  such that movement of actuation wire  212  as handle  216  is manipulated causes coordinated movement of localization element  24  thereby providing an indication that brush device  1000  is being operated. In other embodiments, localization element  24  may be attached to brush  1002 . In certain embodiments, brush device  1000  may have no localization element. Once the target tissue of a patient&#39;s respiratory system is reached by steerable catheter  200 , the physician or other healthcare professional actuates brush device  1000  by manipulating handle  216  which actuates actuating wire  212  thereby causing brush  1002  to extend and rotate, removing tissue  1005  from the patient. The physician or other healthcare professional may then withdraw brush  1002  into brush housing  1001  whereby removed tissue  1006  is scraped from brush  1002  by aperture  1004 . Additionally, in another embodiment, elongate flexible shaft  230  further comprises a vacuum channel and the proximal end of brush housing  1001  further comprises at least one hole to which a vacuum pressure can be applied. Additionally, a vacuum pressure may be applied at proximal end portion  232  of elongate flexible shaft  230  wherein this pressure acts on the vacuum channel and the at least one opening in the proximal end of brush housing  1001  to aid in the removal of the patient&#39;s tissue. In certain embodiments, brush device  1000  may also comprise a tissue collection region where the removed tissue can be collected. In other embodiments, the applied vacuum pressure may be used to pull the removed tissue into tissue collection region. In yet other embodiments, tissue collection region of brush device  1000  may have a viewing window through which the removed tissue can be inspected from outside brush device  1000  (see  FIG.  27   ). 
     In yet other embodiments, brush device  1000  may be visible via fluoroscopic imaging wherein an angled or directionally arranged radiopaque marker pattern  115  is at or near the proximal end and/or the distal end of brush device  1000  (see  FIGS.  20 A,  20 B, and  20 C ). In yet other embodiments, brush device  1000  may be visible via fluoroscopic imaging wherein a radiopaque marker pattern  115  comprising generally circular radiopaque markers  116  is placed around brush device  1000  (see  FIGS.  21 A,  21 B, and  21 C ). In yet other embodiments, brush device  1000  may be visible via ultrasonic imaging an echogenic pattern comprising a plurality of grooves  113  is in brush device  1000  (see  FIG.  23   ). In yet other embodiments, brush device  1000  may be visible via ultrasonic imaging wherein an echogenic pattern comprising a plurality of partially spherical indentations  114  is in brush device  1000  (see  FIG.  22   ). 
     In another embodiment of a brush device, as brush is pushed out of the brush housing the brush is squeezed through a smaller opening to collect the sampled tissue that was trapped when extended. When fully extended, the brush device end would be open so that the brush can be retracted and the sampled tissue can be pulled into the instrument. The brush device would then close as the brush is extended out and the sampled tissue could be scraped/squeezed from the brush bristles and collected in a reservoir. In certain embodiments, a vacuum pressure may be added to this device in conjunction or in lieu of the scrapping process to clean the brush. 
     In yet another embodiment, biopsy device  220  is extendable is extendable along a path from a position within the outer wall  236  through a side exit to a position outside the outer wall  236  at an angle of at least 30 degrees relative to the longitudinal axis, wherein the path of biopsy device  220  can be calibrated to the location of an electromagnetic localization sensor positioned at the distal end portion of the elongate flexible shaft and displayed by a surgical instrument navigation system. Various embodiments of biopsy devices exiting from the side of the elongate catheter body can be seen in  FIG.  37   . 
     In these and other embodiments, a portion of biopsy device  220  may be bent at an angle relative longitudinal axis  207 . A bend in biopsy device  220 , may allow the physician or other healthcare professional to rotate biopsy device  220  and sample the region (or tissue) of interest via several different pathways or positions. This may also increase the amount of region (or tissue) of interest that may be sampled in a single pass, and may improve targeting of regions (or tissue) of interest to be sampled. Moreover, a bend in biopsy device  220  may assist in targeting a region that is not necessarily directly in a patient pathway (e.g., an airway), but may be next to the pathway, thus enabling the physician or other healthcare professional to direct biopsy device  220  to a desired location off the axis of the airway. 
     The method or procedure of guiding the steerable catheter  200  of certain embodiments to a desired target tissue in the respiratory system of a patient comprises: (i) inserting a flexible lumen into the patient, (ii) inserting into the flexible lumen steerable catheter  200 , (ii) navigating steerable catheter  200  through the respiratory system of the patient, (iii) manipulating steering actuator  218  to cause a deflection in longitudinal axis  207 , and (iv) performing a medical procedure at the region (or tissue) of interest. In embodiments where steerable catheter  200  is a navigated catheter, the method or procedure of guiding the steerable catheter  200  of certain embodiments to a desired target tissue of a patient includes the additional steps of: (i) displaying an image of the region of the patient, (ii) detecting a location and orientation of localization element  24 , and (iii) displaying, in real-time, biopsy device  220  on the image by superimposing a virtual representation of steerable catheter  200  and biopsy device  220  on the image based upon the location and orientation of localization element. 
     A method or procedure of guiding steerable catheter  200  of certain embodiments to a desired target tissue in the respiratory system of a patient may comprise inserting a flexible lumen into the patient, and inserting into the flexible lumen steerable catheter  200 . Steerable catheter  200  may then be navigated to the region of interest and steering actuator  218  may be manipulated to cause a deflection in longitudinal axis  207 . Medical procedure may then be performed at the region (or tissue) of interest. In embodiments where steerable catheter  200  is a navigated catheter, the method or procedure of guiding steerable catheter  200  of certain embodiments to a region (or tissue) of interest may comprise the additional steps of displaying an image of the region (or tissue) of interest and detecting a location and orientation of localization element  24 . Then biopsy device  220  may be displayed, in real-time, on the image by superimposing a virtual representation of steerable catheter  200  and biopsy device  220  on the image based upon the location and orientation of localization element  24 . 
     In one embodiment of the present invention, surgical instrument  12  (see  FIG.  1   ) comprises a surgical catheter having a side exit (referred to herein as “side exiting catheter”) which may be used in a medical procedure to gain access to, manipulate, remove or otherwise treat tissue within the body including, for example, heart or lung tissue. Generally, surgical catheters of the present invention have a distal end portion which can be remotely manipulated via a proximally located handle. 
     In accordance with one embodiment of the present invention and referring now to  FIG.  35   , side exiting catheter  100  comprises actuating handle  110  and elongate flexible shaft  130 . Elongate flexible shaft  130  has proximal end portion  132 , distal end portion  134 , longitudinal axis  109  extending from proximal end portion  132  to distal end portion  134 , outer wall  136  comprising a biocompatible material extending from proximal end portion  132  to distal end portion  134 , and a side exit  105  at distal end portion  134  of elongate flexible shaft. In certain embodiments, the biocompatible material is a biocompatible polymer. The stiffness properties of elongate flexible shaft  130  allow elongate flexible shaft  130  to be advanced in patient  13  in a desired direction to a desired region (or tissue of interest) via the application of torsional or linear force applied to handle  110  at proximal end portion  132  of elongate flexible shaft  134 . 
     A localization element  24  may be positioned at distal end portion  134  of elongate flexible shaft  130 . In general any of a number of localization elements  24  may be used, including, but not limited to, for example, electromagnetic sensors, radiopaque markers visible via fluoroscopic imaging, or echogenic materials or patterns that increase visibility of the tip component under an ultrasonic beam. In this embodiment, localization element  24  comprises a six (6) degree of freedom (6DOF) electromagnetic sensor. In other embodiments, localization element  24  comprises a five (5) degree of freedom (5DOF) electromagnetic sensor. A localization element lead  103  extends from localization element  24  to proximal end portion  132  of elongate flexible shaft  130 . In an alternative embodiment, localization element  24  and the electromagnetic field generator may be reversed, such that localization element  24  positioned at distal end portion  134  of elongate flexible shaft  130  emits a magnetic field that is sensed by external sensors. 
     Side exiting catheter  100  further comprises medical instrument  108  that may be extended from a position within outer wall  136  and through side exit  105  to a position outside outer wall  136  of elongate flexible shaft  130  by manipulation of handle  110 . For ease of illustration, only the portion of medical instrument  108  that is extended outside elongate flexible shaft  130  appears in  FIG.  35   ; the remaining portion of medical instrument  108  which is attached to handle  110  is hidden from view (see  FIGS.  51 A and  51 B ). In one embodiment, medical instrument  108  extends through side exit  105  along a path at an angle of at least 10 degrees relative to longitudinal axis  109 . 
     In certain embodiments, by using localization element  24  (which in certain embodiments comprises a 6DOF sensor as described herein), the physician or other healthcare professional can have the location and direction of side exit  105  of elongate flexible shaft  130  displayed by surgical instrument navigation system  10 . A real time two- or three-dimensional virtual reconstruction of side exit  105  and several centimeters of distal end portion  132  of elongate flexible shaft  130  may be displayed by surgical instrument navigation system  10 . Visualization of the location and orientation of side exit  105  may allow for more intuitive advancement of side exiting catheter  100  to a region (or tissue) of interest. An image plane may be generated that is at side exit  105 , as opposed to a point or position distal to distal end portion  134  of elongate flexible shaft  130 . In certain embodiments, this may allow easier targeting of lesions, or other region(s) (or tissue) of interest, that may not be directly in the airway or other pathways, but rather partially or even completely outside of the airway or other pathways. In accordance with an exemplary method of using the device, side exiting catheter  100  may be steered slightly past the region (or tissue) of interest to align side exit  105 . Medical instrument  108  (e.g., forceps, needle, brush, fiducial delivery device, etc.) may then be extended out elongate flexible shaft  130  through side exit  105 . The directional aspect of distal end portion  134  and medical instrument  108  can be viewed on display  18  (see  FIG.  1   ) and a simulated medical instrument can be shown to demonstrate to the physician or other healthcare professional which region (or tissue) of interest will be sampled. These applications may be particularly useful in the sampling of lymph nodes that are outside the patient airways. In some embodiments, for example, side exiting catheter  100  may be capable of creating an endobronchial ultrasound (EBUS)-like view. For example, an image plane oriented with side exit  105  plane may be created and medical instrument  108  may be shown sampling the region (or tissue) of interest on this plane. In various alternative embodiments, the image(s) may be oriented in a plane or orthogonally. Additionally in other embodiments, various curve fitting algorithms may be provided based upon the type and flexibility of the elongate flexible shaft used. These algorithms enable estimated curved trajectories of elongate flexible shaft  130  to be displayed to assist the physician or other healthcare professional. 
     In accordance with another embodiment, systems and methods may be used to provide the initial location of a localization element (e.g., an electromagnetic sensor) in a surgical instrument (e.g., a steerable surgical catheter, a side exiting catheter, a steering or shape sensing device such as a robotic articulating arm, fiber optic shape tracking device, or micro-actuator/flex systems, etc.). In one embodiment, a calibration jig system may be employed. The calibration jig system comprises at least three reference localization elements (e.g., electromagnetic sensors) positioned substantially in a plane and a tool/calibration channel may be positioned in a known location relative to the localization element plane. A surgical instrument may then be inserted into the tool/calibration channel and the surgical instrument pathway shape may be recorded along with the localization element(s) (e.g., 5DOF and/or 6DOF electromagnetic sensors) in the surgical instrument with respect to the location of the reference localization elements in the localization element plane. By using this calibration jig system, the alignment of the localization element(s) within the surgical instrument may be determined relative to the alignment of the surgical instrument. Additionally, or alternatively, other sensing mechanisms that report position and/or shape can be correlated relative to the reference localization element coordinates and therefore may define the complete or substantially complete physical coordinate system. Because the position of the jig tool channel is known relative to the position of the reference localization elements, the position of sensing mechanisms placed within the surgical instrument may be determined relative to the calibration jig and therefore relative to each other. 
     In certain embodiments, as illustrated in  FIG.  36   , after calibration of the alignment of localization element  24  (e.g., an electromagnetic sensor) in side exiting catheter  100  using the calibration jig system, path  122  of a medical instrument (not shown) may be calibrated relative to the position of localization element  24 . During calibration, the location/coordinates of the tip of medical instrument  108  will be measured relative to the position of localization element  24  for an initial position X 0 . After medical instrument  108  is advanced in elongate flexible shaft  130  a distance X 1  to extend medical instrument  108  through side exit  105  to a position outside the elongate flexible shaft  130  the location/coordinates of the tip of medical instrument  108  can be measured at x tip1 , y tip1 , and z tip1  relative to local coordinate system  120  of localization element  24 . Similarly, after medical instrument  108  is advanced in elongate flexible shaft  130  a distance X 2  to extend medical instrument  108  to a further position outside the elongate flexible shaft  130  the location/coordinates of the tip of medical instrument  108  can be measured at x tip2 , y tip2 , z tip2  relative to local coordinate system  120  of localization element  24 . As medical instrument  108  extends through side exit  105  (see  FIG.  35   ) the path  122  of medical instrument  108  is at angle ⊖ relative to longitudinal axis  109 . As such, the location/coordinates of the tip of medical instrument  108  can be measured at a plurality of positions (e.g., 2, 3, 4, or more) within and outside elongate flexible shaft  130 . The calibration can be along the range of distances for which medical instrument  108  may be advanced. Accordingly, after path  122  of medical instrument  108  is determined, the path  122  can be displayed by surgical instrument navigation system  10  (see  FIG.  1   ) as a virtual path to aid the physician or other healthcare professional in extending the medical instrument to the desired region (or tissue) of interest. 
     Referring again to  FIG.  35   , in one embodiment, medical instrument  108  can be a flexible instrument, which in certain embodiments, may be an aspiration needle. In certain embodiments, the flexible instrument may be comprised of flexible nitinol. In another embodiment, medical instrument  108  can be constructed of a flexible coil having a stainless steel tip. In yet another embodiment, medical instrument  108  may be a relatively rigid (non-flexible). In yet other embodiments, medical instrument  108  may comprise a shape memory alloy, as described in greater detail elsewhere herein. As illustrated in  FIG.  37   , medical instrument  108  may comprise a variety of biopsy devices at the end  140  of medical instrument  108 , including, but not limited to, for example, a forceps device  37 A, an auger device  37 D, a boring bit device  37 B, and a brush device  37 C. In addition to biopsy devices, in yet other embodiments, a variety of medical instruments may be used such as fiducial delivery devices, diagnostic imaging devices (such as OCT), or therapy devices (such as an ablation device, an RF emitter, a microwave emitter, a laser device, a device to deliver a radioactive seed, a cryogenic therapy delivery device, a drug delivery device, or a fluid delivery device, among others), or combinations thereof, and the like. In other embodiments, medical instrument  108  may be used to deliver therapy to a surgical site (e.g., fluids, drugs, radioactive seeds, combinations thereof, or the like). 
     In one embodiment, as illustrated by  FIG.  38   , medical instrument  108  extends through side exit  105  along a path at an angle ⊖ of at least 10 degrees relative to longitudinal axis  109 . Typically, medical instrument  108  extends through side exit  105  along a path at an angle from about 10 degrees to about 70 degrees relative to longitudinal axis  109 . By way of example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 10 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 15 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 20 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 25 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 30 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 35 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 40 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 45 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 50 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 55 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 60 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 65 degrees relative to longitudinal axis  109 . By way of further example, in certain embodiments, medical instrument  108  extends through side exit  105  along a path at an angle of about 70 degrees relative to longitudinal axis  109 . 
     Referring now to  FIG.  39   , another embodiment of the side exiting catheter is shown wherein a side exiting tip component  101  is at distal end portion  134  of elongate flexible shaft  130 . Side exiting tip component  101  has a proximal and a distal end and a side exit  105 . In certain embodiments, localization element(s)  24  is positioned at or near the proximal end and/or near the distal end of side exiting tip component  101 . In this embodiment, medical instrument  108  extends through channel  106  of side exiting tip component  101  and channel  107  of elongate flexible shaft  130 . Additionally, a medical instrument  108  is shown extended through side exit  105  along a path at an angle. 
     In yet another embodiment, side exiting tip component  101  may comprise medical instrument  108  formed from a shape memory alloy which transitions between a first and second shape upon the application or release of stress. In certain embodiments, medical instrument  108  may be made of a superelastic material such as Nickel-Titanium (Ni—Ti) alloy (commercially available as nitinol) that has a martensitic to austenitic transformation temperature below body temperature and below normal room temperature. In other embodiments, other suitable shape memory materials for medical instrument  108  can include elastic biocompatible metals such as stainless steel, titanium, and tantalum or superelastic or psuedoelastic copper alloys, such as Cu—Al—Ni, Cu—Al—Zi, and Cu—Zi. When formed, medical instrument  108  comprising shape memory alloy will have a bend at a desired location with a bend angle (i.e., the first shape) and when housed within elongate flexible shaft  130 , medical instrument  108  becomes relatively straight (i.e., the second shape). When medical instrument  108  is advanced and extends through side exit  105 , the stress is removed and medical instrument  108  will return back to its preformed (first) shape. Accordingly, medical instrument  108  comprising shape memory alloy may be able to interact with regions (or tissues) of interest at additional angles than can be achieved the by a medical instrument  108  comprising a non-shape memory material extending through side exit  105 . As illustrated in  FIG.  40   , the longitudinal axis of the portion of medical instrument  108  extending outside distal end portion  134  is at an angle of approximately 90 degrees relative to the longitudinal axis  109 . 
     In yet another embodiment, medical instrument  108  comprising shape memory alloy may be used with a catheter having an exit at the distal end, wherein medical instrument  108  exits the catheter along a longitudinal axis. By using a medical instrument comprising a shape memory alloy with a catheter having an exit along a longitudinal axis, a physician or other healthcare provider is able to target lesions, or other targets, that may not be directly in the airway or other pathways, but rather partially or even completely outside of the airway or other pathways. Such targeting may not be possible with a catheter having an exit at the distal end and non-shape memory instruments. Similar to  FIG.  37   , medical instrument  108  comprising shape memory alloy may comprise a variety of biopsy devices, including, but not limited to, for example, a forceps device  37 A, an auger device  37 D, a boring bit device  37 B, a brush device  37 C, and an aspiration needle device. In addition to biopsy devices, in yet other embodiments, a variety of shape memory instruments may be used such as fiducial delivery devices, diagnostic imaging devices (such as OCT), therapy devices (such as an ablation device, an RF emitter, a microwave emitter, a laser device, a device to deliver a radioactive seed, a cryogenic therapy delivery device, a drug delivery device, or a fluid delivery device, among others), or combinations thereof, and the like. 
     As shown by  FIGS.  41 A,  41 B,  41 C and  41 D , in various embodiments of medical instrument  108  used in steerable catheter  100 , wherein medical instrument  108  is in the extended position it may be disposed at various angles relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 20 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 30 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 40 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 50 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 60 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments wherein medical instrument  108  is in the extended position it may be disposed at least about 70 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 80 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments wherein medical instrument  108  is in the extended position it may be disposed at least about 90 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 100 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments wherein medical instrument  108  is in the extended position it may be disposed at least about 110 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 120 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 130 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 140 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 150 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 160 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at least about 170 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . By way of further example, in certain embodiments, wherein medical instrument  108  is in the extended position it may be disposed at about 180 degrees relative to longitudinal axis  109  of elongate flexible shaft  130  at side exit  105 . 
     As shown in  FIG.  17 G , in an embodiment of the present invention, elongate flexible shaft  130  of side exiting catheter  100  can be steerable wherein elongate flexible shaft  130  comprises a steering mechanism comprising a steering actuator  218  at proximal end portion  132  and a pull wire connected to steering actuator  218  wherein distal end portion  134  may be moved relative to proximal end portion  132  by manipulating steering actuator  218  to apply a tension to the pull wire. Referring now to  FIG.  41 E , medical instrument  108  is shown in the extended position through side exit  105  of a steerable catheter comprising elongate flexible shaft  230 . Medical instrument  108  extends through side exit  105  along a path at an angle ⊖ of at least 10 degrees relative to longitudinal axis  207 . As described in greater detail elsewhere herein, in one embodiment, manipulation of steering actuator  218  (see  FIGS.  18 A and  18 B ) introduces an arc of β degrees into elongate flexible shaft  230 . Distal end portion  234  may be moved to a distance that separates two regions of elongate flexible shaft  230  located at opposing ends of a chord X connecting to two points separated by β degrees on the arc. 
     Typically, the outer diameter of elongate flexible shaft  130  of side exiting catheter  100  is less than 5 mm. By way of example, in certain embodiments, the outer diameter elongate flexible shaft  130  of side exiting catheter  100  is less than 1 mm. By way of further example, in certain embodiments, the outer diameter of elongate flexible shaft  130  of side exiting catheter  100  is less than 2 mm. By way of further example, in certain embodiments, the outer diameter of elongate flexible shaft  130  of side exiting catheter  100  is less than 3 mm. By way of further example, in certain embodiments, the outer diameter of elongate flexible shaft  130  of side exiting catheter  100  is less than 4 mm. By way of further example, in certain embodiments, the outer diameter of elongate flexible shaft  130  of side exiting catheter  100  is less than 5 mm. 
     However, in other embodiments, in addition to, or in place of, localization element  24 , side exiting catheter  100  may be navigated wherein elongate flexible shaft  130  or medical instrument  108  may further comprise radiopaque markers visible via fluoroscopic imaging, or echogenic materials or patterns that increase visibility of the tip component under an ultrasonic beam. In yet other embodiments, side exiting catheter  100  may be navigated via other types of sensors, such as conductive localization elements, fiber optic localization elements, or any other type of localization element. 
     In one embodiment, side exiting tip component  101 , illustrated by  FIGS.  42 A,  42 B, and  42 C , may be visible via fluoroscopic imaging. An angled or directionally arranged radiopaque marker pattern  115  at or near the proximal end and/or the distal end of side exiting tip component  101 . The radiopaque marker pattern  115  may be made of stainless steel, tantalum, platinum, gold, barium, bismuth, tungsten, iridium, or rhenium, alloys thereof, or of other radiopaque materials known in the art. Radiopaque marker pattern  115  allows for tracking of the location and orientation of side exit  105 . Based upon the orientation of radiopaque marker pattern  115  with respect to the incident fluoroscopic beam, a distinct image is visible on a fluoroscope. As side exiting catheter  100  is navigated and rotated into position at the region (or tissue of interest), the orientation of radiopaque marker pattern  115  with respect to the incident fluoroscopic beam will be altered resulting in a corresponding change to the fluoroscopic image, thereby allowing the physician or other healthcare professional to know the location and orientation of side exit  105 . Accordingly, the physician or other healthcare professional can then extend medical instrument  108  at the region (or tissue) of interest. Additionally, radiopaque marker pattern  115  may assist the physician or other healthcare professional in avoiding the passage of the elongate flexible shaft  130  and the medical instrument  108  into healthy tissue, a blood vessel, or other undesired patient area. In other embodiments, radiopaque marker pattern  115  may be on distal end portion  134  of elongate flexible shaft  130  of side exiting catheter  100 . In one embodiment radiopaque marker pattern  115  may replace a six (6) degree of freedom (6DOF) electromagnetic sensor. In other embodiments, radiopaque marker pattern  115 , may supplement a six (6) degree of freedom (6DOF) electromagnetic sensor. 
     As illustrated in  FIGS.  43 A,  43 B, and  43 C , in another embodiment radiopaque marker pattern  115  comprises generally circular radiopaque markers  116  placed around side exiting tip component  101 , with 3 radiopaque markers on one side of side exiting tip component  101  and 1 radiopaque marker on the opposite side of side exiting tip component  101 . By way of example, in certain embodiments, 4 radiopaque markers are placed on one side of side exiting tip component  101  and 2 radiopaque markers are placed on the opposite side of side exiting tip component  101 . By way of further example, in certain embodiments, 5 radiopaque markers are placed on one side of side exiting tip component  101  and 3 radiopaque markers are placed on the opposite side of side exiting tip component  101 . In other embodiments, radiopaque marker pattern  115  may be on distal end portion  134  of elongate flexible shaft  130  of side exiting catheter  100 . 
     In yet another embodiment, at least one ring of radiopaque material  115  may surround side exit  105 . By way of example, in one embodiment illustrated in  FIGS.  44 A,  44 B, and  44 C , side exit  105  of side exiting tip component  101  is surrounded by a first ring of radiopaque material  115  that is concentric to and in immediate connection with side exit  105  of the side exiting tip component  101 . This first ring of radiopaque material  115  is further surrounded by additional separate rings that are concentric to side exit  105  and the first ring of radiopaque material  115 . By way of example, in certain embodiments, side exit  105  is surrounded by 1 ring of radiopaque material  115 . By way of further example, in certain embodiments, side exit  105  is surrounded by 2 rings of radiopaque material  115 . By way of further example, in certain embodiments, side exit  105  is surrounded by 3 rings of radiopaque material  115 . By way of further example, in certain embodiments, side exit  105  is surrounded by 4 rings of radiopaque material  115 . By way of further example, in certain embodiments, side exit  105  is surrounded by 5 rings of radiopaque material  115 . By way of further example, in certain embodiments, side exit  105  is surrounded by 6 rings of radiopaque material  115 . In other embodiments, radiopaque marker pattern  115  may be on distal end portion  134  of elongate flexible shaft  130 . 
     In certain embodiments, all or a portion of side exiting tip component  101  and/or distal end portion  134  of elongate flexible shaft  130  of side exiting catheter  100  may be echogenic such that it may be viewed via ultrasonic imaging. Several approaches of enhancing the ultrasonic signature of medical devices through modification of the device surface reflectivity are known in the prior art and can be applied to certain embodiments of the present invention. In one embodiment, an echogenic pattern can be positioned around the side exiting tip component  101  and/or around distal end portion  134  of elongate flexible shaft  130 , such that the echogenic pattern covers the exterior circumference of side exiting tip component  101  and/or distal end portion  134  of elongate flexible shaft  130 . Typically an echogenic pattern is on the exterior surface of side exiting tip component  101  defined as a length from the distal end of side exiting tip component  101  toward the proximal end of side exiting tip component  101 . By way of example, in one embodiment, the echogenic pattern has a length of about 1 cm from the distal end of side exiting tip component  101 . By way of further example, in another embodiment, the echogenic pattern has a length of about 2 cm from distal end of the side exiting tip component  101 . 
     In one embodiment, as illustrated by  FIG.  45    and  FIG.  45 A , the echogenic pattern comprises a plurality of grooves  113  are cut into the exterior surface of side exiting tip component  101  such that the grooves increase the reflective coefficient of side exiting tip component  101 . The plurality of grooves  113  cause constructive interference of the ultrasonic beam to affect an amplification of the reflecting beam along the line of the incident beam. In other embodiments, plurality of grooves  113  may be in distal end portion  134  of elongate flexible shaft  130  of side exiting catheter  100 . 
     By way of further example, another embodiment of side exiting tip component  101  with an echogenic pattern is shown in  FIG.  46    and  FIG.  46 A . In this embodiment, the echogenic pattern comprises a plurality of partially spherical indentations  114  on the exterior surface of side exiting tip component  101 , such that the radius of the partially spherical indentations is less than the wavelength of the incident ultrasonic beam. The plurality of partially spherical indentations  114  cause constructive interference of the ultrasonic beam to affect an amplification of the reflecting beam along the line of the incident beam; such amplification occurs at any incident ultrasonic beam angle. In other embodiments, plurality of partially spherical indentations  114  may be in distal end portion  134  of elongate flexible shaft  130  of side exiting catheter  100 . 
     In certain embodiments, as shown in  FIG.  47   , all or a portion of medical instrument  108  may be echogenic such that it may be viewed via ultrasonic imaging. Several approaches of enhancing the ultrasonic signature of medical devices through modification of the device surface reflectivity are known in the prior art and can be applied to certain embodiments of the present invention. 
     In certain embodiments, as discussed herein, localization element  24  is positioned at or near distal end portion  134  of elongate flexible shaft  130 . In one embodiment, as shown in  FIG.  48   , localization element  24  comprises a six (6) degree of freedom (6DOF) electromagnetic sensor in the distal end portion  134  of the elongate flexible shaft  130 . A localization element lead  103  extends from localization element  24  to proximal end portion  132  (not shown) of elongate flexible shaft  130 . By way of further example, in another embodiment, an angled or directional pattern may be on the outside of elongate flexible shaft  130  that is visible via fluoroscopic imaging. Accordingly, embodiments of the present invention are not limited to one type and position of localization elements  24 . In certain embodiments, a combination of different localization element  24  types or a series of the same localization element  24  types may positioned at or near distal end portion  134  of elongate flexible shaft  130  of side exiting catheter  100 . 
     Another embodiment, with a radiopaque marker pattern positioned at or near the distal portion  134  of the elongate flexible shaft  130  is illustrated by  FIGS.  49 A,  49 B, and  49 C . In this embodiment a radiopaque marker pattern  115  comprising generally circular radiopaque markers  116  may be placed around distal end portion  134  of elongate flexible shaft  130 , with 3 markers on one side of the distal end portion  134  of elongate flexible shaft  130  and 1 marker on the opposite side of distal end portion  134  of elongate flexible shaft  130 . By way of example, in certain embodiments, 4 markers are placed on one side of distal end portion  134  of elongate flexible shaft  130  and 2 markers are placed on the opposite side of distal end portion  134  of elongate flexible shaft  130 . By way of example, in certain embodiments, 5 markers are placed on one side of distal end portion  134  of elongate flexible shaft  130  and 3 markers are placed on the opposite side of distal end portion  134  of elongate flexible shaft  130  of side exiting catheter  100 . 
     A method or procedure of guiding the side exiting catheter  100  of certain embodiments to a desired target tissue in the respiratory system of a patient may comprise displaying an image of the region of the patient, inserting a flexible lumen into the patient, and inserting into the flexible lumen side exiting catheter  100 . Side exiting catheter  100  typically comprises an electromagnetic localization element at distal end portion  134 . Side exiting catheter may then be navigated to the region of interest and the location and orientation of the electromagnetic localization element is detected. Then medical instrument  108  may be displayed, in real-time, on the image by superimposing a virtual representation of side exiting catheter  100  and medical instrument  108  on the image based upon the location and orientation of localization element  24 . Then a medical procedure may be performed at the region (or tissue) of interest. In certain embodiments, side exiting catheter  100  further comprises an elongate flexible shaft  130  having a proximal end portion  132 , an opposite distal end portion  134 , a longitudinal axis  109 , and an outer wall  136  comprising a biocompatible material extending from proximal end portion  132  to distal end portion  134 . Side exiting catheter  100  may also comprise a handle  110  attached to proximal end portion  132 , and a medical instrument  108  housed within distal end portion  134  of elongate flexible shaft  130  that is extendable along a path from a position within outer wall  136  through side exit  105  to a position outside outer wall  136  at an angle of at least 30 degrees relative to the longitudinal axis  109 . 
     As illustrated in  FIGS.  50 A and  50 B , another embodiment of the present invention includes an offset device to control the extension of a biopsy device or medical instrument. The offset device may comprise, for example, features (e.g., offsets) that snap-on or may be otherwise affixed to handle  216  that are capable of holding a biopsy device  220  in a known or preset (i.e., predetermined) location to maintain the biopsy device  220  extension and free the hands of the physician or other healthcare professional. In one embodiment, for example, the offset device includes one or more offset portions that can be adjusted by combining and/or removing multiple offset segments. In another embodiment, for example, the offset device includes one or more offset portions that can be adjusted by the removal of one or more removable offset segments separated by perforations (i.e., in a disposable fashion). In yet another embodiment, the offset device includes an offset that is capable of adjustment using a screw mechanism (i.e., the length of the offset can be adjusted by screwing the offset in and out). In various embodiments, each offset can be represented on the navigation screen showing offset distance from the distal end portion of the elongate flexible shaft. This representation is accomplished via sensors on the offset devices that would register the selected offset position. In additional embodiments, sensors (e.g., electromagnetic sensors, proximity sensors, limit switch sensors) at the handle may register the presence or contact with an offset device such that the extension depth of the biopsy device can be measured and represented on the navigation screen. The surgical catheter, in various embodiments, may include one or more offsets, two or more offsets, three or more offsets, four or more offsets, or five or more offsets. In other embodiments, more than five offsets may be included (e.g., 6-12 offsets, 6-18 offsets, 6-24 offsets, or more). An embodiment of offset device wherein the biopsy device is a brush is shown in  FIGS.  50 A and  50 B . Another embodiment of the offset device wherein the medical instrument is a side exiting tip component is shown in  FIGS.  51 A and  51 B . 
     As illustrated in  FIGS.  50 A and  50 B , handle  216  attached to elongate flexible shaft  230  of steerable catheter  200  may include one or more offset devices  1501 . The offset device(s)  1501  may be capable of holding the biopsy device  220 , depicted as a brush, in place and provide a substantially fixed distance or length of extension out of elongate flexible shaft  230  to take a biopsy. As shown, multiple offsets  1501  can be provided in stages that allow extension of biopsy device  220  (e.g., at 1 cm, 2 cm, 3 cm, and so on) whereby the physician or other healthcare professional can adjust the offsets by removal or repositioning (removed offsets  1501 R, for example, are depicted in dashed lines within the port in  FIG.  50 B ). Thus,  FIG.  50 A  shows biopsy device  220  prior to extension, whereas  FIG.  50 B  shows biopsy device extended (e.g., 2 cm of extension) by the removal or repositioning of two offsets  1501 R. 
     As shown in  FIGS.  51 A and  51 B , another embodiment of the present invention is directed to an offset device for use with a medical instrument  108  that exits the side of elongate flexible shaft  130  of side exiting catheter  100 . Handle  110  attached to elongate flexible shaft  130  may include one or more offset devices  1501 . The offset device(s)  1501  may be capable of holding the medical instrument  108 , depicted as an aspiration needle, in place and provide a substantially fixed distance or length of extension out of elongate flexible shaft  130  to take a biopsy. As shown, multiple offsets  1501  can be provided in stages that allow extension of medical instrument  108  (e.g., at 1 cm, 2 cm, 3 cm, and so on) out the side exit  105  of the elongate flexible shaft  130  whereby the physician or other healthcare professional can adjust the offsets by removal or repositioning (removed offsets  1501 R, for example, are depicted in dashed lines within the port in  FIG.  51 B ). Thus,  FIG.  51 A  shows medical instrument  108  prior to extension, whereas  FIG.  51 B  shows medical instrument  108  extended (e.g., 2 cm of extension) out side exit  105  of the elongate flexible shaft  130  by the removal or repositioning of two offsets  1501 R. 
     Typically, biopsy device  220  may be extended a distance (extended distance) correlated to movement of handle  216  wherein extended distance may be from about 0.5 cm to about 4.0 cm. By way of example, in certain embodiments, the extended distance is at least about 0.5 cm. By way of further example, in certain embodiments, the extended distance is at least about 1.0 cm. By way of further example, in certain embodiments, the extended distance is at least about 1.5 cm. By way of further example, in certain embodiments, the extended distance is at least about 2.0 cm. By way of further example, in certain embodiments, the extended distance is at least about 2.5 cm. By way of further example, in certain embodiments, the extended distance is at least about 3.0 cm. By way of further example, in certain embodiments, the extended distance is at least about 3.5 cm. By way of further example, in certain embodiments, the extended distance is about 4.0 cm. 
     Typically, medical instrument  108  may be advanced a distance (advanced distance) correlated to movement of handle  110  wherein advanced distance may be from about 0.5 cm to about 4.0 cm. By way of example, in certain embodiments, the advanced distance is at least about 0.5 cm. By way of further example, in certain embodiments, the advanced distance is at least about 1.0 cm. By way of further example, in certain embodiments, the advanced distance is at least about 1.5 cm. By way of further example, in certain embodiments, the advanced distance is at least about 2.0 cm. By way of further example, in certain embodiments, the advanced distance is at least about 2.5 cm. By way of further example, in certain embodiments, the advanced distance is at least about 3.0 cm. By way of further example, in certain embodiments, the advanced distance is at least about 3.5 cm. By way of further example, in certain embodiments, the advanced distance is about 4.0 cm. 
     In another embodiment, as shown in  FIGS.  52 A,  52 B,  52 C, and  52 D , a localization element  24  (e.g., electromagnetic sensor) can be attached to an existing, non-navigated surgical instrument or device  70  (e.g., steerable catheter, non-steerable catheter, bronchoscope, forceps device, auger device, boring bit device, aspiration needle device, brush device, side exiting tip component, etc.) for use in the systems and methods described herein. In one embodiment, as illustrated in  FIG.  52 A , a plastic or polymer sheath or condom  72  is placed over a localization element lead wire  103  and localization element  24 . Then, as illustrated in  FIG.  52 B , the sheath or condom  72  may then be shrink-fitted to surgical instrument or device  70  via the application of a temperature differential. Typically the application of a heat treatment causes sheath or condom  72  to shrink to surgical instrument or device  70  and localization element lead wire/localization element combination, thus converting existing, non-navigated surgical instrument or device  70  to a navigated surgical instrument or device  70 . While heat treating is a common way to apply a temperature differential, it is understood that the existing, non-navigated surgical instrument or device  70  can be cooled before the plastic or polymer sheath or condom  72  is placed over existing, non-navigated surgical instrument or device  70 . In another embodiment, as shown in  FIG.  52 C  more than one localization element  24  may be attached to an existing, non-navigated surgical instrument or device  70  using a stretchable plastic or polymer sheath or condom  72 . As illustrated in  FIG.  52 D , the stretchable plastic or polymer sheath or condom  72  may extend past the end of surgical instrument or device  70  such that a lip  74  is created when the sheath or condom  72  is affixed to non-navigated surgical instrument or device  70 . This lip  74  may assist in registration of surgical instrument or device  70 . In other embodiments, localization element  24  may be wireless, such that a localization element lead wire  103  is not required. 
     Other embodiments include, for example, a plastic or polymer sheath or condom that is custom sized to fit over an existing, non-navigated surgical instrument or device  70  and may be placed over a localization element lead wire  103  and localization element  24  to add a localization element  24  (e.g., an electromagnetic sensor), thus converting existing, non-navigated surgical instrument or device  70  to a navigated surgical instrument or device  70 . In this embodiment, the plastic or polymer sheath or condom may be held in place on the existing, non-navigated surgical instrument or device  70  by a friction fit. In yet other embodiments, an elastic or stretchable plastic or polymer sheath or condom may be expanded and placed over a localization element lead wire  103  and localization element  24  to add a localization element  24  (e.g., an electromagnetic sensor), thus converting the existing, non-navigated surgical instrument or device  70  to a navigated surgical instrument or device  70 . In this embodiment, the elastic or stretchable plastic or polymer sheath or condom may also be held in place on the existing, non-navigated surgical instrument or device  70  by a friction fit. 
     In yet other embodiments, a localization element  24  may be affixed to an existing, non-navigated surgical instrument or device  70  with tape. In certain embodiments, localization element  24  may be wireless. In other embodiments, localization element  24  may be affixed to an existing, non-navigated surgical instrument or device  70  via an adhesive. 
     In addition to or in place of localization element  24 , steerable catheter  200  and/or side exiting catheter  100  may be equipped with one or more sensing devices at or near the distal end portion of the elongate flexible shaft and/or at the biopsy device  220  or medical instrument  108  of the respective catheters described herein. Additional sensing devices may include electrodes for sensing depolarization signals occurring in excitable tissue such as the heart, nerve or brain. In one embodiment, for use in cardiac applications, the sensing device may include at least one electrode for sensing internal cardiac electrogram (EGM) signals. In other embodiments, the sensing device may be an absolute pressure sensor to monitor blood pressure. In still other embodiments, surgical instrument  12  may be equipped with other sensing devices including physiological detection devices, localization elements, temperature sensors, motion sensors, optical coherence tomography (OCT) sensors, endobronchial ultrasound (EBUS) sensors, or Doppler or ultrasound sensors that can detect the presence or absence of blood vessels. 
     The accompanying Figures and this description depict and describe certain embodiments of a navigation system (and related methods and devices) in accordance with the present invention, and features and components thereof. It should also be noted that any references herein to front and back, right and left, top and bottom and upper and lower are intended for convenience of description, not to limit the present invention or its components to any one positional or spatial orientation. 
     It is noted that the terms “comprise” (and any form of comprise, such as “comprises” and “comprising”), “have” (and any form of have, such as “has” and “having”), “contain” (and any form of contain, such as “contains” and “containing”), and “include” (and any form of include, such as “includes” and “including”) are open-ended linking verbs. Thus, a method, an apparatus, or a system that “comprises,” “has,” “contains,” or “includes” one or more items possesses at least those one or more items, but is not limited to possessing only those one or more items 
     Individual elements or steps of the present methods, apparatuses, and systems are to be treated in the same manner. Thus, a step that calls for modifying a segmented image dataset for a region of a respiratory system to match the corresponding anatomy of a patient&#39;s respiratory system, that includes the steps of: (i) forming a respiratory-gated point cloud of data that demarcates anatomical features in a region of a patient&#39;s respiratory system at one or more discrete phases within a respiration cycle of a patient, (ii) density filtering the respiratory-gated point cloud, (iii) classifying the density filtered respiratory-gated point cloud according to anatomical points of reference in a segmented image dataset for the region of the patient&#39;s respiratory system, and (iv) modifying the segmented image dataset to correspond to the classified anatomical points of reference in the density filtered respiratory-gated point cloud, but also covers the steps of (i) comparing the registered respiratory-gated point cloud to a segmented image dataset to determine the weighting of points comprised by the classified respiratory-gated point cloud, (ii) distinguishing regions of greater weighting from regions of lesser weighting, and (iii) modifying the segmented image dataset to correspond to the classified respiratory-gated point cloud. 
     The terms “a” and “an” are defined as one or more than one. The term “another” is defined as at least a second or more. The term “coupled” encompasses both direct and indirect connections, and is not limited to mechanical connections. 
     Those of skill in the art will appreciate that in the detailed description above, certain well known components and assembly techniques have been omitted so that the present methods, apparatuses, and systems are not obscured in unnecessary detail. 
     While various embodiments of the invention have been described above, it should be understood that they have been presented by way of example only, and not limitation. Thus, the breadth and scope of the invention should not be limited by any of the above-described embodiments, but should be defined only in accordance with the following claims and their equivalents. 
     The previous description of the embodiments is provided to enable any person skilled in the art to make or use the invention. While the invention has been particularly shown and described with reference to embodiments thereof, it will be understood by those skilled in art that various changes in form and details may be made therein without departing from the spirit and scope of the invention. For example, the elongate flexible shafts, biopsy device, medical instruments, and localization elements can be constructed from any suitable material, and can be a variety of different shapes and sizes, not necessarily specifically illustrated, while still remaining within the scope of the invention.