O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Animal Tracking Status (ORNL)

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY ORNL “Track” Team Shaun S. Gleason, Ph.D. James S. Goddard, Ph.D. Michael J. Paulus, Ph.D. Justin S. Baba, Ph.D. John C. Turner

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Internal Anatomic Reference from X-ray CT Real Time Optical Tracking with Reference Markers External Anatomic Reference from X-ray CT Gamma-ray Functional Image

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Recent ORNL Animal Tracking Progress/Challenges Tracking Hardware –System architecture –Camera changes –Animal burrow –Illumination adjustments/experiments –Calibration tools Tracking software –Improved image acquisition code –Improved camera calibration routine –Enhanced segmentation –Faster pose measurement Phantom tracking/SPECT study Animal studies

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Tracking Hardware

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY System Architecture System ClockMotion Control PC SPECT Data Acquisition PC Optical Tracking PC Time-Stamped Pose File Time-Stamped Gantry Position File Time-Stamped SPECT Event Files SPECT Gantry with Optical Tracking

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Tracking/SPECT Gantry CMOS Cameras SPECT Detectors IR Strobe Mounts CalibrationPhantom

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Stereo Camera System Imrpovements –Adjusted the vertical view angle from 0 degrees to degrees above SPECT gantry rotation axis. –Moved cameras closer together in the horizontal plane (30-degrees) to improve view between SPECT detectors. –Firmware updated to allow hardware trigger. 30-degrees

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Animal Burrow- Reflection Elimination Why are reflections a problem? See image on bottom-right. Contracted with Deposition Sciences Inc. (DSI) to apply AR coating on the exterior and interior surfaces to eliminate reflections. DSI claimed to have a low pressure chemical vapor deposition (LPCVD) method that would get coating up into the inside end of tube. Glass tubes returned, and reflections from the outside surface were eliminated. Reflections from inside surface of glass are still present: little or no AR coating on the inside end of the tube. LED reflection merged with marker Animal within burrow

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Illumination Adjustments –Built a trigger circuit to allow the IR LEDs to be strobed Increased short-term power to LEDs Freezes motion –Polarization experiments for reflection suppression: Linear polarization of light source Laser illumination Cross-polarization filter on camera Circular polarizing reflectors

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Polarization Experiments for Reflection Elimination Polarized white light source Reflector sheet rotates polarization Cross-polarization filter on camera Eliminates reflection Need spherical IR reflectors that rotate polarization Coherent, polarized source (red laser) Retro reflector (diffuses polarization) Cross-polarization filter on camera Eliminates reflection Requires IR laser illumination Requires higher power laser to cover animal burrow Polarized IR LED light source Retro reflector (preserves polarization) Polarization filter on camera Eliminates reflection from opposite source Does not eliminate direct reflection w/out polarization with polarization

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Calibration Tools –Camera Calibration Tool for: intrinsic (focal length, lens distortion) and extrinsic (camera-to-camera) calibration Checkerboard target mounted to a plate INSIDE glass tube Plate is adjustable using a “joystick” mounted to back of plate –Optical Tracking and SPECT Coordinate System Alignment Tool Optical tracking coordinates relative to optical axis of camera #1 SPECT coordinates relative to gantry axis-of-rotation Tool contains: –Retro-reflective markers for optical system –Co-located Co-57 sources for SPECT system Pin-hole collimator optical-to- SPECT coordinate calibration tool Stereo camera calibration tool

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Tracking Software

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Optical Tracking Software Progress Changed acquisition code to acquire true simultaneous images with strobe using hardware trigger Added MATLAB camera calibration routine with more sophisticated optimization (for intrinsic and extrinsic calibration) Segmentation improvements: –threshold for seed points now software adjustable (new) –region growing –contour analysis –filtering based on correspondence (derived from fundamental matrix, F) (new) –filter on size/aspect-ratio (new) –centroid calculation Least squares optimization for closest epipolar line that matches each pair of corresponding centroid points Speed improvements by writing more efficient code (from 9 meas/sec to 15 meas/sec)

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Phantom Study

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY I Rod Phantom Tracking/SPECT Study Three capillaries filled with liquid I-125 were mounted to the inside of a plastic tube. Retro reflectors were mounted to the outside of the tube. The tube was fixed to a 6 degree-of- freedom translation mount. Two ~1.5 hour SPECT scans were performed: –Scan 1: the phantom was translated axially 4 times, 2.0 mm per step –Scan 2: the phantom was translated laterally 4 time, 2.5 mm per step Parallel- and pin-hole SPECT data were acquired for each scan. 3-rod phantom in plastic tube Translation mount

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY I Rod Phantom Tracking/SPECT Study Axial MotionLateral Motion Movies of parallel-hole SPECT projections

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY I Rod Phantom Tracking/SPECT Study Plot of Measured (blue) vs. Actual (black dotted) Motion of Phantom Axial Motion (2mm per step)Lateral Motion (2.5 mm per step) 2.8 mm SPECT event data, pose data and timestamp data being analyzed by our JLAB partners for pose-corrected reconstruction software development.

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Most Recent Animal Tracking Study

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Awake Animal Tracking Study Balb/c mouse anesthetized using ketamine/xylazene. Retro reflective markers placed on head of animal. Animal allowed to wake up, then placed within the animal burrow on the SPECT gantry for tracking. Animal was tracked for about 20 minutes. Successful measurement of animal’s 3D position was accomplished ~99% of the total time.

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Awake Animal Tracking Study (cont) Animal preferred to be within the burrow towards the closed end. Motion was primarily constrained to lateral and vertical (nodding) motion of the head. Tracking system was able to stay “locked” onto the motion 99% of the time.

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Animal Tracking Study (cont) Live video of computer screen showing stereo camera views and real-time segmentation/correspondence measurements (green) Camera 1 ViewCamera 2 View

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Next Step: Awake Animal Tracking with Simultaneous SPECT Data Acquisition We have recently put in place all hardware/software and protocols necessary to acquire SPECT data of animals in motion: –Robust awake animal tracking New camera configuration More robust/faster pose measurement software Strobed illumination Partial reflection elimination Animal handling protocols Experience with animal behavior –Optical Tracking/SPECT coordinate system calibration tools We can now begin acquiring SPECT data with motion: –Additional phantom studies (point sources, line sources) –Awake animal studies

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY SPECT Reconstruction Algorithm Development Status for Static & Dynamic Animal Studies

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Reconstruction Tools We have created a suite of reconstruction tools for use in static animal SPECT studies: –2D Filtered Backprojection Parallel-hole –3D ML-EM (w/ J. Gregor, Univ. of TN) Parallel- and Pin-hole –3D OS-EM (w/ J. Gregor, Univ. of TN) Non-overlapping ordered subsets Parallel and Pin-hole A new data merging tool has been developed to serve as a platform for dynamic animal SPECT studies: –Time-Stamped SPECT Events –Time-Stamped Gantry Position Data –Time-Stamped Pose Measurements

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Reconstruction Comparisons on Phantom with 3 Capillary Tubes (I-125) FBP (Parallel-hole)OS-EM (Parallel-hole)OS-EM (Pin-hole) Trans-axial Slices

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Reconstruction Comparisons on Phantom with 3 Capillary Tubes (I-125) FBP (Parallel-hole)OS-EM (Parallel-hole)OS-EM (Pin-hole) Volume Renderings

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY Reconstruction Software Architecture Time-Stamped Pose File Time-Stamped Gantry Position File Time-Stamped SPECT Event Files “DataMerger” (ORNL) Compressed Events “GAM” file Event Remapping (JLAB) Pose-corrected SPECT Events Pose-Corrected Reconstruction (JLAB) “Static” Tomographic Data File Pose-corrected SPECT images FBP, ML-EM, OSEM Reconstruction (Static) Static SPECT images

O AK R IDGE N ATIONAL LABORATORY U.S. DEPARTMENT OF ENERGY “DataMerger”