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OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Animal Tracking Status (ORNL)
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Tracking Hardware
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
System Architecture
System ClockMotion Control PC SPECT Data Acquisition PC
Optical Tracking PC
Time-StampedPose File
Time-StampedGantry Position File
Time-StampedSPECT Event Files
SPECT Gantry with Optical Tracking
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Tracking/SPECT Gantry
CMOS CamerasCMOS Cameras SPECT DetectorsSPECT Detectors
IR StrobeIR StrobeMountsMounts
CalibrationCalibrationPhantomPhantom
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Stereo Camera System Imrpovements
– Adjusted the vertical view angle from 0 degrees to 10-15 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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Polarization Experiments for Reflection Elimination
Polarized white light source Reflector sheet rotates polarizationCross-polarization filter on cameraEliminates reflectionNeed spherical IR reflectors that rotate polarization
Coherent, polarized source (red laser)Retro reflector (diffuses polarization)Cross-polarization filter on cameraEliminates reflectionRequires IR laser illuminationRequires higher power laser to cover animal burrow
Polarized IR LED light source Retro reflector (preserves polarization)Polarization filter on cameraEliminates reflection from opposite sourceDoes not eliminate direct reflection
w/out polarization with polarization
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Tracking Software
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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)
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Phantom Study
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
I-125 3-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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
I-125 3-Rod Phantom Tracking/SPECT Study
Axial Motion Lateral Motion
Movies of parallel-hole SPECT projections
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
I-125 3-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.
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Most Recent Animal Tracking Study
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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.
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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.
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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 View Camera 2 View
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
SPECT Reconstruction Algorithm Development Status for Static & Dynamic Animal Studies
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
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
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
Reconstruction Software Architecture
Time-StampedPose File
Time-StampedGantry Position File
Time-StampedSPECT Event Files
“DataMerger” (ORNL)
Compressed Events“GAM” file
Event Remapping (JLAB)
Pose-corrected SPECT Events
Pose-CorrectedReconstruction (JLAB)
“Static” Tomographic Data File
Pose-corrected SPECT images
FBP, ML-EM, OSEMReconstruction (Static)
Static SPECT images
OAK RIDGE NATIONAL LABORATORY
U.S. DEPARTMENT OF ENERGY
U.S. DEPARTMENT OF ENERGY
“DataMerger”