Small Animal Cone Beam CT

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• Small Animal Cone Beam CT
• Project Checkpoint
• Sungjun Kim, Owen Gray and Pinak Pujari

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Overview

• Deliverables
• Schedule
• Dependencies
• Work to date

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Deliverables
Deliverables

• Minimum
• Working intensity correction, rudimentary image
  dewarping and reconstruction of multiple planar
  images into standard DICOM volumetric formats
• Expected
• Functional GUI for 2D image correction and
  display/manipulation of 3D volumetric data.
• Software module to correct for variation in
  attenuation due to pose of subject/angle of CT
  turn table.
• Maximum
• Interactive GUI for characterization of
  misalignment in translation stage

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Data Flow Diagram
Deliverables
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Block Diagram
Deliverables
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Overview

• Deliverables
• Schedule
• Dependencies
• Work to date

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Schedule
Implementation Slightly behind schedule, but
currently on track for delivery
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UI Development Schedule
Actual Time Line
Projected Timeline
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Overview

• Deliverables
• Schedule
• Dependencies
• Work to date

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Prerequisites
Dependencies

• Access to existing source
• JHMI CVS access granted
• Test Data Availability
• Sufficient test data for development debugging
  acquired in appropriate formats
• Additional data may be necessary for robust final
  testing

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Development Tools
Dependencies

• NetBeans IDE
• Initial difficulties with NetBeans environment
  resolved
• Platform is still suboptimal
• SWIG
• Tool for wrapper generation for C/Java Interop
• C image processing code successfully wrapped
• Preliminary testing of native code from Java
  complete

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Third-party libraries
Dependencies

• JAI (Java Advance Imaging) API
• API posed greater development challenges than
  anticipated
• Development is now on track, but learning curve
  was steep
• Provides many functions that we had anticipated
  having to build from scratch
• Potential reduction in anticipated work

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File I/O
Dependencies

• .RBF Input
• .RBF is proprietary format, may not be used in
  future (deviation form initial specification)
• Reader for .RBF files (raw camera output)
• .TIF Intermediate Output
• .TIF conversion not yet complete
• .TIF format for intermediate images was a change
  from original spec to accommodate different
  detector modalities

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DICOM Output
Dependencies

• PixelMed
• Third-party toolkit for DICOM manipulation
• May be overkill for the project
• API poorly understood at this time
• Existing JHMI PixelMed code base probably not
  usable
• Resolution Investigate alternative APIs,
  collaborate with 4D CT group on DICOM output

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Overview

• Deliverables
• Schedule
• Dependencies
• Work to date

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Image Display/ROI Selection
Work To Date

• Completed
• Design/Develop working JAI Image
  Loader/Renderer/Viewer.
• Reads directories containing Images of any format
  and displays them (demo included)
• Code provides robust memory management
• Necessary due to size of files (2.7 MB per raw
  image) and number of images (360 with current
  specification)
• Imaging libraries installed on fast machines in
  Ugrad lab
• enable fast debugging of resource-intensive code

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Image Display/ROI Selection
Work To Date

• In Process
• Develop ROI analyzer with different Image
  Statistics (Histogram, User specified dynamic
  range).
• ROI resampling (up and down)
• Integration of display components with mainline
  code base

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File I/O
Work To Date

• Completed
• .RBF File reader
• .TIF file reader
• In Process
• .TIF conversion
• Resampling of user designated ROI to appropriate
  size for Feldkamp input (500x500 pixels)

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General UI
Work To Date

• Completed
• UI design complete
• Prototype/demo functioning
• All controls necessary to meet specification in
  place
• In Process
• Integration of GUI components with advanced
  display code base

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Image processing/Reconstruction
Work To Date

• Completed
• Pre-processing/Intensity correction
• Feldkamp reconstruction (.RBF input only)
• In Process
• Feldkamp reconstruction (with .TIF input)
• Threading model for online image processing
• Begin processing as soon as camera saves a frame
• Images processed/reconstructed asynchronously

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Conclusions

• Currently, we are on track to for expected
  deliverables
• There is still risk/uncertainty inherent in
  integration of various modules
• Will be able to deliver a working application
• Performance improvements may be necessary for
  handling large image files

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Conclusions

• Maximum deliverable (integrated UI for
  dewarp/calibration) unlikely by May 14th
• Appropriate hooks/APIs for integration at a
  future date will be included
• Detailed specification/class design for
  calibration component expected, but not committed

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