ITK Release 4/Microscopy/File Formats/Hackathon August 2011

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Goals

TIFF Update

  • Background
  • Tasks
    • Complete update of TIFF 4.0 library
    • Verify usage for TIFF files larger than 4Gb
    • Verify usage for TIFF streaming
    • Verify usage for TIFF extra resolutions

JPEG2000 Review

  • Background
  • Tasks
    • Verify usage for JPEG2000 files larger than 4Gb
    • Verify usage for JPEG2000 streaming
    • Verify usage for JPEG2000 extra resolutions

ITK IO API

  • Propose API for managing multi-resolution files
  • Image Interpretation layer
  • Issues
    • Some file formats ( i.e. TIFF ) support multi-images in a single file
    • This can be used for multi-resolution or volumes, how should this be accessed? Should a Image IO present a set of images?
    • The current ITK Image Pyramid is designed to maintain the physical center of the images. However for many sized images this lead to changing of physical locations of scale-space extrema.
    • How do we indicate what type of operator was used to generate the multi-resolutions? Can we even know for certain filter formats?

TIFF Microscopy Units

  • What to do about lack of units in ITK spacing ?
    • mm ?
    • Introduce an enum type ? a class ?
    • Introduce a units conversion class ?
      • To centralize the computation and prevent inconsistent units conversion.
        • Think of the Mars Rover...

Bioformats Patch

  • Review Gaetan's patch to interface to Bioformats ?

Participants

On Site

  • Brad Lowekamp
  • Curtis Lisle
  • Matt McCormick
  • Luis Ibanez
  • Andinet Enquobahrie

Remote

  • Arnaud Gelas
  • Kishore Mosilaganti

Venue

  • NLM - Bethesda
    • NIH Campus

UnAgenda

Day 1

  • 9:30 Computers / Network setup
  • 10:00 Live Code Review of TIFF Gerrit patch
  • 12:00 Merge of TIFF Gerrit patch
  • 12:30 Lunch
  • 1:30 Tests of 6Gb files
  • 3:30 Streaming tests on TIFF files
  • 5:30 Adjourn

Day 2

  • 9:30am Image interpretation layer (database ?)(Channels/Resolutions/Size)
  • 10:30am Managing files with internal multi-resolution
  • 11:30am Managing TIFF files with J2K compression
  • 12:30pm Lunch
  • 1:30pm Tests of JPEG2000 streaming
  • 3:30pm Tests of JPEG2000 multi-resolution
  • 4:00pm Adjourn


Results

Completed

  • Have working Gerrit patch with TIFF 4.0 Beta 7

http://review.source.kitware.com/#change,2510

    • Five failing tests
      • Only on Linux
      • Only when reading FAX images
      • These failing tests turned out to be the result of a misuse of "#cmakedefine" in the tif_config.h.in (Bad Luis...). The expression was used as
        • #cmakedefine FOOBAR @FOOBAR@, while it should be
        • #define FOOBAR @FOOBAR@
    • Passes all tests on Windows and Mac
  • The Patch finally build in all platforms and has been merged.
  • Succeeded to read a TIFF image larger than 4Gb
  • Succeeded to write a TIFF image larger than 4Gb
  • Uploaded Example Aperio files to MIDAS
  • Converted the Visible Human dataset to a single file, multi-frame TIFF image of size 13 Gb

Work in Progress

  • OpenSlideImageIO class for ITK
  • AperioImageIO class for ITK
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