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

Goals

TIFF Update

• Background
  • TIFF 4.0
  • ITK-159
• 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
  • JPEG2000
• 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
  • ODP
  • PDF
• 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
  • http://midas.kitware.com/community/view/61
• 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