ITK Release 4/Microscopy/File Formats

Overview

Microscopy applications use a very specific set of file formats, many of which are not supported in ITK by the version 3.20.

Among the initiatives of ITKv4, we are improving the support for file formats that are relevant to the microscopy image analysis community.

Bio-Formats

The Bio-Formats library is probably the most complete collection of readers and writers for image file formats of interest to the microscopy community.

The Bio-Formats library is implemented in Java and it is distributed under the GPL license. ITKv4 now carries adaptors to this library that can be enabled at CMake configuration time.

• Bio-Formats

JPEG2000

• ITKv4 has adopted a branch of the openjpeg repository (from the v2 branch)
• There are failing tests in some of the Windows builds, that still have to be addressed.
• Now that openjpeg is preparing to do a new release of the v2 branch, we should look at updating the version in ITK again.

TIFF 4.0

The Source

• http://www.remotesensing.org/libtiff/
• ftp://ftp.remotesensing.org/pub/libtiff/
• Master Download Site
  • http://download.osgeo.org/libtiff/

BigTIFF

From: http://www.remotesensing.org/libtiff/BigTIFFProposal.html

BigTIFF logically extends the original TIFF file format (referred to as 'ClassicTIFF' from this point on), breaking the 4 gigabyte boundary, in theory allowing files up to 18,000 petabytes in size. The BigTIFF specification is the result of work by a variety of parties on the LibTiff mailing list, including the current LibTiff maintainers, Joris Van Damme and Adobe staff. The BigTIFF specification has not yet been officially approved by the TIFF specification owner (Adobe) but implementation within LibTiff could accelerate that process.

Our Plan

• We are trying to update to libTIFF 4.0
• The current version of TIFF in ITK is: 3.7.2
• The current Stable release of TIFF is: 3.9.5
• We made a first cut at updating to libTIFF 4.0 beta 6
  • This is in Gerrit at: http://review.source.kitware.com/#change,76
• As of July 13 - 2011, the most recent release of libTIFF is
  • libTIFF 4.0 beta 7
  • ftp://ftp.remotesensing.org/pub/libtiff/tiff-4.0.0beta7.tar.gz
  • http://download.osgeo.org/libtiff/tiff-4.0.0beta7.tar.gz
  • We will aim to update this library by the ITKv4 Beta release.

Hackathon August 2011

• Hackathon August 2011