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Ticket #724 (closed defect: fixed)

Opened 2011-08-15T14:23:39-05:00

Last modified 2011-09-01T12:30:14-05:00

Preserve Original Metadata

Reported by: hinerm Owned by: hinerm
Priority: major Milestone: imagej-2.0-alpha5
Component: bf-itk Version:
Severity: serious Keywords:
Cc: Blocked By:


Ensure BF-ITK plugin is preserving the original image's metadata throughout the read/write process.

If not, modify the plugin to maintain additional key-value pairs as appropriate.

Change History

comment:1 Changed 2011-08-17T14:26:51-05:00 by curtis

To facilitate this, Mark is working on a  test program for outputting the key/value pairs from the metadata dictionary.

comment:2 Changed 2011-08-24T14:47:18-05:00 by hinerm

  • Status changed from new to accepted

A test program, itkBFImageInfo has been added to the bf-itk-pipe build. It prints image information both from Bio-Formats, and the itkImageIOBase.

comment:3 Changed 2011-09-01T12:30:14-05:00 by hinerm

  • Status changed from accepted to closed
  • Resolution set to fixed

The only metadata found as not being preserved was Pixel Type and Number of Components.

ITK has a suspected bug in that if the tiff PLANAR_CONFIGURATION is set to 2, it forces PixelType to rgba and Number of Components to 4. In fact, it should probably be checking the SamplesPerPixel, as if that value is 1 PLANAR_CONFIGURATION is irrelevant. A potential bug report will be filed in ITK's bug tracker.

Bio-Formats' Tiff writer also did not check SamplesPerPixel when setting the PLANAR_CONFIGURATION value, purely relying on the interleaved status.

Resolved in commit 00c2936718db62353f3d4a6bc12d790a0d29f3b4 :
The Bio-Formats Tiff writer will now set PLANAR_CONFIGURATION to 1 (chunky) if SamplesPerPixel is 1, else based on the interleaved status.