[SCIFIO] spacing lost

Michael Meuli michael.meuli at gmail.com
Wed Jul 15 09:52:39 CDT 2015


Hi,

I have a .tif image with z-stacks of three channels (cropped version
attached).

With Fiji I can see that the spacing is set correctly:
Voxel size: 0.0616x0.0616x0.1998 micron^3

If I do:
./SCIFIOTestDriver itkSCIFIOImageIOTest /home/mmeuli/Bioimage/ITK/1-1.tif
/home/mmeuli/Bioimage/ITK/test.ome.tiff -w -a -d 5

The spacing in test.ome.tiff is lost:
Voxel size: 1x1x1 cm^3

If I set the spacing with itk::ChangeInformationImageFilter the spacing is
nicely set in itk but not written correctly to .ome.tiff or .tiff ...
I've compiled ITK on 29th June with an up to date master-branch.

No validation errors found:
mmeuli at mmeuli:~/Bioimage/Bio-Formats 5.1.2/bftools$ ./tiffcomment
../test.ome.tiff | ./xmlvalid
Parsing schema path
http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd
Validating <stdin>
No validation errors found.


Best regards
Michael
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