Open melissalinkert opened 1 week ago
Reported in https://forum.image.sc/t/issues-mrxs-to-tiff-using-bioformat2raw/100695; private sample data is in automated-tests/inbox/imagesc-100695/.
automated-tests/inbox/imagesc-100695/
The problematic dataset has an extra Slide zoom mask level inserted between the Slide zoom level and Slide filter level (the "real" data). Looking at a diff of Slidedat.ini against the Slidedat.ini for https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/CMU-1.zip is useful.
Slide zoom mask level
Slide zoom level
Slide filter level
Slidedat.ini
https://github.com/melissalinkert/bioformats2raw/commit/905daf48e125c00bb8431cca32fd9780115ce0ed is a start at fixing the channel count detection, but that does not result in correct image data. I suspect that pyramidDepth needs to be calculated and recorded separately for each hierarchy so that the index file is read properly, but more investigation is needed.
pyramidDepth
Reported in https://forum.image.sc/t/issues-mrxs-to-tiff-using-bioformat2raw/100695; private sample data is in
automated-tests/inbox/imagesc-100695/.The problematic dataset has an extra
Slide zoom mask levelinserted between theSlide zoom levelandSlide filter level(the "real" data). Looking at a diff ofSlidedat.iniagainst theSlidedat.inifor https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/CMU-1.zip is useful.https://github.com/melissalinkert/bioformats2raw/commit/905daf48e125c00bb8431cca32fd9780115ce0ed is a start at fixing the channel count detection, but that does not result in correct image data. I suspect that
pyramidDepthneeds to be calculated and recorded separately for each hierarchy so that the index file is read properly, but more investigation is needed.