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ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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CZI: Failed to read pre-stitched image with no pyramid #3919

Open dgault opened 1 year ago

dgault commented 1 year ago

This issue was raised on forum thread https://forum.image.sc/t/czi-pyramidal-with-bioformat/73215/10 and a set of sample files provided (https://wetransfer.com/downloads/5021c67300c122c50c8394172155318c20221201105414/b5cb3f, Note: David to upload sample files to repo inbox). When attempting to open the stitched image with Bio-Formats 6.11.1 you instead see 42 series (comes from 21 mosaics with 2 channels) and the pixel data appears skewed.

While debugging the issue, if you modify the values at https://github.com/ome/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java#L832, keeping the seriesCount at 1 and setting prestitched to true, that is enough to allow the file to be opened correctly a single stitched image. This can likely be fixed by correcting this section of code to recognise a prestitched image when no pyramids are present.

imagesc-bot commented 1 year ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/czi-pyramidal-with-bioformat/73215/19

dgault commented 1 year ago

Sample files are now located under inbox/imagesc-73215