Opening CZI compressed with ZSTD does not allow access to series (pyramid levels)

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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Opening CZI compressed with ZSTD does not allow access to series (pyramid levels) #4110

Closed sebi06 closed 4 months ago

sebi06 commented 8 months ago

Dear BF Team,

i created two CZI image datasets
one is uncompressed the other one compressed via ZSTD (which will become the new default compression for ZEN)
when I open the uncompressed CZI using the latest BF I get what I expect (5 pyramid levels)
when I open the compressed CZI it opens directly while not offering the series selection (only the highest level is read)

CZI Data:

https://www.dropbox.com/scl/fi/wauh69abwh9qdmj7l7bo6/TR_M-29_uncompressd.czi?rlkey=hbdh7k906ogdcavbccqysx56l&dl=0

https://www.dropbox.com/scl/fi/igjapws4kn5x0mvkpktbb/TR_M-29_ZSTD.czi?rlkey=2cdp4gzkv614huwpndiixqsb6&dl=0

imagesc-bot commented 8 months ago

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

https://forum.image.sc/t/quick-start-zeiss-czi-reader/83733/11

dgault commented 8 months ago

Thanks @sebi06 for opening the issue, I can confirm that I can reproduce the issue with Bio-Formats 7.0.1, the same issue can be seen in all versions since ZSTD compression was implemented. The provided sample files have been copied to inbox/imagesc-83733

dgault commented 4 months ago

Closing as resolved by https://github.com/ome/bioformats/pull/4138