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czbiohub-sf / iohub

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
https://czbiohub-sf.github.io/iohub/
BSD 3-Clause "New" or "Revised" License
29 stars 6 forks source link

New `tifffile` version breaks the OME-TIFF reader #94

Closed ziw-liu closed 1 year ago

ziw-liu commented 1 year ago 
          > Tifffile v2023.3.15 includes a new parser for MMStack series and reverts the MicroManager specific optimizations for OME series. Positions are now returned as a dimension in the series rather than as separate series. The dimension order is parsed from the MM metadata and might differ from OME. I only have a limited number of test files, many of which are corrupted in one way or another. Hope it works for you.

@cgohlke Thanks for letting us know! I have yet to change the related code here, so I have to pin the tifffile version on the main branch for now to avoid this breaking change.

Originally posted by @ziw-liu in https://github.com/czbiohub/iohub/issues/66#issuecomment-1472914679

ziw-liu commented 1 year ago

A temporary pin of the dependency is necessary before the reader gets fixed so that users can still install and use iohub from the main branch.