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mehta-lab / waveorder

Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.
BSD 3-Clause "New" or "Revised" License
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acquisitions that are stopped early produce incorrect zarr outputs #25

Closed bryantChhun closed 3 years ago

bryantChhun commented 3 years ago

problem

A micro-manager acquisition that stops early (either from a crash or manually) does not update the ome.xml metadata, which is determined based on defined experiment parameters at the start of acquisition. Consequently, tifffile, zarr, and our io.MicromanagerReader expect a larger dataset than exists. The result is a written file that has a larger dimensionality than the source file.

solution

Unclear right now. It's possible the ome.tiff structure has something in place to signify "empty data" or similar... Will need some research

bryantChhun commented 3 years ago

Fixed in PR #28