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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
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Test with a real HCS OME-TIFF dataset #163

Open ziw-liu opened 1 year ago

ziw-liu commented 1 year ago 
          I'm looking at this now, I can make you a small test dataset

EDIT: Check if this fits the bill: cm.mantis/2023_07_21_mm_hsc_dataset/mm_hsc_dataset_2

Originally posted by @ieivanov in https://github.com/czbiohub-sf/iohub/issues/159#issuecomment-1646341451

ziw-liu commented 1 year ago

@ieivanov thanks for making this! I think this is a nice example to test against. One very minor point is that it would be nice to have non-single digit column numbers (e.g. 12) to prevent future regressions.

ieivanov commented 1 year ago

Yup, I can make that happen. I'll have to re-acquire this dataset anyway as we saw that the data is of the wrong file size due to a MM bug somewhere (https://github.com/micro-manager/micro-manager/issues/1746)

ieivanov commented 1 year ago

One wrinkle we missed yesterday - an important feature of the iohub readers is adding singleton dimensions where they may be missing. In the test data we should include acquisitions with fewer than 5 dimensions to test that iohub correctly turns those into TCZYX datasets

ziw-liu commented 1 year ago

In the test data we should include acquisitions with fewer than 5 dimensions to test that iohub correctly turns those into TCZYX datasets

This is already tested with the older (2020-gamma) MM datasets. I don't think we need to acquire the full suite of the combinations unless we aim to replace the old ones completely.

ieivanov commented 1 year ago

Ah, right, OK!