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fmi-faim / faim-ipa

A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)
BSD 3-Clause "New" or "Revised" License
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Add legacy STK support #125

Open jeskowagner opened 6 months ago

jeskowagner commented 6 months ago

Enabled by the great refactoring of faim-hcs to faim-ipa, #18 can now be tackled. This PR hijacks metadata extraction of metaseries created with ImageXpress to enable users to feed legacy STK-formatted tif files seamlessly. However, this approach currently only support single-plane acquisitions (in this line) simply because I do not have access to multi-plane acquisitions to test any other format.

I am marking this as draft PR because

Beyond that it seems to work as expected, producing valid zarr files.

jeskowagner commented 6 months ago

I just noticed that this was also enabled by the tifffile package adding better metadata extraction support for STK's, without which the StagePosition field is not populated (which is needed by faim-ipa). Specifically, the required PR was this. Very cool to see others working to push what can be done with these legacy files. Note that this PR also suggests that getting this metadata is supported for single-plane STK's only, so this limitation would likely be insurmountable.