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akhanf
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Nov 12, 2025
akhanf
commented
- updates for getting metadata from imaris files, writing into bids microscopy json fields
- fallback when OME metadata isn't present that relies on standardized location of tif files relative to the imaris data (this is very site-specific, ie works for our folder structure -- in a future refactor spimprep would have the ability to set multiple input paths rather than just one)..
was indexing wrong field (DataAxis3), fixes it and also adds in all the metadata into the json
instead of res-3x use level-3 (like spimquant)
With some pre-conversion workflows, omero metadata isn't embedded in the imaris file. This uses standardized folder structure to find the associated tif and grab from there..
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