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khanlab / SPIMprep

A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
MIT License
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SPIM.metadata.json file not bids-compliant #19

Closed akhanf closed 5 months ago

akhanf commented 5 months ago

Should be named SPIM.json, and should have the required BIDS json entries for SPIM data, bare minimum being e.g.:

    "PixelSize": [
        0.1,
        0.0027083330000000003,
        0.0027083330000000003
    ],
    "PixelSizeUnits": "mm",

but should try to include as much info as possible from the existing OMERO or Blaze metadata..