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Support for MACSima data

Open berombau opened this issue 1 year ago • 0 comments

A reader to support reading data from the Miltenyi MACSima platform. It should support the published datasets:

  • [ ] Liver Cell Atlas (old data stitched and already processed)
  • [x] Lung_adc_demo (stitched data they provide if you ask)
  • [ ] still on the look-out for more...

It should also help users to read newer private datasets:

  • [ ] from the RawData output folder with AntigenCycle and BleachCycle, similar to https://github.com/SchapiroLabor/multiplex_macsima
  • [x] from a single .ome.tiff folder like Lung_adc_demo, similar to https://github.com/gustaveroussy/sopa/blob/master/sopa/io/reader/macsima.py
  • [ ] from multiple .ome.tiff folder where the folder name is a different ROI/sample/condition (in-house VIB data)

Some nice building blocks that would help with this:

  • [x] lazy-loading the SpatialData object by only reading the metadata, image files will only be read on demand
  • [x] channel names are parsed from the OME.TIFF metadata or from a channel list metadata file or from the filename
  • [x] allow subsetting to easy debugging
  • [ ] load multi samples as different coordinate-systems
  • [x] support channel cycle number metadata
  • [x] support physical pixels size
  • [ ] support metadata if the channel is a marker, repetitive DAPI or autofluorescence

berombau avatar Jun 11 '24 15:06 berombau