Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Support for MACSima data #155

Open
10 of 13 tasks
berombau opened this issue Jun 11, 2024 · 0 comments
Open
10 of 13 tasks

Support for MACSima data #155

berombau opened this issue Jun 11, 2024 · 0 comments

Comments

@berombau
Copy link

berombau commented Jun 11, 2024

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)
  • 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:

Some nice building blocks that would help with this:

  • lazy-loading the SpatialData object by only reading the metadata, image files will only be read on demand
  • channel names are parsed from the OME.TIFF metadata or from a channel list metadata file or from the filename
  • allow subsetting to easy debugging
  • load multi samples as different coordinate-systems
  • support channel cycle number metadata
  • support physical pixels size
  • support metadata if the channel is a marker, repetitive DAPI or autofluorescence
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant