The Single Cell Expression Atlas would like to show data from spatial omics experiments. In order to pick best standards for new data, I’m trying to wrangle a published dataset into the IDR style I see in git.
In a related topic I saw you mention pattern files and companion OME files. I wondered if you had some standards about these files for multiplex FISH or Visium? We use MAGE-TAB for single-cell RNA-seq and I see very similar files in IDR. I wondered if the attributes here are controlled or required?
I’m also interested to understand how you generate and validate these files? Do you do this from OME-TIFF automatically?
Our resource is mainly interested in the expression matrix (cellxgene), plus some extra metadata about targets and cells rather than the raw images (although we would like to link to them if possible). Do you have any examples with these matrices yet so I can see how to format highly multiplexed datasets?
Thanks for your help,