I was wondering if some people were working on reading FCS files. It seems scanpy was mostly designed for scRNA-seq data, but I think anndata and scanpy fit well with any kind of cytometry data too (and as it’s single-cell data, I think it would make sense to support it).
I’m already using scanpy to analyze my FCS files, but currently, I have to use an external library to read an FCS file and then convert it back to an anndata instance. Maybe I’m missing something, but if it’s not supported yet, I think it could be great to have it. If you want so, I would be happy to contribute to implementing it.
Also, more generally, is there a reason not to consider cytometry?