Quentin Blampey

Thanks for trying on `linux`! For now I don't have enough bandwidth to reproduce and try fixing this issue (mostly because it's Windows specific), but I keep this open and...

Hi @emartinki, indeed, Resolve data is not yet supported in Sopa. It should be relatively easy and/or quick to add it, because I just need to add the corresponding reader....

Thanks for the extra information @emartinki. I just added the reader, you can try it on the `main` branch from sopa (install it in development mode) or wait for the...

Yes, indeed, `region` would be in your case `"A1-2"` for the first sample, then `"A1-3"`, etc. I decided to call this argument `region` to make it consistent with the other...

I'll close the issue since this reader is now released, but don't hesitate to re-open if needed

Hi @jonas2612, I assume there is a ComSeg issue on a single patch, maybe on a small patch. I saw there is an open issue [here](https://github.com/fish-quant/ComSeg/issues/13) on the ComSeg repository,...

Thanks for sharing @jonas2612. Normally, when running `sopa.make_transcript_patches` with the argument `write_cells_centroids=True`, you should have a `centroids.csv` file inside each patch cache directory. Could you maybe re-run `sopa.make_transcript_patches` and check...

Thanks @jonas2612 for investigating, I think it totally makes sense! There are potentially three things we need to update/fix: 1. Sopa should always create a `centroids.csv`, even if there are...

Thanks, I think we have enough info to fix it, we'll let keep you updated 😊

I had a quick look, and normally, ComSeg shouldn't run on the patches without any prior cell. But the current implementation already prevents that. Normally, when running `sopa.make_transcript_patches`, you should...