Quentin Blampey

I meant something like `self.sdata_path = Path("data/zarrs/{sample}.zarr")` in `utils.py:L43`, but I'm not sure it would work

Hey, sorry to hear it's still not working. I have to say I still find Snakemake confusing sometimes, so I don't really know how to make this work without many...

Hello @Yifan-debug, This error seems to be related to the issue https://github.com/gustaveroussy/sopa/issues/85, but it has been fixed since then. Which versions of Sopa do you use? You should have `sopa>=1.1.1`...

Hi @pakiessling, Sometimes the Xenium Explorer can be a little bit buggy, have you tried to close and re-open it? Else, have you seen any specific warning when running Sopa?...

Hum, okay, let me know if it happens again. Normally it should be very rare, so I'm surprised that it happened 3 times before working Do you have the recent...

I'm closing the issue for now, don't hesitate to let me know if it happens again!

Hello @mamyAndrianteranagna, thanks for referring to this issue. Can you list which versions of `sopa`, `spatialdata`, and `spatialdata-io` do you use? And can you confirm that you read the data...

Actually, the reader should be the same (`sopa.io.merscope` is a simple wrapper around `spatialdata_io.merscope`). But, still, it's good to re-run it with the latest versions, since it appears that your...

Hello @mamyAndrianteranagna, Despite the weird "c" channel in the transformation, there is something weird happening before. Starting from `spatialdata-io==0.1.3`, the main coordinate system for MERSCOPE data is "global" (i.e. the...

Well, everything should work whatever the main coordinate system, for both Cellpose and Baysor. My guess is that there is nothing wrong with Sopa or SpatialData, but instead, there is...