Quentin Blampey

I think the MERSCOPE data format has been the same since approximately early 2023, so everything should be good. Processing the data with VPT will not help (we read the...

Hi @mamyAndrianteranagna, it's good to see that now you can see the "global" coordinate system, but sorry to hear that the alignment is still wrong. Do you still have the...

Hello! What file format is it? `.ome.tif` I suppose? And does it come from a specific machine? According to your error, it seems you were using the Snakemake pipeline, not...

I'm closing this issue as I didn't receive an answer to my question above. Please feel free to re-open if you still have this issue!

Hello @xiao233333, thanks for reporting this. I already experienced this issue, but I don't really understand what is happening. I currently believe that it's a strange Snakemake issue, which triggers...

Hi @KunHHE, For any downstream analysis, you can use [Scanpy](https://scanpy.readthedocs.io/en/stable/), which should contain all you need. For the preprocessing, you can use [Pytometry](https://github.com/scverse/pytometry). You can also use Scyan, although it's...

Hi @hrj21, thanks for reporting. Unfortunately, I don't have any experience in `reticulate` so it's difficult for me to debug. Does everything work as expected using the python package directly?...

I think what you want is the `key_added` argument from [sopa.aggregate](https://gustaveroussy.github.io/sopa/api/aggregation/#sopa.aggregate)? For instance, `sopa.aggregate(sdata, aggregate_channels=False, expand_radius_ratio=1, key_added = "table_xxx")` Be careful, `expand_radius_ratio=1` means that the cell will be expanded by...

Your code looks good @NadineBestard! I think we can slightly update it to make it smoother: - You don't need to precise `shapes` in `sdata.shapes['nuclei_boundaries']`, you can use `sdata['nuclei_boundaries']` directly....

Hi @jeffquinn-msk, How many cells do you have? I'm surprised about your ETA. Would you mind sharing your shapes (as a GeoPandas parquet file)? This way I can compare the...