Quentin Blampey

I couldn't reproduce the issue yet. Meanwhile, a few questions: - Do you have the same issue with the CLI using `sopa==1.0.9`? For example, if you run the command line...

This is probably a Windows issue related to how strings are handled in the command line. This should be solved in the master branch, can you `git pull` and try...

Hello @mariavigovaldoleiros, Actually, we can use cell radius expansion, but only to compute the channel intensity for each cell (see the `expand_radius_ratio` parameter [here](https://github.com/gustaveroussy/sopa/blob/580c8e6130f63f76792007292b403a4311a4ce58/workflow/config/example_commented.yaml#L73)). Yet, indeed, we don't display it...

Hello @josenimo, these operations can actually be done easily outside of Sopa, using only the SpatialData object: 1. to expand your shapes, you can do `geo_df = sdata["cell_boundaries"].buffer(expand_radius)`, where `expand_radius`...

Hello @mariavigovaldoleiros, did my comments answer your question? I'm closing this issue, feel free to re-open

Hello @HSvitina, Thanks for your interest in Sopa, I will be happy to help! First, I have a few questions to understand the issue better: - are you using the...

Hello, thanks for these details @HSvitina, I was able to reproduce the issue for the conversion to the Xenium Explorer. Actually, this happens only when using the API, but this...

Indeed it seems that it reads it as `"'merscope'"` instead of `'merscope'`. I have to say that I don't understand why this happens, because I tried on Linux/MacOS/Windows, and I...

Hello @HSvitina, luckily this is still the same issue with the quotes. I updated the snakemake pipeline to use double quotes by default. You can `git pull`, and the pipeline...

Indeed @HSvitina only one layer is used by default, but you can use them all if desired. As mentioned in the doc [here](https://gustaveroussy.github.io/sopa/api/io/#sopa.io.merscope), you can do `sopa.io.merscope("/path/to/region", z_layers=[0, 1, 2,...