Quentin Blampey

I'm closing this issue, but feel free to re-open if you need extra information!

Hello @mariavigovaldoleiros, thanks for creating this issue, you're actually not the first one to ask for a `.czi` file reader. I'll work on this and come back to you very...

This is available in `sopa==1.0.11`, via a new reader called [aicsimageio](https://gustaveroussy.github.io/sopa/api/io/#sopa.io.aicsimageio). It uses AICSImageIO, which supports reading multiple formats, including CZI. Note that, as the docs mentions, you'll need to...

I'm closing this issue, but feel free to re-open if you need extra information!

Hello @andrea-de-micheli, **TL;DR**: I suggest using the Snakemake pipeline, which will do all the parallelization and the boring stuff for you. Using the CLI is recommended if you want to...

Hello, I'm surprised it didn't finish after 18+ hours. Have you tried using a Snakemake profile or did you instead use `--cores 16` in the snakemake command? For example, there...

Thanks for the info @andrea-de-micheli! Concerning your log, it seems that the error is indeed not there. But, I see that the error rule had `jobid: 59`, do you know...

Actually `cell_key: cell_id` is when you want to use the default Vizgen segmentation as a prior. Instead, to use cellpose as a prior, simply delete `cell_key` and it will use...

Bonjour @andrea-de-micheli, Yes, you can re-execute the same snakemake command, it will start again where it failed! Snakemake re-runs other rules only if it detects changes (like code change or...

Hello @andrea-de-micheli, yes it has been added. Can you check that you have the right version on your `sopa` conda environment? (I'm precising the `sopa` environment because it is the...