Quentin Blampey

Hey @cstrlln, I just released a new version `1.1.1` of sopa, which now includes [ComSeg](https://github.com/fish-quant/ComSeg) by @tdefa! We also contacted the author(s) of `proseg` to see if they want to...

Hi @KunHHE, no update regarding Proseg, sorry (we are still discussing it with its author). I'm also discussing with the author of [segger](https://github.com/EliHei2/segger_dev) to integrate it inside Sopa

Hi @Jwong684, Indeed, it seems that the file format has changed. Currently, I'm using: - The columns `x_global_px`, `y_global_px`, and `target` for the transcript file - All the images inside...

I don't think that renaming the columns is a good solution because I think that your transcript "x"/"y" columns are in microns instead of pixels, right? Same for the `_fov_positions_file`...

Nice @cstrlln! So the format didn't change? Is it just a matter of using one specific export module?

Indeed @Jwong684, as mentioned in this issue, I was using the second CSV column as the pandas index. But it seems that the FOV column is not always the second...

This should be fixed in `sopa==1.0.12`, can you try?

This is fixed, and the docs are updated. Closing the issue :)

Hello @altunbulakli, Indeed Sopa should run baysor, but in your case it seems it didn't. Can you show me the full log? You should have a text file called `TC_070.zarr/.sopa_cache/patches_file_baysor`,...

Actually, it looks as expected (it just a list of patches IDs). Each ID corresponds to the name of a directory inside `TC_070.zarr/.sopa_cache/baysor_boundaries`, do you have such directories? Also, have...