Quentin Blampey

Yes, I have a transformation implementation for MERFISH. For non-standard data, I could indeed enforce a specific file format, but the users would need to create this file before reading...

Hi @Marius1311, Thanks for reporting this. In your case, I imagine you have multiple images (one per z-stack), so the `get_spatial_image` can't find which image is the default image to...

Not necessarily: it would mean that, if you don't choose any z-stack, then it will use the middle one. But you would still be able to load all z-stacks, play...

Thanks @lardenoije for your feedback! I'm working on a new version of the API (`sopa==2.0.0`) which should ease its usage but also make it more flexible, so I'll try to...

Hi all, sorry for the delay! I’m happy to announce that `sopa==2.0.0` is now released :) Don’t hesitate to check the new documentation, or the [migration guide](https://github.com/gustaveroussy/sopa/discussions/138) to smoothly get...

Hello @Marius1311, we currently don't support 3D cellpose segmentation, but this is definitely something I can work on! Baysor might already work in 3D, but I'm not sure, I need...

Hi @lguerard, sorry for the delay, I forgot to answer Yes, the Baysor output is not very straightforward to use in 3D. I'm thinking about it, but it would involve...

Hi @Marius1311, @lguerard and I recently added [`proseg`](https://github.com/dcjones/proseg) to the available segmentation methods. It uses the `z` transcript location by default, so the corresponding table will take the 3D information...

Okay, perfect, so in that case it means you would be satisfied with the approach I proposed? That is, running 3D segmentation to compute the cell-by-gene table, but storing the...

In `sopa==2.0.4`, recently released, there is now a [tutorial for `proseg`](https://gustaveroussy.github.io/sopa/tutorials/api_usage/#proseg), which uses the 3D information (when a `z` column is present in the transcript dataframe)! @lguerard, regarding cellpose this...