Quentin Blampey

Hello @Yifan-debug, can you show me which line of code you used to get this error? My guess is that you provided `shapes_key=["cell_circles"]` instead of `shapes_key="cell_circles"`. Indeed, the key should...

I think I understand the error now, but this is due to the fact that your data is not formated as an output of Sopa. Indeed, the `sopa.io.write` function expects...

Okay, thanks for giving a try. I'll try to fix `sopa.io.write` to make it more general, i.e. handle non-sopa outputs. What is your actual use case? I have a few...

Thanks for sharing these details! In that case, since you want to use Sopa for segmentation, you should do the following: 1. Read only the `morphology_focus` and `transcripts` elements in...

Hi @LucaMarconato! In the current PR for the CLI (https://github.com/scverse/spatialdata-io/pull/239), they call `ShapesModels.parse()` inside `spatialdata-io` instead of moving the function itself. Which option do you prefer? I'm fine with both....

`z_index = 0` was used because the polygons are duplicated for all z-indices. I was not aware of the possibility of segmenting every z-level using VPT, thanks for letting us...

Hi @wangjiawen2013, yes, this is possible. There is a [tutorial here](https://gustaveroussy.github.io/sopa/tutorials/advanced_segmentation/#multi-step-segmentation) that details how to do it. Let me know if you experience any issues or need more help to...

I'm closing the issue, as it is inactive, but feel free to re-open if desired!

Hi @KunHHE, can you try to directly use `spatialdata_io` as below? It should be able to read the Vizgen segmentation. Inside this spatialdata object, you'll have an AnnData object that...

Hi @KunHHE, normally the MERSCOPE outputs a `micron_to_mosaic_pixel_transform.csv` file under the `images` directory. Here, this file is not existing, so spatialdata-io can't read the data. Are you sure you transferred...