sopa

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I trained a cellpose model and used it with a morphology2D file outside of sopa and got pretty good results, however when running it with the same image on sopa...

cstrlln

CosMx input file format requirements

11

Hi Sopa development team, Sopa looks like a perfect fit for what I've been trying to do with integrating IF stains with Baysor re-segmentation. However, I've been having trouble figuring...

Jwong684

[help wanted] Other segmentation options

4

Thanks for the software, it's a very comprehensive effort. We just got some CosMX data and are pretty unhappy with the default segmentations. We were on the way of training...

cstrlln

sdata object has no cellpose or baysor boundaries

3

Hello to the SOPA creators. I am quite a beginner to Python and the Command Line Interface. I have attempted to run the Ready made Snakemake pipeline for Xenium data...

altunbulakli

Overlay custom segmentation using cell segmentation resolver

12

Hi, Thank you for SOPA, it looks really helpful. I'd love to use the cell segmentation resolver. However, I'm struggling a little with how best to implement. I have custom...

EST09

[Feature] how to handle updated output from different technologies.

5

**Is your feature request related to a problem? Please describe.** I think the output of CosMX files has changed since sopa was developed. **Describe the solution you'd like** Could you...

cstrlln

Add nextflow pipeline

2

The `snakemake` pipeline should be translated to `nextflow` to reach more users. Don't hesitate to comment this issue to show your interest, else we keep it as a low priority...

quentinblampey

[Feature] Use .CZI data in SOPA

2

**Feature request** I am using multiplexed images (Opal dyes - fluorescence data) acquired with a Zeiss microscope that generates **.czi** files, but this format is not compatible with SOPA. **Suggested...

mariavigovaldoleiros

[Feature] Cellpose - artificially define an area of cytoplasm

1

**Feature request / question** In the absence of a general membrane marker, Sopa/cellpose (using only DAPI) will not "expand" the detected nuclei to generate an artificial cell membrane/cytoplasm area. In...

mariavigovaldoleiros

Where is the tuto.zarr from the tuto.zarr?

4

snakemake --config sdata_path=tuto.zarr --configfile=config/toy/uniform_cellpose.yaml --cores 1 --use-conda i did not find the tuto.zarr in the workflow or anywhere in the snakemake folder

suhridbuddha