cstrlln

proseg output support

10

could you suggest how to appropriately import the output data from proseg into voyager? https://github.com/dcjones/proseg

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...

[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...

[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...

I was not sure where in the SCE community to ask but here it goes: Is there a tool to integrate new single cell datasets to a reference 'atlas' as...

protein info from CosMX

1

Thank you for the tool! any suggestions on how to reintegrate the surface protein staining data from CosMX (e.g CD45, panCK) after segmenting with proseg?

drop unused levels in barplot

1

wanted to know what would be the simplest way of dropping unused levels in barplots, specially when splitting by different variables this gets tricky. Thank you!