[Feature] Multiple run of Cellpose/Baysor

[lguerard]

Hi !

I put this as a feature, but maybe it's already available (I guess maybe through API mainly).

We're in the parameters optimization step of our pipeline and would like to run Cellpose and/or Baysor with different settings. Is it possible to add more and more Shapes layer in the SpatialData object ?
If so, how do I select the one for Baysor segmentation and/or for the different steps of conflicts or aggregation ?

Thanks a lot !

[quentinblampey]

Hi @lguerard,

Yes, indeed, I recommend using the API for this. Basically, when running segmentation, you can choose the name of the new shapes layer that will be added to your SpatialData object.
So, you can create multiple shapes layers, and compare them afterwards.

I'll soon release sopa==2.0.0, probably this week or next week, and I highly recommend waiting for this new version because it will be much easier to use. I'll add extra details on how to do that after releasing the new version!

[lguerard]

Thanks for the answer !

And really looking forward to test 2.0.0 ! :)