Fix compatibility with latest version of Baysor

[lguerard]

Latest version of Baysor outputs either segmentation_polygons2D.json or segmentation_polygons3D.json depending on input data. This very basic fix would reestablish compatibility, in case users aren't running both 2D and 3D and outputting results in same folder

[lguerard]

Actually, there's way more changes inside the Json output. The format completely changed, another option is needed to be passed to Baysor. I'll try it and come back here if I manage to have some fix(es).

[quentinblampey]

Thanks for diving into this! Let me know if you need some help
It indeed seems that there are several issues with the new Baysor version...

[lguerard]

I'm having an issue but I don't know if that's on sopa's side or Baysor :

https://github.com/lguerard/sopa/blob/938b7dbf82666c5a5025f7e901a7feca2640fdb7/sopa/segmentation/transcripts.py#L127

gives an error because the loom files contains cells that aren't in the JSON. Do you know why that would be ?

[quentinblampey]

Sorry @lguerard I don't know what happened, it automatically closed the PR when I wanted to push some stuff to your PR
For some reasons I couldn't push, even though being up to date with your changes

[quentinblampey]

I'm going to create a new PR with your changes

[lguerard]

No worries at all, but it might not yet be fully working, it's quite WIP at the moment...