Daniel C. Jones

I'll definitely investigate this some more. I did fix a bug in the connectivity checking recently, but haven't released a new version yet. That should make `--check-connectivity` more useful. One...

I'm glad that improved things. I think it's clear that the "consensus polygons" are the source of a lot of the disconnection. I'll think about if there are improvements I...

I definitely agree that there should be a way to report the negative controls without necessarily using them in segmentation. That should be pretty easy to implement, so I'll try...

In fact, I think you can do this now without a special option if you're willing to write a ton of arguments to describe the input format: ```sh proseg \...

This is a spatialdata-io issue (I just created an issue, see the mention above), so they'll have to add support for this. In the mean time, the best you can...

`proseg-to-baysor` will lose a small number of cells because it filters out cells that have zero assigned transcripts. This really wasn't by choice, but because including them caused errors with...

This may be better is proseg 3. The umaps will look slightly different after importing because proseg will output expected counts, which can be non-integers, but that's not something xenium...

This seems fine, but you've disabled any 3d segmentation here with `--nbglayers 1` and `--no-z-layer-doubling`. Allowing some 3d segmentation usually improves the accuracy of transcript assignments in my testing on...

Huh, not sure what might cause this. If you're able, can you try proseg 3 and see if you get the same error?

The current release doesn't work particularly well with xenium 5k (or high plex data in general), as you've noticed. I'm working on a new model that will, but it's still...