Daniel C. Jones

This may change in future versions (I'd like to have a more precise model of optical crowding), but currently negative controls are not use directly, and in fact are excluded...

Hi, thanks for using proseg. Version 3 was was inadvertently outputing a different polygon estimation (unioned polygons) than version 2 (consensus 2d polygons), which made the the overlap seem worse...

Hi Amit, Because proseg tries to construct cell boundaries to explain the observed transcripts, usually when I see implausible large cells has a few possible causes: 1. There should be...

That's an interesting example. Unfortunately, I don't yet have a great plan how to improve this situation. Proseg does it's best to explain the observed transcripts with the cells it's...

Ah this looks like a bug. Proseg was assuming the same cell id doesn't occur in multiple fovs, which was to work around cosmx assigning non-unique cell ids. That seems...

This is fixed now in version 3.0.1 which I just published.

I'll try to write up some kind of tutorial, but probably your best bet is to use the [spatialdata-plot](https://github.com/scverse/spatialdata-plot) library. For example, here's a simple plot of cell boundaries. ```python...

I've just added a little example of how to do this here: https://github.com/dcjones/proseg/blob/main/examples/visiumhd-cellpose.sm

Proseg 3 has a different prior on morphology. I have seen some cases of producing weird cells like these in cases with quite sparse transcript density, but nothing this bad....

Actually, could you tell me how the transcripts subset you shared here was constructed? I see the coordinates are not the same as what was in the original file.