Daniel C. Jones

Hi, thanks for using proseg! Performance is an issue that I'm actively working on, so hopefully it will improve, but it is memory hungry for large datasets. The CosMx performance...

I don't know exactly what's happening here, but there can be fov effects which can manifest as reduced detection of transcripts along the edges of a fov. Because proseg is...

I'll definitely try to release some code to reproduce this analysis, I just don't have it in a very usable form right now.

I can't say for sure what's going on, but I suspect some subset of cells has extremely low coverage (the median is pretty low here). Proseg infers cell boundaries using...

This is odd, and I do see the same thing in xenium explorer with the counts not necessarily corresponding to what's shown. I'll investigate this some more, but also should...

Yes, proseg itself will output a number of tables, most importantly: * `expected-counts.csv.gz`: Give the cell-by-gene count matrix * `cell-metadata.csv.gz`: Spatial cell positions and other information. I don't have tutorials...

1. I think this is due to xenium explorer not supporting cells being multi-polygons, which is the case when you have these voxels that are only connected along the diagonal....

1. That's correct. Proseg produces MultiPolygons, which are usually one polygon, but can sometimes have disconnected parts. Baysor (and thus xeniumranger) only support single polygons, so the rule used in...

It might not be necessary, I'll try to look at some more recent CosMx data. The issue is that CosMx output is a mess, completely undocumented, and keeps changing, which...

Thanks for trying proseg. Just to verify, because I fixed a similar bug a while ago, is this with the latest version (1.0.5)? Also, I haven't yet extensively tested proseg...