Daniel C. Jones

To clarify, the counts that proseg reports (in the expected-counts file) are always with respect to the 3d cells, which is what's being used internally. The flattened 2D polygons are...

Hi Luc, There's really no attempt at this point to tweak default parameters based on the platform. That may change in the future with more testing, but all `--merscope` does...

Hi Luc, These polygons look a little peculiar to me. I'm not sure what you're using to plot these, but it's doing some sort of simplification or modification of the...

Ok, these look much more like what I'd expect to see. Especially in cells with a relatively low number of transcripts, you might expect to see peculiar voxel "appendages", but...

My suspicion is that the nuclear segmentation that proseg is initialized with oversegmented and split these into multiple cells. Currently proseg is somewhat anchored to this input. It can't merge...

It does use the the `CellComp` column, rather than the DAPI stain directly. Those transcript assignments derived from the image-based segmentation are used in two ways: 1. Voxel assignments are...

You should be able to filter these transcripts out with `--min-qv 20`. I should probably make these the default, but it's typically a very small number of transcripts. Right now...

The main difficulty proseg would have with these cases (and multi-nucleated cells in general) is that it is initialized and constrained by prior cell segmentation. If it's initialized with nuclear...

Hi Anna, Rounding the nearest integer should be completely fine. I do that pretty regularly when a downstream analysis assumes integer counts.

I don't think I've run this particular dataset. I have a set of datasets that regularly rerun proseg on to test changes. I'll see about adding this to it to...