Daniel C. Jones

Thanks for letting me know! I just released 2.0.2 which should fix this.

That's interesting. It looks to me like the initial nuclear segmentation missed some cells here and proseg is trying to compensate by making one huge cell. Currently proseg doesn't have...

In this case, it seems like a glitch drawing the polygons. Because proseg is voxel based, it can't produce diagonal lines like this, so there's either an error in it's...

I just released 2.0.4 which should fix this. I'd also suggest using the `--no-z-layer-doubling` argument, otherwise voxel layers get subdivided to 40 by the end of sampling in the default...

Hi Alexis, 1. That's correct, there's no compartment information in MERSCOPE, so the whole cell is used. In my paper I resegmented nuclei using cellpose to for some analyses. 2....

Yeah, in principle you should be able to use the polygons that proseg outputs, but it would probably require a little work to get mean intensities using these. First, proseg's...

Thanks for the interest! IMC data is pretty different than transcriptomic data and would involve a different set of assumptions in the model, so it isn't trivial to add support,...

The biggest issue is just RNA vs protein more than anything. Proseg takes advantage of the fact most RNA is distributed fairly randomly throughout the cell to segment transcriptomic data....

Something definitely seems off, unless it is a truly massive dataset. I've never seen it take this long or use this much memory. My best guess is that the coordinate...

I can confirm that it does seems to use quite a lot of memory. Part of this is just that it's a large dataset and CosMx 6k has lot of...