Daniel C. Jones

No guarantees, but I think this bug was fixed with 1.0.5. There have been no changes to the actual model between 1.0.3 and 1.0.5, so it should not introduce batch...

Great question! I don't have a solution for this right now. In principle, you would compute the aggregate marker intensity across the polygons that proseg outputs, but I don't have...

These are being computed slightly differently, which I agree that is confusing so I'll reconcile these in a future version. Expected counts are from transcript assignments averaged over many samples,...

Hi Yiming, Unfortunately 2.0.2 only introduced run time improvements, memory usage will be similar to 2.0.1. I'm working on some more significant changes to reduce the memory usage, but that...

Probably `--nbglayers 1` is easiest way to reduce memory usage with the least impact. Number of threads will have very little impact on memory. I'm a little surprised you are...

Thanks! This is an interesting use case! As far as input format, it's pretty general, but you minimally need a csv file that has the following columns (where the column...

That shouldn't be needed. That tells it to ignore the cellular compartment column, but if your input doesn't one have that it'll work just the same.

Proseg can lose cells like this if they are very small and smashed together so that they can't be represented with voxels. That's usually a pretty minor effect, though. I've...

That's interesting. I don't see anything remarkable about this sample that would cause this issue. Another thought that occurred to me is that there may be an issue with the...

Hi RL, I think it may depend on what kind of downstream analysis you're doing. I use the 2D consensus polygons for visualizations, since it's more readable, and also for...