I am pretty much stuck at the beginning on this. I have a qptiff file generated from CODEX/Phenocycler panel of 22 markers. I know the next step is to process the data in QuPath and then ultimately I'd like to be able to take the data into Seurat where I am much more comfortable with the typical workflows for single-cell/spatial data.

My problem is I haven't worked with CODEX data at all, it's just something one of our students generated. I would like to process the data to the point where it is compatible with the "Test.csv" example presented in this Github issue

Does anyone have some documentation that could get me started on this?