Valerio Reffo

Everything you need to work with visiumHD data is the fullres image and the files inside the binned_outputs folder, for any bin dimension of your choice the raw/filtered_feature_b5_matrix.h5 (I use...

Since you are away for 2 weeks I'll search for a working solution, so i tried different expand_radius_ratio (0, None, 1) to see if it change much. When i retried...

I may have a problem, I can't remember the samples with which I had problems, do I send you all the boundaries? they are almost 900k nuclei. Also a follow...

My bad, it's the first time I manage a workflow of such scale. I refer to the intensity and transcript filtering yes, the overwriting auto-save on disk and in memory...

No, I don't think it's necessary. In the next days I'll try the potential fix and I'll be back. Thank you anyway.