KunHHE

Hi @quentinblampey Any updates on the proseg added into sopa? That will be very cool!!!

Thanks @wakelin-g. "if you are analysing MERFISH data, you should be using density_prior = uniform instead of density_prior = rna_count_based." Can you clarify to me, MERFISH/Xenium datasets will use density_prior...

Dear @wakelin-g, I did a new tets using the code from your guidance. If I use 'leiden', then I can see the plot_cell_annotation_sc only show the leiden cluster number (the...

Hi @quentinblampey, I ran Xenium using 10X shared datasets but get error that I never see when I run merscope data. I found in the .zarr folder-shapes: no cellpose_boundaries generation,...

Hi @quentinblampey, sorry, re-opened the issue. Tried to open h5ad using spatialdata-io, but not sure why it ask FileNotFoundError: C:\Users\hekun\Downloads\clustering_output.h5ad\images\micron_to_mosaic_pixel_transform.csv not found.? (sopa) C:\Users\hekun>python Python 3.10.16 | packaged by conda-forge...

Thanks @quentinblampey, I guess my h5ad file doesn't have the images directory when I generate AnnData. But usually AnnData doesn't have other directory except the 'Tables"? Or we can put...

> I think the disconnected cell pieces are still happening. I tried to find the same ROIs showed on a R shiny app, and those showed on Vizgen's visualiser. Although...

Thanks very much! I did not know that VPT can convert-geometry. My laptop is windows, I update the .VZG file successfully in VPT.

> Fantastic :) > […](#) Hi @marsdenl do you mind if I keep asking some naive question? I am a new pipeline runner, so we generate .csv.gz and .geojson files...