marsdenl

@quentinblampey @josenimo I have a similar issue on Windows also. .sopa_cache only contains patches and patches_file_image and the run fails after: Writing tiles: 100%|█████████████████████▉| 4796/4797 [07:28 Image of shape (3,...

Hey @josenimo. Yes sorry for the very vague comment and thanks for taking the timer to answer. I've been trying to run it on snakemake yes with the following config:...

That's already super useful to know, thanks for the information :)

Hey @dcjones. Thanks again for listing the settings above. Do you expect them to change the size of the masks generated? I've been having the issue that a single cell...

I used the Vizgen Visualiser and converted the proseg .geojson to Vizgen's .parquet file required using the vizgen VPT post processing tool. Perhaps some modification occurs during these steps so...

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 there...

I see, that makes a lot of sense. I just checked and you're absolutely right. The initial input segmentation has the same errors. The black/white cell in the FOV above...

Hey @KunHHE, Sure! Vizgen's VPT convert geometries function is compatible with .geojson files. Although on Windows it struggles a bit, on MAC I can simply run on the CLI: vpt...

Fantastic :) On Tue, 26 Nov 2024 at 13:21, KunHHE ***@***.***> wrote: > Thanks very much! I did not know that VPT can convert-geometry. My laptop > is windows, I...

No worries at all. Ive done my fair share of asking questions on Github also :) Like I said earlier, there is a cell_ID mismatch between Proseg and VPT so...