Request to update Vizgen Cell Boundaries Polygon generation

[rushin682]

Hello,

Thank you for a great repo and paper!

We noticed that for Vizgen aspect, creating of polygons (Line 140 - 152: preprocess/vizgen.py) uses the old cell boundaries h5 format. However, we have a parquet file for the cell boundaries. Is it possible to add a feature that can take the parquet file as input to create the polygons as well?

Thanks once again for your time. Looking forward to your response.

best,
Rushin

[chenyhvvvv]

Thank you for your interest! Can you show me a public dataset to let me try on it?

[devianggr]

Hi,

Maybe I can help Rushin to share the public dataset with the cell_boundaries.parquet file.
You can download the access dataset through this link:
https://info.vizgen.com/protein-co-detection-showcase?submissionGuid=2e012b62-62b4-4a7e-97d4-cbfbd0a7a903

Best,
Devi

[chenyhvvvv]

Hi, after trying and searching for reading parquet object of Vizgen, I can not find a proper package or code to read it in python. Directly using pandas can not work.

And there is little result of this and still an issue in satijalab/seurat#7080.

But instead, you can use Cellpose to segment the MIP DAPI image. The code include prepare_dapi_for_cellpose in preprocess/vizgen.py to provide MIP image of mosaic_DAPI_z[].tif and segment using script like

python preprocess/cellpose_dapi.py --dapi ./data/vizgen_mouse_brain/mosaic_DAPI_mip_resized.tif --out_dir ./data/vizgen_mouse_brain