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aristoteleo / spateo-release

Spatiotemporal modeling of spatial transcriptomics
https://spateo-release.readthedocs.io/
BSD 2-Clause "Simplified" License
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cell segmentation cs.score_and_mask_pixels function modulenotfounderror #235

Open vivian-huang opened 5 months ago

vivian-huang commented 5 months ago

Hi,

I am trying to follow the Spateo cell segmentation tutorial, but I am throwing a ModuleNotFoundError for fbgbp at this step for segmentation:

st.cs.score_and_mask_pixels( adata, 'nuclear', k=5, method="EM+BP" )

Checking my installed libraries, however, it appears that fbgbp==0.2.1 is already installed.

To try to get around this problem, I directly cloned the fbgbp locally and inserted a path via

sys.path.insert(0, "/Users/lab/Downloads/fbgbp/") import fbgbp

prior to the st.cs.score_and_mask_pixels function, but I am getting a new ModuleNotFoundError: No module named 'fbgbp.binary_belief_propagation'

image

Any help with this would be appreciated. Thanks!

Xiaojieqiu commented 5 months ago

Hi Vivan, I think you will need to update and install the fbgbp package.

@YifanLu2000 can you please fix the version issue and dependency issue for spateo?

github-actions[bot] commented 1 month ago

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