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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Cannot run through example dataset in `3_Pixie_Cluster_Cells.ipynb` #1098

Closed cliu72 closed 6 months ago

cliu72 commented 6 months ago

Describe the bug When running 3_Pixie_Cluster_Cells.ipynb directly (WITHOUT running 2_Pixie_Cluster_Pixels.ipynb) before it, I get this error: image

I don't think the example dataset in Hugging Face was updated after some code changes.

Expected behavior Run through notebook 3 completely using example dataset with no errors.

To Reproduce Delete any existing example_dataset folders and run notebook 3 only (don't run notebook 2).

cliu72 commented 6 months ago

Ah sorry my bad, it's because I had some old versions of the example dataset in the cache, so it was using the cached version instead of the new version.