angelolab / angelolab/ark-analysis
Allow for a subset of FOVs in k-means clustering notebook
- Lingua principale
- Jupyter Notebook
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Descrizione
**Describe the bug**
There is no option to choose a subset of FOVs in the k-means neighborhood notebook. Discovered by Avery.
Currently, the notebook gets all FOVs in the cell table (`all_fovs = all_data[settings.FOV_ID].unique()` in the notebook), then uses all FOVs in the segmentation directory to calculate the distance matrix (https://github.com/angelolab/ark-analysis/blob/main/src/ark/analysis/spatial_analysis_utils.py#L37). If you manually change `all_fovs` in the notebook to try to run k-means only on a subset of FOVs, it errors out.
**Expected behavior**
Allow users to choose a subset of FOVs to run k-means on.
**To Reproduce**
Change `all_fovs` in the kmeans notebook to be a subset of FOVs.
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