Repository for analysis performed in Unraveling cellular complexity with unlimited multiplexed superresolution imaging.
conda create -n golgi python=3.9
pip install numpy anndata scanpy umap-learn scikit-learn dask[complete] matplotlib pandas tables
golgi_features.py - Computes feature matrices from FLASH-PAINT images in Picasso format.
plot_golgi_matrices.py - Creates clustermap from ROIs of FLASH-PAINT images in Picasso format.
plot_golgi_umap.py - Computes and plots UMAP embedding of features generated by golgi_features.py.
plot_umap_and_image.py - Plot UMAP next to original image with ROI highlighted.
cluster_analysis.py - Tools for clustering and investigating UMAP embedding.
util.py - Common functions used by all scripts.
231211_DistanceHeatmapBrefeldinA.ipynb - Computes a distance heatmap for the Brefeldin A condtion.
231211_DistanceHeatmapControl.ipynb - Computes a distance heatmap for the Ilimaquinone condtion.
231211_DistanceHeatmapIlimaquinone.ipynb - Computes a distance heatmap for the control sample.
231211_DistanceHeatmapNocodazole.ipynb - Computes a distance heatmap for the Nocodazole condtion.
240118_DrugDataAbundance2.ipynb - Computs abundance box plots.