Spatial multiplex immunofluorescence data from thymic slices. Tissues are stained with phenocycler (CODEX) workflow. The goal is to understand how aging affects thymic tissue.
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AKOYA_clustering_comparison_functions.R contains the functions that I use to automate the downstream analysis of spatial multiplex immunofluorescence clustering
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floodfill_multiprocessing_to_color_images.py is a script to parallelize the coloring by cell type of cell segmentation masks for images that aren't labeled during segmentation.
Comparison of multiplex immunofluorescence image of corticomedullary junction of a mouse thymus and single-cell overlay of Mesmer cell segmentation colored by cell type cluster.
