Scripts for the analysis of tumor-immune cell interactions in Imaging Flow Cytrometry data.
Note: This GitHub site is currently mostly a placeholder. Instructions on how to run them will follow 'soon'.
The two .ijm Fiji macros currently have different functionalities, but will at some point be merged into a single script.
Analyze_ImageStream_stack_2celltypes_+_membrane_intensity_analysis_1.5.ijm can be used to separate tumor cells from immune cells and to quantify 'marker of interest' enrichment at the interface between these cells and visualize this in various ways.
ClassifyCellTypes_2_8.ijm is a more general script that works for more cell types. First, tumor cells and immune cells are determined using K-means clustering. Next, immune cell marker abundance is classified as positive or nagative, compared to a user-set or automatic threshold level. This script currently lacks the membrane enrichment quantification and visualizations.
Finally, the Jupyter Notebook Summarize_Interactions.ipynb can be used to quantify interactions between different cells types, for example:
For combining exported ImageStream images to create input tiff files for the macros, see our ImageStreamCombiner repository.