This repository contains supporting code for "Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states".
additional_scripts
Contains environment creation scripts and aggregate runner scripts for Mesmer/mIF analysis.
analysis_and_figure_creation_notebooks
mif_analysis
Multiplexed Immunofluorescence Analysis Files
multislide_analysis
Multiregion H&E Slide Analysis Files
primary_analysis
TCGA & CM-025 Primary Figures Analysis
til_analysis
TIL-specific Analysis Files
ml_inference
Scripts for inference using trained neural networks.
ml_training
Scripts and Hyperparameters used for neural network training.
packages
checkmate_imports.py
Utility code used during general analysis
image-graphs
Utility code for creating and manipulating graphs
mc_lightning
Toolkit developed in PyTorch Lightning for model training and inference
vision-helpers
Additional convenience and helper code
preprocessing_and_qc_scripts
Scripts used for HistoQC and tile generation
pytorch_models
Information regarding where to find the pytorch model files