NSCLC_Distinct_ecologies

Code for paper 'Distinct tumor-immune ecologies in NSCLC patients predict progression and define a clinical biomarker of therapy response'. Link

Description for each folder

• FoV analysis: Outline code to process a single Field of View (FoV)
• Non-spatial analysis: Code to handle pixel based analysis of images.
• Predictions using NN SDM: Refer to an implementation of the NN SDMs here.
• RoGM_analysis: Code that generates the Kaplan Meier survival curves a) for SD/PD groups, and b) using the ratio of geometric means (RoGM) values for SD/PD groups.
• Fig3_code: Code outlines to generate neighborhoods from cell segments and quadrats.
• Fig5_predictions: Code outlines to generate disease progression predictions using SVMs.
• Fig6_Mistic_code: Run Mistic as detailed here.