Occident-Paper

Code for creating figures from Occident paper "Dynamic phenotyping of CAR T-cell-cancer cell interactions with live-cell imaging and cellular behavior analysis". In particular, this repo contains notebook to generate graphs in Figures 3, 4, and 5. This repository uses many functions from the occident library https://github.com/bee-hive/occident to perform the underlying analysis. For Figure 2 code, see here.

Data

Live cell images with segmentation and tracking will be made available on bioimage aarchive shortly.

Environment

Code is written in Python 3.11.9. The following packages are required:

1. numpy 1.26.4
2. matplotlib 3.8.2
3. statsmodel 0.14.2
4. pandas 2.1.4
5. scipy 1.11.4
6. skimage 0.23.2
7. tifffile 2024.5.10

Organization

Each folder contains notebooks to produce the associated figure.