This repository contains codes for the Geometric Scattering Trajectory Homology (GSTH) method from the paper "Tissue-wide coordination of calcium signaling regulates the epithelial stem cell pool during homeostasis".
GSTH recognizes and visualizes patterns of calcium signaling in microscopy data, using a combination of data geometry and topology. It models Ca2+ imaging as signals over a cell adjacency graph and uses a multi-level wavelet-like transform (called a scattering transform) to extract signaling patterns from high dimensional in vivo datasets.
To run the codes, the following packages need to be installed:
- Numpy (>1.20.3)
- Scipy (>1.5.2)
- Networkx (>2.5)
- Eirene (https://github.com/Eetion/Eirene.jl)
- PHATE (>1.0.7)
Numpy, Scipy and Networkx can be installed by running the following from a terminal:
pip install numpy
pip install scipy
pip install networkx
The Python version of PHATE can be installed by running the following from a terminal:
pip install --user phate