This repo contains all materials related to the manuscript on "Machine-Learning Analysis of Reaction–Diffusion–Based Pigmentation Patterns in Monkeyflowers (Mimulus)" by Nathan Schaumburger, Reesha J Patel, Timothy Kuliyev, Yao-Wu Yuan, and Michael L Blinov.
- SupplementalMaterial contains all running Jupyter Notebooks to run image classification, visualization and parameter estimation. It also contains all images simulated using Virtual Cell modeling and simulation software, dataframes with image features, dataframes with classification and PCA added, and all outputs of visualization scripts.
- OlderStuff contains additional files that are not in the final manuscript version. Specifically, it has CNN classification based on manual classification.
- Ua - Degradation rate for NEGAN
- Ui - Degradation rate for RTO
- Ga - Self-activation of A by A
- Gi - Activation of I by A
- Ba - Inhibition of A by I
- Da - Diffusion rate of A
- Di - Diffusion rate of I