Contains the scripts for running predRNN on CADES (https://cades.ornl.gov/), for predicting microbial growth of a population made of Pseudomonas Aeruginosa and mutant. Scripts for obtaining population curves and colony areas are also included.
predRNN is a Recurrent Neural Network: https://github.com/thuml/predrnn-pytorch
Relevant papers on P. Aeruginosa for this repo:
https://www.frontiersin.org/articles/10.3389/fmicb.2018.00033/full
https://www.jove.com/t/55701/assembly-tracking-microbial-community-development-within-microwell
Video frame prediction of microbial growth with a recurrent neural network: https://www.frontiersin.org/articles/10.3389/fmicb.2022.1034586/full