Virtual live/apoptotic cell staining using cGAN

Train and evaluate conditional generative adveserial networks to virtually stain phase contrast images.

This project is powered by DeepTrack 2.0

Installation

Clone the repository using git clone https://github.com/softmatterlab/Live-apoptotic-virtual-staining

Installing dependencies using pip

Requires python >= 3.6

Open a terminal and run pip install -r misc/requirements.txt

For use with a GPU, please refer to tensorflow

Running

Train a model to virtually stain phase-contrast images

Open a terminal and run python train.py setup -i [MODEL_INDEX] -e [NUMBER_OF_EPOCHS] -r [NUMBER OF REPETITIONS]

Use a trained model to virtually stain phase-contrast images

Open a terminal and run python evaluate.py -t [DATASET]