Spring 2022 Bioimage Informatics (Self-Study) project
This project explores using a deep generative adversarial network (GAN) to perform semi-supervised image segmentation on the 2015 MICCAI Gland Challenge dataset.
Version 2 of the code exists here.
Executes octopus for a single configuration file.
One time setup
bash /path/to/octopus/bin/mount_drive
bash /path/to/octopus/bin/setup_wandb
For each run
python /path/to/octopus/run_octopus.py --filename=/path/to/octopus/configs/remote/config001.txt
wandb conducts a search over your hyperparameters. Set the configuration file within the sweep yaml file.
One time setup
bash /path/to/octopus/bin/mount_drive
bash /path/to/octopus/bin/setup_wandb
For each sweep
wandb sweep /path/to/octopus/sweeps/remote/sweep001.yaml
# execute wandb agent as specified by wandb
octopus is designed to handle ConfigParser configuration files. For this project, ConfigParser config files are
organized into local and remote configs.
Sweeps are a tool wandb uses to search over a hyperparameter space. For this project, sweep configuration files are organized into local and remote sweeps.