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Torch Integrated Cell

Model Architecture

Image-driven generative cell modelling with adversarial autoencoders: https://arxiv.org/abs/1705.00092

For the updated 3D version, please see:

Building a 3D Integrated Cell
Manuscript: https://www.biorxiv.org/content/early/2017/12/21/238378
GitHub: https://github.com/AllenCellModeling/pytorch_integrated_cell

Installation

Installing on linux is recommended.

prerequisites

Running on docker is recommended, though not required.

  • install torch on docker / nvidia-docker as in e.g. this guide: https://github.com/gregjohnso/dl-docker
  • download the training images: aws s3 cp s3://aics.integrated.cell.arxiv.paper.data . --recursive --no-sign-request

Steps:

After you clone this repository, you will need to edit the mount points for the images in run_docker.sh to point to where you saved them. Once those locations are properly set, you can start the docker image with

bash run_docker.sh

Once you're in the docker container, you can train the model with

bash train_model_2D.sh

This will take a while, probably about 12-18 hours.

Project website

Example outputs of this model can be viewed at http://www.allencell.org

Citation

If you find this code useful in your research, please consider citing the following paper:

@article{johnson2017generative,
   title={Generative Modeling with Conditional Autoencoders: Building an Integrated Cell},
   author={Gregory R. Johnson, Rory M. Donovan-Maiye, Mary M. Maleckar},
   journal={arXiv preprint arXiv:1705.00092},
   year={2017},
   url={https://arxiv.org/abs/1705.00092}
}

Contact

Gregory Johnson E-mail: gregj@alleninstitute.org

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.