No description or website provided.
Branch: paper_release
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
doc/images
models
.gitignore finished readme except arxiv link Apr 27, 2017
DataProvider2D.lua Initial Commit Apr 7, 2017
imtools.lua Initial Commit Apr 7, 2017
plot error.ipynb Initial Commit Apr 7, 2017
printFigs2D.ipynb
readme.md
run_docker.sh
setup.lua Initial Commit Apr 7, 2017
train.lua Initial Commit Apr 7, 2017
train_model_2D.lua updates Apr 25, 2017
train_model_2D.sh
utils.lua

readme.md

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/.