https://github.com/allencellmodeling/torch_integrated_cell

https://github.com/allencellmodeling/torch_integrated_cell

biolog cell-analysis machine-learning neural-network torch

Last synced: 7 months ago
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• Host: GitHub
• URL: https://github.com/allencellmodeling/torch_integrated_cell
• Owner: AllenCellModeling
• Created: 2017-04-24T17:04:19.000Z (almost 9 years ago)
• Default Branch: paper_release
• Last Pushed: 2018-08-13T21:30:04.000Z (over 7 years ago)
• Last Synced: 2025-04-30T12:17:10.074Z (10 months ago)
• Topics: biolog, cell-analysis, machine-learning, neural-network, torch
• Language: Jupyter Notebook
• Size: 9.95 MB
• Stars: 46
• Watchers: 11
• Forks: 8
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md

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README

          
Torch Integrated Cell

===============================

![Model Architecture](doc/images/model_arch.png?raw=true "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 .