{"id":19091961,"url":"https://github.com/allencellmodeling/torch_integrated_cell","last_synced_at":"2025-07-18T13:32:31.165Z","repository":{"id":91697911,"uuid":"89266164","full_name":"AllenCellModeling/torch_integrated_cell","owner":"AllenCellModeling","description":null,"archived":false,"fork":false,"pushed_at":"2018-08-13T21:30:04.000Z","size":10438,"stargazers_count":46,"open_issues_count":0,"forks_count":8,"subscribers_count":11,"default_branch":"paper_release","last_synced_at":"2025-04-30T12:17:10.074Z","etag":null,"topics":["biolog","cell-analysis","machine-learning","neural-network","torch"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/AllenCellModeling.png","metadata":{"files":{"readme":"readme.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2017-04-24T17:04:19.000Z","updated_at":"2025-02-20T19:15:34.000Z","dependencies_parsed_at":null,"dependency_job_id":"fe477fe0-7bcd-4aa3-9da3-7f990a45bf40","html_url":"https://github.com/AllenCellModeling/torch_integrated_cell","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/AllenCellModeling/torch_integrated_cell","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Ftorch_integrated_cell","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Ftorch_integrated_cell/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Ftorch_integrated_cell/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Ftorch_integrated_cell/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenCellModeling","download_url":"https://codeload.github.com/AllenCellModeling/torch_integrated_cell/tar.gz/refs/heads/paper_release","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenCellModeling%2Ftorch_integrated_cell/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265768338,"owners_count":23825103,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biolog","cell-analysis","machine-learning","neural-network","torch"],"created_at":"2024-11-09T03:17:39.974Z","updated_at":"2025-07-18T13:32:31.130Z","avatar_url":"https://github.com/AllenCellModeling.png","language":"Jupyter Notebook","readme":"Torch Integrated Cell\n===============================\n\n![Model Architecture](doc/images/model_arch.png?raw=true \"Model Architecture\")\n\nImage-driven generative cell modelling with adversarial autoencoders: https://arxiv.org/abs/1705.00092\n\n## For the *updated 3D version*, please see:  \n**Building a 3D Integrated Cell**  \nManuscript: https://www.biorxiv.org/content/early/2017/12/21/238378  \nGitHub: https://github.com/AllenCellModeling/pytorch_integrated_cell  \n\n## Installation\nInstalling on linux is recommended.\n\n### prerequisites\nRunning on docker is recommended, though not required.\n\n- install torch on docker / nvidia-docker as in e.g. this guide: https://github.com/gregjohnso/dl-docker\n- download the training images: `aws s3 cp s3://aics.integrated.cell.arxiv.paper.data . --recursive --no-sign-request`\n\n### Steps:\nAfter 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.\nOnce those locations are properly set, you can start the docker image with\n\n`bash run_docker.sh`\n\nOnce you're in the docker container, you can train the model with \n\n`bash train_model_2D.sh`\n\nThis will take a while, probably about 12-18 hours.\n\n## Project website\nExample outputs of this model can be viewed at http://www.allencell.org\n\n## Citation\nIf you find this code useful in your research, please consider citing the following paper:\n\n    @article{johnson2017generative,\n       title={Generative Modeling with Conditional Autoencoders: Building an Integrated Cell},\n       author={Gregory R. Johnson, Rory M. Donovan-Maiye, Mary M. Maleckar},\n       journal={arXiv preprint arXiv:1705.00092},\n       year={2017},\n       url={https://arxiv.org/abs/1705.00092}\n    }\n    \n## Contact\nGregory Johnson\nE-mail: gregj@alleninstitute.org\n\n## License\nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License\nalong with this program.  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