{"id":20063750,"url":"https://github.com/geometric-intelligence/herbrain","last_synced_at":"2025-05-05T17:33:18.988Z","repository":{"id":252436296,"uuid":"827974965","full_name":"geometric-intelligence/herbrain","owner":"geometric-intelligence","description":null,"archived":false,"fork":false,"pushed_at":"2025-04-17T04:22:50.000Z","size":46542,"stargazers_count":3,"open_issues_count":1,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-17T18:30:26.249Z","etag":null,"topics":[],"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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/geometric-intelligence.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"2024-07-12T19:41:38.000Z","updated_at":"2025-04-17T04:22:53.000Z","dependencies_parsed_at":"2024-08-09T19:27:47.898Z","dependency_job_id":"7d1e674d-4573-4be4-904a-6960a8efaf1c","html_url":"https://github.com/geometric-intelligence/herbrain","commit_stats":null,"previous_names":["geometric-intelligence/herbrain"],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fherbrain","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fherbrain/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fherbrain/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fherbrain/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/geometric-intelligence","download_url":"https://codeload.github.com/geometric-intelligence/herbrain/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252542502,"owners_count":21764978,"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":[],"created_at":"2024-11-13T13:43:41.374Z","updated_at":"2025-05-05T17:33:13.975Z","avatar_url":"https://github.com/geometric-intelligence.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 🧠 HerBrain\nHerBrain uses AI for quantifying changes in the female brain during menstruation, pregnancy, and menopause.\n\n[![DOI](https://zenodo.org/badge/827974965.svg)](https://zenodo.org/doi/10.5281/zenodo.13356094)\n\n\n## 🎬 HerBrain App Demo ##\n\n[![Demo](/images/HerBrainDemo_thumbnail.png)](https://youtu.be/zUucJbwaaO4)\n\n## 🎤 Our Public Talk on Womens' Brain Health and AI ##\n\n[![BBB Talk](/images/bbb_thumbnail.png)](https://youtu.be/BsdNQUcwb1M)\nVisual on thumbnail slide taken from: Caitlin M Taylor, Laura Pritschet, and Emily G Jacobs. The scientific body of knowledge–whose body does it serve? A spotlight on oral contraceptives and women’s health factors in neuroimaging. Frontiers in neuroendocrinology, 60:100874, 2021.\n\n## 🤖 Installing HerBrain\n\n1. Clone a copy of `herbrain` from source:\n```bash\ngit clone https://github.com/geometric-intelligence/herbrain\ncd herbrain\n```\n2. Create an environment with python \u003e= 3.10\n```bash\nconda create -n herbrain python=3.10\n```\n3. Install `herbrain` in editable mode (requires pip ≥ 21.3 for [PEP 660](https://peps.python.org/pep-0610/) support):\n```bash\npip install -e .[all]\n```\n4. Install pre-commit hooks:\n```bash\npre-commit install\n```\n\n## 🌎 Bibtex ##\nIf this code is useful to your research, please cite:\n\n```\n@misc{myers2023geodesic,\n      title={Geodesic Regression Characterizes 3D Shape Changes in the Female Brain During Menstruation},\n      author={Adele Myers and Caitlin Taylor and Emily Jacobs and Nina Miolane},\n      year={2023},\n      eprint={2309.16662},\n      archivePrefix={arXiv},\n      primaryClass={cs.CV}\n}\n```\n\n## 🏃‍♀️ How to Run the Code ##\n\nOnce you download the data,\n\n1. Choose whether to launch pregnancy or menstrual cycle app. Pregnancy app is in the `project_pregnancy` folder, and menstrual app is in the `project_menstrual` folder.\n2. Run the `main_3_dash_app.py` file by running:\n\n```\npython main_3_dash_app.py\n```\n\n## 👩‍🔧 Authors ##\n[Adele Myers](https://ahma2017.wixsite.com/adelemyers)\n\n[Nina Miolane](https://www.ninamiolane.com/)\n\n## How to Set up Your Environment\n\n```shell\n$ conda create -n herbrain --file conda-linux-64.lock\n$ conda activate herbrain\n$ poetry install --no-root\n```\nWe use `--no-root` because we don't have a module named `herbrain`\nIf you are on Mac, make and use `conda-osx-64.lock` instead.\n\n# Dev\n\nOnly run if changes are made to the environment files.\n\nTo recreate the conda lock, after modifying conda.yaml:\n```shell\npip install conda-lock\nmake conda-linux-64.lock\n```\nNote that you may need to install conda-lock not in your base env.\n\nTo recreate the poetry lock, after modifying pyproject.toml:\n```shell\nmake poetry.lock\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgeometric-intelligence%2Fherbrain","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgeometric-intelligence%2Fherbrain","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgeometric-intelligence%2Fherbrain/lists"}