🧠 HerBrain

HerBrain uses AI for quantifying changes in the female brain during menstruation, pregnancy, and menopause.

🎬 HerBrain App Demo

🎤 Our Public Talk on Womens' Brain Health and AI

Visual 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.

🤖 Installing HerBrain

1. Clone a copy of herbrain from source:

git clone https://github.com/geometric-intelligence/herbrain
cd herbrain

2. Create an environment with python >= 3.10

conda create -n herbrain python=3.10

3. Install herbrain in editable mode (requires pip ≥ 21.3 for PEP 660 support):

pip install -e .[all]

4. Install pre-commit hooks:

pre-commit install

🌎 Bibtex

If this code is useful to your research, please cite:

@misc{myers2023geodesic,
      title={Geodesic Regression Characterizes 3D Shape Changes in the Female Brain During Menstruation},
      author={Adele Myers and Caitlin Taylor and Emily Jacobs and Nina Miolane},
      year={2023},
      eprint={2309.16662},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}

🏃‍♀️ How to Run the Code

Once you download the data,

1. 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.
2. Run the main_3_dash_app.py file by running:

python main_3_dash_app.py

👩‍🔧 Authors

Adele Myers

Nina Miolane

How to Set up Your Environment

$ conda create -n herbrain --file conda-linux-64.lock
$ conda activate herbrain
$ poetry install --no-root

We use --no-root because we don't have a module named herbrain If you are on Mac, make and use conda-osx-64.lock instead.

Dev

Only run if changes are made to the environment files.

To recreate the conda lock, after modifying conda.yaml:

pip install conda-lock
make conda-linux-64.lock

Note that you may need to install conda-lock not in your base env.

To recreate the poetry lock, after modifying pyproject.toml:

make poetry.lock