Installation Guide¶

Quick Installation¶

octopi is available on PyPI and can be installed using pip:

pip install octopi

Development Installation¶

If you want to contribute to octopi or need the latest development version, you can install from source:

git clone https://github.com/chanzuckerberg/octopi.git
cd octopi
pip install -e .

MLflow Setup¶

To use MLflow for experiment tracking, create a .env file in your project root with the following content:

MLFLOW_TRACKING_USERNAME = <Your_CZ_email>
MLFLOW_TRACKING_PASSWORD = <Your_mlflow_access_token>

You can get a CZI MLflow access token from here.

Verification¶

To verify your installation, run:

python -c "import octopi; print(octopi.__version__)"

Next Steps¶

• Import Your Data - Learn how to import your tomograms into a copick project.
• Quick Start Guide - Run your first particle picking experiment.
• Learn the API - Integrate Octopi into your Python workflows.