Install

This project uses a single uv environment. Clone the repository in your location of choice and enter the directory using

git clone https://github.com/QI2lab/merfish3d-analysis
cd merfish3d-analysis

Create and sync the environment with CUDA 12.9 GPU dependencies:

uv sync

For development tools, include the dev group:

uv sync --group dev

All package entry points can then be run through uv run, for example uv run qi2lab-preprocess /path/to/experiment.

(Optional) Installing Proseg

Please follow the Proseg documentation to install the command line tool used for downstream RNA-based segmentation refinement.

Documentation

To build the documentation, install using uv sync --group docs. Then execute uv run mkdocs build --clean or uv run mkdocs serve. The documentation is available in your web browser at http://127.0.0.1:8000/.

The Documentation GitHub Actions workflow builds and deploys the site after every push to main and can also be started manually. It uses only the docs dependency group on a standard CPU runner, so deployment does not require a CUDA-capable host. In the repository settings, set Pages → Build and deployment → Source to GitHub Actions.