EM_recon_pipeline

Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

Setup

1. If necessary, install pixi. This downloads pixi, puts it in ~/.pixi/bin, and adds it to the PATH definition. You then need to restart your shell to get access to the pixi command.

Create Environment and Install

git clone https://github.com/JaneliaSciComp/EM_recon_pipeline.git

cd EM_recon_pipeline

pixi install --environment fibsem     # to install or update the FIBSEM tools environment

# NOTE: During install, you can ignore warnings like:
#
#         WARN Skipped running the post-link scripts because `run-post-link-scripts` = `false`
#         - bin/.librsvg-pre-unlink.sh
#
#         WARN The package `fsspec==2026.1.0` does not have an extra named `s3`

Running Scripts

# Run a script using the pixi environment
pixi run --manifest-path .../EM_recon_pipeline/pyproject.toml --environment fibsem --frozen python src/python/janelia_emrp/fibsem/dat_converter.py --help

# Or activate a shell with the environment
pixi shell --manifest-path .../EM_recon_pipeline/pyproject.toml --environment fibsem --frozen
python src/python/janelia_emrp/fibsem/dat_converter.py --help

Development Library Management

• Environment is managed using pixi with dependencies defined in pyproject.toml.
• To add/update dependencies, edit the [project] or [tool.pixi.dependencies] sections in pyproject.toml and run pixi install, or use pixi add [--pypi] <package>.