EM_recon_pipeline

Pipeline scripts and tools for reconstructing Electron Microscopy volumes.

Setup

1. If necessary, install miniforge.

Create Environment and Install

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

cd EM_recon_pipeline

conda env create -f janelia_emrp.environment.yml
conda activate janelia_emrp

poetry install

Development Library Management

• Using conda with poetry as described here.
• To change/update dependencies, edit pyproject.toml or use poetry add and then run poetry install.