neuron_morphology_tools

Algorithms and analysis tools for networkx graph objects representing individual neurons output through the mesh processing pipeline outline in the following study: https://www.biorxiv.org/content/10.1101/2023.03.14.532674v1

🚀 Getting Started with Docker

You have two options for setting up the Docker environment:

1. Pull the Prebuilt Image

docker pull celiib/neuron_morphology:latest

2. Build the Image Locally

Navigate to the /docker folder and build the image using docker-compose:

cd docker
docker-compose build

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▶️ Running the Environment

1. Create a ./notebooks directory in the repository root (this will be mounted into the container for your work):

   cd docker
   mkdir notebooks

2. Start the container from the /docker folder:

   docker-compose up

   This will launch JupyterLab at http://localhost:8890.

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⚙️ Installing the Repository Inside the Container

Once inside JupyterLab:

1. Open a terminal in the JupyterLab interface.
2. Run the following command to install the repository in editable mode:

   pip3 install -e ./neuron_morphology_tools

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📓 Running Example Notebooks

After installation, you can open and run any of the example notebooks in the Applications folder to explore the functionality of the tools.

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🧰 Requirements

• Docker
• Docker Compose

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📝 Notes

• The ./notebooks directory is bind-mounted so your work will persist outside the container.
• The container exposes JupyterLab on port 8890.

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