neuroglancer-scripts

Tools for converting volumetric images and surface meshes to the pre-computed format of Neuroglancer.

Installation

The easiest way to install the latest stable version of neuroglancer-scripts is through pip. Using a virtual environment is recommended:

python3 -m venv venv/
. venv/bin/activate
pip install neuroglancer-scripts

Usage

See the documentation.

Development

The code is hosted on https://github.com/HumanBrainProject/neuroglancer-scripts.

Useful commands for development:

git clone https://github.com/HumanBrainProject/neuroglancer-scripts.git

# Install in a virtual environment
cd neuroglancer-scripts
python3 -m venv venv/
. venv/bin/activate
pip install -e .[dev]

# Tests
pytest  # run tests
pytest --cov=neuroglancer_scripts --cov-report=html  # detailed test coverage report
tox  # run tests under all supported Python versions

# Please install pre-commit if you intend to contribute
pre-commit install  # install the pre-commit hook

Contributing

This repository uses pre-commit to ensure that all committed code follows minimal quality standards. Please install it and configure it to run as a pre-commit hook in your local repository (see above). Also, please note that the code quality checks may need a more recent version of Python than that required by neuroglancer_scripts itself (> 3.8 at the time of this writing).

Acknowledgments

cloud-volume (BSD 3-Clause licensed) for compressed morton code and shard/minishard mask implementation.