neuroglancer-scripts
Tools for converting volumetric images and surface meshes to the pre-computed format of Neuroglancer_.
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Installation
The easiest way to install the latest stable version of neuroglancer-scripts is
through pip
. Using a virtual environment is recommended:
.. code-block:: shell
python3 -m venv venv/
. venv/bin/activate
pip install neuroglancer-scripts
Usage
See the documentation <http://neuroglancer-scripts.readthedocs.io/>
_.
Development
The code is hosted on https://github.com/HumanBrainProject/neuroglancer-scripts.
Useful commands for development:
.. code-block:: shell
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).
.. _Neuroglancer: https://github.com/google/neuroglancer
.. _pre-commit: https://pre-commit.com/
Acknowledgments
cloud-volume <https://github.com/seung-lab/cloud-volume>
_ (BSD 3-Clause licensed) for compressed morton code and shard/minishard mask implementation.