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.