https://github.com/humanbrainproject/neuroglancer-scripts
Conversion of neuroimaging data for display in Neuroglancer
https://github.com/humanbrainproject/neuroglancer-scripts
neuroimaging
Last synced: 9 months ago
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Conversion of neuroimaging data for display in Neuroglancer
- Host: GitHub
- URL: https://github.com/humanbrainproject/neuroglancer-scripts
- Owner: HumanBrainProject
- License: mit
- Created: 2016-10-06T11:26:17.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-12-05T16:59:27.000Z (over 1 year ago)
- Last Synced: 2025-06-26T12:16:00.733Z (9 months ago)
- Topics: neuroimaging
- Language: Python
- Homepage:
- Size: 473 KB
- Stars: 28
- Watchers: 15
- Forks: 18
- Open Issues: 5
-
Metadata Files:
- Readme: README.rst
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README
neuroglancer-scripts
====================
Tools for converting volumetric images and surface meshes to the pre-computed format of Neuroglancer_.
.. image:: https://img.shields.io/pypi/v/neuroglancer-scripts.svg
:target: https://pypi.python.org/pypi/neuroglancer-scripts
:alt: PyPI Version
.. image:: https://github.com/HumanBrainProject/neuroglancer-scripts/actions/workflows/tox.yaml/badge.svg
:target: https://github.com/HumanBrainProject/neuroglancer-scripts/actions/workflows/tox.yaml
:alt: Build Status
.. image:: https://codecov.io/gh/HumanBrainProject/neuroglancer-scripts/branch/master/graph/badge.svg
:target: https://codecov.io/gh/HumanBrainProject/neuroglancer-scripts
:alt: Coverage Status
.. image:: https://readthedocs.org/projects/neuroglancer-scripts/badge/?version=latest
:target: http://neuroglancer-scripts.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
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 `_.
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 `_ (BSD 3-Clause licensed) for compressed morton code and shard/minishard mask implementation.