Metadata-Version: 2.1
Name: brainrender
Version: 2.1.5
Summary: Visualisation and exploration of brain atlases and other anatomical data
Author-email: "Federico Claudi, Adam Tyson, Luigi Petrucco" <hello@brainglobe.info>
License: BSD-3-Clause
Project-URL: Homepage, https://brainglobe.info/
Project-URL: Source Code, https://github.com/brainglobe/brainrender
Project-URL: Bug Tracker, https://github.com/brainglobe/brainrender/issues
Project-URL: Documentation, https://brainglobe.info/documentation/brainrender/index.html
Project-URL: User Support, https://forum.image.sc/tag/brainglobe
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.9.0
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: bg-atlasapi>=1.0.0
Requires-Dist: brainglobe-space>=1.0.0
Requires-Dist: h5py
Requires-Dist: imio
Requires-Dist: k3d
Requires-Dist: loguru
Requires-Dist: morphapi>=0.2.1
Requires-Dist: msgpack
Requires-Dist: myterial
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pooch
Requires-Dist: pyinspect>=0.0.8
Requires-Dist: pyyaml>=5.3
Requires-Dist: requests
Requires-Dist: tables
Requires-Dist: vedo>=2023.5.0
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: coverage; extra == "dev"
Requires-Dist: tox; extra == "dev"
Requires-Dist: black; extra == "dev"
Requires-Dist: mypy; extra == "dev"
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Requires-Dist: ruff; extra == "dev"
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Requires-Dist: imio; extra == "dev"
Provides-Extra: nb
Requires-Dist: jupyter; extra == "nb"
Requires-Dist: k3d; extra == "nb"


# Brainrender
<p align="center">
  <img width="1200" src="https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/three_atlases.png">
</p>

[![Python Version](https://img.shields.io/pypi/pyversions/brainrender.svg)](https://pypi.org/project/brainrender)
[![PyPI](https://img.shields.io/pypi/v/brainrender.svg)](https://pypi.org/project/brainrender)
[![tests](https://github.com/brainglobe/brainrender/workflows/tests/badge.svg)](https://github.com/brainglobe/brainrender/actions)
[![codecov](https://codecov.io/gh/brainglobe/brainrender/graph/badge.svg)](https://codecov.io/gh/brainglobe/brainrender)
[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)


**`brainrender` is a python package for the visualization of three dimensional neuro-anatomical data. It can be used to render data from publicly available data set (e.g. Allen Brain atlas) as well as user generated experimental data. The goal of brainrender is to facilitate the exploration and dissemination of neuro-anatomical data by providing a user-friendly platform to create high-quality 3D renderings.**

## Docs
:books: [brainrender docs](https://brainglobe.info/documentation/brainrender/index.html)

📖 [brainrender paper](https://doi.org/10.7554/eLife.65751)

## Installation
You can [install `brainrender`](https://brainglobe.info/documentation/brainrender/installation.html) with:

```
pip install brainrender
```

## Contributing
Contributions to brainrender are more than welcome. Please see the [developers guide](https://brainglobe.info/community/developers/index.html). Note that some tests are only run locally, by specifying `--runslow --runlocal` in `pytest`.

## Citing brainrender
If you use `brainrender` in your work, please cite:
```
Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R.,  Branco, T. (2021) "Visualizing anatomically registered data with Brainrender&quot; <i>eLife</i> 2021;10:e65751 [doi.org/10.7554/eLife.65751](https://doi.org/10.7554/eLife.65751)
```

## Examples
The following images were created for the publication of the [brainrender paper](https://doi.org/10.7554/eLife.65751). References to the original data being visualised can also be found in the paper.

<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/cellfinder_cells_3.png' width=500 style='margin:auto'></img>
</p>
<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/gene_expression.png' width=500 style='margin:auto'></img>
</p>
<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/human_regions.png' width=500 style='margin:auto'></img>
</p>
<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/injection_2.png' width=500 style='margin:auto'></img>
</p>
<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/mouse_neurons_2.png' width=500 style='margin:auto'></img>
</p>
<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/probes.png' width=500 style='margin:auto'></img>
</p>
<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/zfish_functional_clusters_2.png' width=500 style='margin:auto'></img>
</p>
<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/zfish_neurons.png' width=500 style='margin:auto'></img>
</p>
<p align="center">
<img src='https://raw.githubusercontent.com/brainglobe/brainrender/main/imgs/zfish_regions.png' width=500 style='margin:auto'></img>
</p>
