Metadata-Version: 2.1
Name: mousebrains
Version: 0.0.2
Summary: Transforms to map between different mouse (template) brains
Home-page: https://github.com/navis/navis-mousebrains
Author: Philipp Schlegel
Author-email: pms70@cam.ac.uk
License: GNU GPL V3
Keywords: mouse brains template registration brain navis transform
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: gitpython
Requires-Dist: navis >=0.6.0
Requires-Dist: numpy
Requires-Dist: pandas
Provides-Extra: extras

# navis-mousebrains
Transforms and meta data to map between different mouse template brains. This package is intended to be used with [navis](https://github.com/schlegelp/navis) and is analogous to [`navis-flybrains`](https://github.com/schlegelp/navis-flybrains).

Currently `mousebrains` ships with:

- meta data and surface meshes the Allen CCF mouse brain template

## Installation
You can install `mousebrains` from PyPI:

```bash
pip3 install mousebrains
```

To install the dev version from Github:
```bash
pip3 install git+https://github.com/navis-org/navis-mousebrains.git
```

### External dependencies
In order to use CMTK-based transforms, you will need to have
[CMTK](https://www.nitrc.org/projects/cmtk/) installed.

For the Elastix-based transforms, you will need to download
[elastix](https://elastix.lumc.nl/index.php) and make sure that the path
to the binaries is in your `PATH` variable.

## Usage

TODO

## Changes

TODO

## Acknowledgements

TODO

## Citing

TODO

When in doubt, feel free to open an [issue](https://github.com/navis-org/navis-mousebrains/issues/new) to ask for advice.
