Metadata-Version: 2.4
Name: mousebrains
Version: 0.0.4
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
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: provides-extra
Dynamic: requires-dist
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Dynamic: summary

# 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 mesh for the Allen CCF mouse brain template
- transforms between the CA3 EM and uCT volume by Z. Zheng (Princeton) and the Allen CCF

## 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

```python
import navis
import mousebrains

# Transform some points from the Zheng CA3 dataset to Allen CCF space
points = np.array([[47056, 51152, 2128]])

points_xf = navis.xform_brain(
    points,
    source="Zheng_CA3_EMraw",  # EM voxel space (18x18x45nm)
    target="AllenCCF"  # Allen CCF space (microns)
)
```

## Changes

- 0.0.4:
 - flipped Zheng CA3 uCT -> CCF transforms onto right hemisphere
 - added templates for Zheng CA3 EM and uCT datasets
- 0.0.3: added transforms for the Zheng CA3 dataset

## Acknowledgements

TODO

## Citing

TODO

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