Metadata-Version: 2.1
Name: brainreg-segment
Version: 0.2.16rc0
Summary: Manual segmentation of 3D brain structures in a common anatomical space
Home-page: https://brainglobe.info/
Author: Adam Tyson, Horst Obenhaus
Author-email: code@adamltyson.com
License: BSD-3-Clause
Project-URL: Source Code, https://github.com/brainglobe/brainreg-segment
Project-URL: Bug Tracker, https://github.com/brainglobe/brainreg-segment/issues
Project-URL: Documentation, https://docs.brainglobe.info/brainreg-segment
Project-URL: User Support, https://forum.image.sc/tag/brainglobe
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows :: Windows 10
Classifier: Framework :: napari
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: dev
License-File: LICENSE

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# brainreg-segment
Segmentation of 1/2/3D brain structures in a common anatomical space

`brainreg-segment` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing manual segmentation of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, and visualisation (e.g. in [brainrender](https://github.com/BrancoLab/brainrender)).

`brainreg-segment` and `brainreg` were developed by [Adam Tyson](https://github.com/adamltyson) and [Charly Rousseau](https://github.com/crousseau) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on [aMAP](https://doi.org/10.1038/ncomms11879) by [Christian Niedworok](https://github.com/cniedwor). The work was generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).

## Installation

brainreg-segment comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://docs.brainglobe.info/brainreg/installation).

brainreg-segment can be installed on it's own (`pip install brainreg-segment`), but you will need to register your data with brainreg first.

## Usage

See [user guide](https://docs.brainglobe.info/brainreg-segment/user-guide).

If you have any questions, head over to the [image.sc forum](https://forum.image.sc/tag/brainglobe).

## Contributing
Contributions are very welcome. Please see the [contributing guide](https://github.com/brainglobe/.github/blob/main/CONTRIBUTING.md).

### Citing brainreg-segment

If you find brainreg-segment useful, and use it in your research, please let us know and also cite the paper:

> Tyson, A. L., V&eacute;lez-Fort, M.,  Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T.,  Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867 [doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9)

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The BrainGlobe project is generously supported by the Sainsbury Wellcome Centre and the Institute of Neuroscience, Technical University of Munich, with funding from Wellcome, the Gatsby Charitable Foundation and the Munich Cluster for Systems Neurology - Synergy.

<img src='https://brainglobe.info/images/logos_combined.png' width="550">


