brainreg-segment 0.2.20
Manual segmentation of 3D brain structures in a common anatomical space
License: BSD-3-Clause
Requires Python: >=3.9

# This package is deprecated!

Please use [`brainglobe-segmentation` instead](https://github.com/brainglobe/brainglobe-segmentation).

The old README can be found below.

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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/brainglobe/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://brainglobe.info/documentation/brainreg/index.html).

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://brainglobe.info/documentation/brainreg-segment/index.html).

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 [developers guide](https://brainglobe.info/developers/index.html).

### 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)