Metadata-Version: 2.1
Name: brainglobe-segmentation
Version: 1.0.1
Summary: Manual segmentation of 3D brain structures in a common anatomical space
Author-email: "Adam Tyson, Horst Obenhaus" <code@adamltyson.com>
License: BSD-3-Clause
Project-URL: Homepage, https://brainglobe.info/
Project-URL: Source Code, https://github.com/brainglobe/brainglobe-segmentation
Project-URL: Bug Tracker, https://github.com/brainglobe/brainglobe-segmentation/issues
Project-URL: Documentation, https://docs.brainglobe.info/brainglobe-segmentation
Project-URL: User Support, https://forum.image.sc/tag/brainglobe
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: Microsoft :: Windows :: Windows 10
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: bg-atlasapi
Requires-Dist: brainglobe-napari-io >=0.3.0
Requires-Dist: brainglobe-utils >=0.2.7
Requires-Dist: imio
Requires-Dist: napari >=0.4.5
Requires-Dist: numpy
Requires-Dist: pandas[hdf5]
Requires-Dist: qtpy
Requires-Dist: scikit-image
Requires-Dist: scipy
Requires-Dist: tifffile
Provides-Extra: dev
Requires-Dist: black ; extra == 'dev'
Requires-Dist: gitpython ; extra == 'dev'
Requires-Dist: pre-commit ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: coverage ; extra == 'dev'
Requires-Dist: pytest-cov ; extra == 'dev'
Requires-Dist: pytest-qt ; extra == 'dev'
Requires-Dist: napari-time-slicer ; extra == 'dev'

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# brainglobe-segmentation

Segmentation of 1/2/3D brain structures in a common anatomical space

`brainglobe-segmentation` 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)).
`brainglobe-segmentation` is the successor to [`brainreg-segment`](https://github.com/brainglobe/brainreg-segmentation).

`brainglobe-segmentation` 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

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

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

## Usage

See [user guide](https://brainglobe.info/documentation/brainglobe-segmentation/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 brainglobe-segmentation

If you find brainglobe-segmentation 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)
