Manual segmentation of 3D brain structures in a common anatomical space

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Image segmentationManual segmentation
Image annotationDense image annotationManual segmentation
Image segmentation

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

brainreg-segment is a companion to 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).

brainreg-segment and brainreg were developed by Adam Tyson and Charly Rousseau in the Margrie Lab, based on aMAP by Christian Niedworok. The work was generously supported by the Sainsbury Wellcome Centre.


brainreg-segment comes bundled with brainreg, so see the brainreg installation instructions.

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


See user guide.

If you have any questions, head over to the forum.


Contributions are very welcome. Please see the contributing guide.

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., Vélez-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

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.


  • 0.2.16

Last updated:

  • 15 June 2022

First released:

  • 26 August 2020


  • BSD-3-Clause

Supported data:

Plugin type:

GitHub activity:

  • Stars: 20
  • Forks: 7
  • Issues + PRs: 12

Python versions supported:

Operating system:


  • numpy
  • tables
  • scikit-image
  • pandas
  • napari (>=0.4.5)
  • napari-plugin-engine (>=0.1.4)
  • imlib (>=0.0.26)
  • dask (>=2.15.0)
  • imio
  • brainglobe-napari-io

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