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

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

    brainglobe-segmentation 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). brainglobe-segmentation is the successor to brainreg-segment.

    brainglobe-segmentation 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.


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

    brainglobe-segmentation can be installed on it's own (pip install brainglobe-segmentation), 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 developers guide.

    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., 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


    • 1.0.1

    Last updated:

    • 07 November 2023

    First released:

    • 06 November 2023


    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 24
    • Forks: 9
    • Issues + PRs: 17

    Python versions supported:

    Operating system:


    • bg-atlasapi
    • brainglobe-napari-io >=0.3.0
    • brainglobe-utils >=0.2.7
    • imio
    • napari >=0.4.5
    • numpy
    • pandas[hdf5]
    • qtpy
    • scikit-image
    • scipy
    • tifffile

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