Multi-atlas whole-brain microscopy registration

    Workflow step:
    Image registration
    Image registrationAffine registration

    Python Version PyPI Wheel Development Status Code style: black codecov

    Napari plugin to run brainreg, developed by Stephen Lenzi.


    pip install brainreg-napari


    Documentation for the plugin can be found here, and for more detail, documentation for the original brainreg can be found here and a tutorial is here.

    For segmentation of bulk structures in 3D space (e.g. injection sites, Neuropixels probes), please see brainreg-segment.

    This software is at a very early stage, and was written with our data in mind. Over time we hope to support other data types/formats. If you have any issues, please get in touch on the forum or by raising an issue.


    brainreg is an update to amap (itself a port of the original Java software) to include multiple registration backends, and to support the many atlases provided by bg-atlasapi.

    The aim of brainreg is to register the template brain (e.g. from the Allen Reference Atlas) to the sample image. Once this is complete, any other image in the template space can be aligned with the sample (such as region annotations, for segmentation of the sample image). The template to sample transformation can also be inverted, allowing sample images to be aligned in a common coordinate space.

    To do this, the template and sample images are filtered, and then registered in a three step process (reorientation, affine registration, and freeform registration.) The resulting transform from template to standard space is then applied to the atlas.

    Full details of the process are in the original aMAP paper. reg_process Overview of the registration process


    Contributions to brainreg-napari are more than welcome. Please see the contributing guide.

    Citing brainreg

    If you find brainreg 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

    Please also cite aMAP (the original pipeline from which this software is based):

    Niedworok, C.J., Brown, A.P.Y., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M. and Margrie, T.W., (2016). AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nature Communications. 7, 1–9.

    Lastly, if you can, please cite the BrainGlobe Atlas API that provided the atlas:

    Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668,

    Don't forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas)!

    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.


    • 0.1.1

    Last updated:

    • 06 December 2022

    First released:

    • 13 July 2021


    • MIT

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 6
    • Forks: 5
    • Issues + PRs: 8

    Python versions supported:

    Operating system:


    • napari
    • napari-plugin-engine (>=0.1.4)
    • magicgui
    • qtpy
    • brainglobe-napari-io
    • brainreg
    • brainreg-segment
    • pooch (>1)

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