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Multi-atlas whole-brain microscopy registration

Project description

Python Version PyPI Wheel Development Status Code style: black


Napari plugin to run brainreg, developed by Stephen Lenzi.


pip install brainreg-napari


Documentation for the plugin is to come, but 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.

If you have any other questions, please send an email.


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. process Overview of the registration process

Citing brainreg

If you find brainreg useful, and use it in your research, please let us know and also cite the preprint:

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Obenhaus, H. A., Claudi, F., Lenzi, S. C., Branco, T., Margrie, T. W. (2021) “Tools for accurate post hoc determination of marker location within whole-brain microscopy images’ bioRxiv,

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)!

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Files for brainreg-napari, version 0.0.4rc0
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Filename, size brainreg_napari-0.0.4rc0-py3-none-any.whl (10.3 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size brainreg-napari-0.0.4rc0.tar.gz (14.0 kB) File type Source Python version None Upload date Hashes View

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