Package: brainreg-napari
THIS PACKAGE HAS MOVEDAs of the release ofbrainregversion1.0.0,brainreg-napariis now a part ofbrainreg.
If you are looking to install thebrainglobe-napariplugin, please installbrainregwith it's optionalnaparidependency as detailed in the installation instructions on thewebsiteorrepository.
Before you update, you should also remove the oldbrainreg-naparipackage from your environment using eitherpython-mpipuninstallbrainreg-napari# If you installed via pipcondaremovebrainreg-napari# If you installed via condaYou can find the old documentation and installation instructions below, but please note this version of the package should be considered unmaintained.brainreg-napariNapari plugin to runbrainreg,
developed byStephen Lenzi.Installationpipinstallbrainreg-napariUsageDocumentation and tutorials for the plugin can be foundhere.For segmentation of bulk structures in 3D space
(e.g. injection sites, Neuropixels probes), please seebrainreg-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 touchon the forumor byraising an issue.Detailsbrainreg is an update toamap(itself a port
of theoriginal Java software)
to include multiple registration backends, and to support the many atlases
provided bybg-atlasapi.The aim of brainreg is to register the template brain
(e.g. from theAllen 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 theoriginal aMAP paper.Overview of the registration processContributingContributions to brainreg-napari are more than welcome. Please see thedevelopers guide.Citing brainregIf 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, 867doi.org/10.1038/s41598-021-04676-9Please 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.https://doi.org/10.1038/ncomms11879Lastly, 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,https://doi.org/10.21105/joss.02668Don't forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas)!