Software built by the community#

Tools like the BrainGlobe Atlas API were developed to help establish a community of developers creating interoperable tools. The BrainGlobe core developers have created a number of such tools (cellfinder, brainreg, brainrender etc.). More recently, members of the community have built their own software that leverages the BrainGlobe ecosystem in some way:

Aligning Big Brains & Atlases#

Aligning Big Brains & Atlases (ABBA) is a FIJI plugin for the registration of 2D brain sections to an atlas. Using the Python version allows users to register their data to any BrainGlobe Atlas.


Brainways is a user-friendly tool for mapping single sections to an atlas using deep learning.


MagellanMapper is a graphical tool for 3D reconstruction and automated analysis of whole specimens using BrainGlobe atlases for registration.


Braintracer is an extension of BrainGlobe providing further analysis tools that build upon brainreg and cellfinder.


pAPRica is a package for analysis of large microscopy datasets that incorporates registration using brainreg.


BrainAtlas wraps the BrainGlobe Atlas API into a package for easy use with the Unity video game engine.


ClearFinder is a graphical user interface that allows users without programming experience to use cellfinder and ClearMap for cell counting and reference atlas annotation of the whole volume of adult tissue-cleared mouse brains. Basic statistics and visualization round up the analysis.


if you have developed any software using BrainGlobe tools, please let us know and we can advertise it here.