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.

• Website

• GitHub repository

• ABBA Python

Brainways

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

• Preprint

• GitHub repository

• Napari plugin

MagellanMapper

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

• GitHub repository

• Documentation

Braintracer

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

• GitHub repository

pAPRica

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

• Preprint

• GitHub repository

• Documentation

BrainAtlas

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

• GitHub repository

• Documentation

Hint

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