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#

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

MagellanMapper#

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

Braintracer#

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

pAPRica#

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

BrainAtlas#

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

ClearFinder#

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.

vvasp#

vvasp (pronounced wasp) is a python library for 3D viewing of spatially defined neuroscience data (histology, probe trajectories, neuron locations, etc.). It uses the default PyVista plotter and is fully interoperable with PyVista functionality.

cuisto#

cuisto is a Python package for histological quantification of objects in reference atlas regions. cuisto uses data exported from QuPath used with ABBA to pool data and derive, average and display metrics.

BlenderBrain#

BlenderBrain allows the user to visualise atlas data from the BrainGlobe Atlas API in Blender.

DMC-BrainMap#

DMC-BrainMap is a napari-based tool for the analysis of 2D brain sections, including feature segmentation and atlas registration.

CoperniFUS#

CoperniFUS is a flexible GUI for stereotaxic Focused UltraSound (FUS) experiment planning.

Hint

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