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.

BraiAn#

BraiAn is a Python library for easy navigation, visualisation, and analysis of whole-brain quantification data

PyNutil#

PyNutil is a Python library for brain-wide quantification and spatial analysis of features in serial section images from mouse and rat brain

NeuroCarto#

NeuroCarto is a neural probe channel map editor for the Neuropixels probe family. It allows user to create a blueprint for arranging electrodes in a desired density and generate a custom channel map.

brainreg3D#

brainreg3D is a pipeline for manual pixelwise registration of brain regions using 3D projections onto an experimentally obtained 2D image.

brain-locations-visualizer#

brain-locations-visualizer uses point locations, in 3D coordinates of the Allen Brain Atlas, to create different visualisations for these locations

neuralib#

neuralib is a utility toolkit for rodent systems neuroscience research. It provides wrappers, parsers, and tools for efficient data handling, analysis, and reproducibility in open-source neuroscience workflows.

ConfUSIus#

ConfUSIus is a Python package for handling, visualization, preprocessing, and statistical analysis of functional ultrasound imaging (fUSI) data.

Hint

If you have developed any software using BrainGlobe tools, please let us know and we can advertise it here. Typically we include tools which:

  • Use a BrainGlobe package in some way

  • Are general purpose, i.e. not just replicating figures from a paper

  • Are installable, i.e. not just a collection of scripts