Atlas Suite

A suite to build, analyze volumetric brain atlases.

• atlas-densities — Create the volumetric density data files for brain regions.
• atlas-direction-vectors — Create direction vectors for several brain regions including the cerebellum, the isocortex, and the thalamus of the AIBS P56 mouse brain.
• atlas-placement-hints — Generation of placement hints for circuit building.
• atlas-splitter Workflows — Split brain atlas regions and refine annotations accordingly.
• atlas-alignment-meter — Pythonic tool (CLI and library) to measure the slice-to-slice jaggedness of a volumetric dataset (NRRD file only).
• Deep Atlas Suite — A suite of tools created by the Blue Brain Project to manipulate brain atlas images.
• BioExplorer - Extract and analyze scientific data for visualization and interactive exploration.

atlas-densities

Useful links: GitHub repo, Documentation.

Create the volumetric density data files for brain regions.

This project contains the tools to create the volumetric density data files the BBP Cell Atlas is built on. For example:

• combine AIBS annotation files to reinstate missing mouse brain regions
• combine several AIBS gene marker datasets, to be used as hints for the spatial distribution of glia cells
• compute cell densities for several cell types including neurons and glia cells in the whole mouse brain

atlas-direction-vectors

Useful links: GitHub repo, Documentation.

Create direction vectors for several brain regions including the cerebellum, the isocortex, and the thalamus of the AIBS P56 mouse brain.

This project is used to create direction vectors for several brain regions including the cerebellum, the isocortex, and the thalamus of the AIBS P56 mouse brain. Direction vectors are 3D unit vectors associated to voxels of a brain region. They represent the directions that cross transversely the layers in laminar brain regions.

atlas-placement-hints

Useful links: GitHub repo, Documentation.

Generation of placement hints for circuit building.

This project contains tools to compute placement hints. Placement hints give approximate distances, per voxel, to different layers within the context of a laminar brain region.

atlas-splitter

Useful links: GitHub repo, Documentation.

Split brain atlas regions and refine annotations accordingly.

This project contains tools to split brain atlas regions and refine annotations accordingly. For example, this can be used to split the layer 2/3 of the AIBS mouse isocortex and save modified hierarchy and annotation files.

atlas-alignment-meter

Useful links: GitHub repo, Documentation.

Pythonic tool (CLI and library) to measure the slice-to-slice jaggedness of a volumetric dataset

Measure the displacement of slices in order to smooth the volumetric dataset.

Deep Atlas Suite

The Deep Atlas is a suite of tools created by the Blue Brain Project to manipulate brain atlas images.

https://github.com/BlueBrain/Deep-Atlas

BioExplorer

The Blue Brain BioExplorer is a tool for scientists to extract and analyze scientific data for visualization and interactive exploration

Exploration relies on building software that combines data integration, analysis and interactive visualization to build, modify and navigate through large scientific datasets. For this, Blue Brain built and open-sourced the Blue Brain BioExplorer. It was originally developed to answer key scientific questions related to the Coronavirus as a use case and to deliver a visualization tool. Today, the BioExplorer allows to reconstruct, visualize, explore and describe in detail the structure and function of highly-detailed biological structures such as molecular systems, neurons, astrocytes, blood vessels, and more. You can see the first application of the BioExplorer in A Machine-Generated View of the Role of Blood Glucose Levels in the Severity of COVID-19 study.

Useful links: GitHub repo, Documentation.