Atlas Densities

This project contains the tools to create the BBP Cell Atlas, using datasets from the Allen Institute for Brain Science (AIBS) and collected literature density values. The AIBS datasets files were obtained via experiments performed on P56 wild-type mouse brains. The outcome of this project is a list of volumetric files that provides cell type density estimates for each voxel of the mouse brain volume. The BBP Cell Atlas is the first model required to reconstruct BBP circuits of the mouse brain.

Atlas Direction Vectors

This project contains the commands which 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 of the fiber tracts and their streamlines are assumed to cross transversely layers in laminar brain regions.

Atlas Placement Hints

This project contains tools to compute placement hints. Placement hints are used by the placement algorithm to place 3D cells in the context of circuit building.

Atlas Splitter

This project contains tools to 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).