Data Examples

The AIBS provides volumetric data for cell densities and gene markers free to download from their website. The format is often uchar (8bit) grayscale values volume taken from the reconstructed brain at 25 µm resolution.

  • Download general cell body position (from MouseBrain API search for “atlasVolume:”). These are Nissl stained data.

  • Download glia body positions. These are the gene expression stains of Gfap, so we have density/energy/intensity voxel information at lower resolution.

  • Download inhibitory/excitatory body positions (from MouseBrain API search for ‘Packing of 3-D volumetric data into a 1-D numerical array’). These are the gene expression stains of Gad.

  • Download the atlas (from MouseBrain API, search for “annotation:”). An atlas is a dataset where each voxel maps to a brain region. The format is in uint (32bit) of structural annotation volume at 25 µm resolution. The value represents the ID of the finest level structure annotated for the voxel.

Hierarchy

The Hierarchy object represents the relationship bewteen the regions that compose an atlas. Note that the 3-D mask for any structure is composed of all voxels of the atlas annotated for that structure and for any of its descendants in the structure hierarchy.

Voxcell supports loading JSON files as support for hierarchy data:

from voxcell.nexus.voxelbrain import Atlas
hierarchy = Atlas.open('/path/to/atlas').load_region_map()

Example

The AIBS provides a hierarchy free to download from their website.

Download the structured hierarchy. Structures are organized in a hierarchy where each Structure has one parent denoting a “part-of” relationship.