Connectivity Grid Data

Image data from each Allen Mouse Connectivity Atlas experiment is registered to the Common Coordinate Framework (CCF). This produces a series of CCF-space 3D “grid” volumes which describe the location and extent of that experiment’s injection site (containing infected cell bodies) as well as the distribution of AAV Projection signal throughout the brain.

You can access these grid volumes either via the API or by constructing a allensdk.core.mouse_connectivity_cache.MouseConnectivityCache.

We produce grid volumes from registered images using the grid module. These volumes are then used downstream by the unionize module, which summarizes AAV signal within each annotated brain structure, producing structure unionizes.

Reference

Volume	Description
projection_density	sum of detected projection pixels / sum of all pixels in voxel
injection_fraction	fraction of pixels belonging to manually annotated injection site
injection_density	density of detected projection pixels within the manually annotated injection site
data_mask	binary mask indicating if a voxel contains valid data. Only valid voxels should be used for analysis.

Note that projection density reports detected AAV signal both within and outside the injection site.