Structure Unionize Records

All AAV Projection signal in the Allen Mouse Connectivity Atlas has been registered to the expert-annotated Common Coordinate Framework. This enables signal quantification at all annotated levels of the brain structure ontology. In the AllenSDK and Allen Brain Atlas API we call structure-level signal integration “unionization”.

AAV unionize records are available for download directly through the API or via the MouseConnectivityCache. The following methods return a Pandas DataFrame of records that describe projection signal in all structures in the adult mouse ontology:

allensdk.core.mouse_connectivity_cache.MouseConnectivityCache.get_structure_unionizes()

allensdk.core.mouse_connectivity_cache.MouseConnectivityCache.get_experiment_structure_unionizes()

Take a look at the Structure Signal Unionization section of the Mouse Connectivity Jupyter notebook to see how these methods can be used.

Record Properties

Property	Description
experiment_id	ID of the experiment (a.k.a SectionDataSet)
structure_id	ID of the structure (e.g. 315 for Isocortex)
hemisphere_id	ID of the hemisphere (1 = left, 2 = right, 3 = both)
is_injection	If true, numbers only include voxels from injection site. If false, numbers only include voxels outside of the injection site.
sum_pixels	Number of valid pixels in the structure in this experiment. Valid pixels are those not manually annotated as invalid data.
sum_projection_pixels	Number of pixels identified as projecting in this structure.
sum_pixel_intensity	Sum of intensity values in this structure.
sum_projection_pixel_intensity	Sum of intensity values in projecting pixels in this structure.
projection_density	sum_projection_pixels / sum_pixels
projection_intensity	sum_projection_pixel_intensity / sum_projection_pixels
projection_energy	projection_density * projection_intensity
volume	volume of valid pixels in structure. Valid pixels are those not manually annotated as invalid data.
projection_volume	volume of projection signal in structure in mm3
normalized_projection_volume	projection_volume / total volume of signal in the injection site.
max_voxel_density	density of projection signal in 10um3 grid voxel with largest density.
max_voxel_x	x coordinate in um of grid voxel with largest density.
max_voxel_y	y coordinate in um of grid voxel with largest density.
max_voxel_z	z coordinate in um of grid voxel with largest density.