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:
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. |