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  • projection density = sum of detected pixels / sum of all pixels in division
  • projection energy = sum of detected pixel intensity / sum of all pixels in division
  • injection_fraction = fraction of pixels belonging to manually annotated injection site
  • injection_density = density of detected pixels within the manually annotated injection site
  • injection_energy = energy of detected pixels within the manually annotated injection site
  • data_mask = xxxxxx

For each summation type, grid files can be downloaded at 10, 25, 50 and 100 μm isotropic voxel resolution.


3-D grids were updated in the May 2015 release to reflect the remapping to the new Allen Mouse Common Coordinate Framework (CCFv3), higher resolution computation and new compress data format. 3-D grids from the October 2014 release (mapped to CCFv2) can be access through our data download server (see instructions).

Grid data for each SectionDataSet can be downloaded for each SectionDataSet using the 3-D Grid Data Service. The service returns a zip file containing the volumetric data for density, intensity and/or energy in an uncompressed format with a simple text header file in MetaImage format. Structural annotation for each grid voxel can be obtained via the ReferenceSpace gridAnnotation volume file at 100 µm grid resolution.

Voxels with no data are assigned a value of "-1".



compressed NRRD(Nearly Raw Raster Data) format. To download a particular grid file, the user specifies the SectionDataSet ID, the type of grid and the resolution.


  • Download projection_density for a VISp injection SectionDataSet at 50 μm resolution
    Code Block

Example Matlab code snippet to read in the 100 µm density grid volume: