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Each image in a dataset is divided into a 100 10 x 100 10 µm grid. Pixel-based statistics are computed using information from the primary image and the segmentation mask. In each division, the sum of the number of detected pixels and the sum of detected pixel intensity were collected. A second set of these same summations was computed for the regions manually identified as belonging to the injection site for injection site quantification. The resulting 3-D grid is then transformed into the standard reference space using linear interpolation to generate sub-grid values.

From these summation we obtained measures for:

  • projection density = sum of detected pixels / sum of all pixels in division
  • projection intensity = sum of detected pixel intensity / sum of detected pixels
  • projection energy = projection intensity * projection density



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 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.