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?(? bit) anatomical template of CCFv3 - a shape and intensity average of 1675 specimen brains


?(? bit) reconstructed Allen Reference Atlas Nissl deformably registered to the anatomical template of CCFv3


UINT (32bit) structure gray matter and fiber tract annotation of CCFv3





  • atlasVolume: uchar (8bit) grayscale Nissl volume of the reconstructed brain at 25 µm resolution.
  • annotation: uint (32bit) structural annotation volume without fiber tracts at 25 µm resolution. The value represents the ID of the finest level structure annotated for the voxel. Note: the 3-D mask for any structure is composed of all voxels annotated for that structure and all of its descendents in the structure hierarchy.
  • annotationFiber: uint (32bit) fiber tracts annotation volume at 25 µm resolution.
  • averageTemplate: ushort (16bit) average brain template used as registration target at 25 µm resolution.
  • gridAnnotation - 100 µm: uint (32bit) combined structural and fiber tract annotation volume at grid (100 µm) resolution for projection analysis.


UINT (32bit) structure annotation extracted from the coronal Allen Reference Atlas and deformably registered to CCFv3


UINT (32bit) structure annotation extracted from the P56 Allen Developing Mouse Brain Reference Atlas and deformably registered to CCFv3

All volumetric data is compressed NRRD (Nearly Raw Raster Data) format. The raw numerical data is stored as a 1-D array raster as shown in the figure below.

Figure: Packing of 3-D volumetric data into a 1-D numerical array raster.

Example Matlab code snippet to read in the 25µm atlas and annotation volumes: