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Data | Description |
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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 | |
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- 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.
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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:
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