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Reference Histological Data
A set of anatomic reference data to provide additional information on the cytoarchitecture, myeloarchitecture and chemoarchitecture of the mouse brain.
Staining Type Stain Target Staining Pattern
Histological staining Nissl Nissl substances Pan-cellular, cell bodies and dendrites
Histological staining AchE Synaptic protein Acetylcholinesterase Axons and cell bodies of cholinergic neurons
Immunohistochemistry Pvalb Ca2+ binding protein Parvalbumin Cell-type marker: a subset of GABAergic interneurons (fast-spiking)
SMI-32 Neurofilament-H (non-phosphorylated) Cell bodies, dendrites and thick axons
Immunohistochemistry Calb1 Ca2+ binding protein Calbindin, 28 kDa Cell-type marker: a subset of GABAergic Interneurons
SMI-99 Myelin basic protein Myelinated axons, oligodendrocytes
Immunohistochemistry NeuN Nuclear protein Fox3 Cell-type marker: Pan-neuronal
NF-160 Neurofilament-M Cell bodies, dendrites and axons
Allen Mouse Brain Common Coordinate Framework (CCF) - Transgene Expression Data

The Allen Mouse Brain Common Coordinate Framework (CCFv3) is an annotated 3D reference space with 10µm voxel resolution. An average template brain was created from images of 1,675 young adult C57BL/6J mouse brains acquired using serial two-photon tomography.

Using multimodal reference data (e.g., histological stains, immunohistochemistry, transgene expression, connectivity patterns, endogenous gene expression) we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures.

Please see the reference atlases portal for more information.

The following transgenic line datasets were used in the annotation of the CCFv3: