The basic cell types of the brain

The brain includes different cell types, and subclasses of the different cells. Neurons are the main signaling units, communicating with each other via synapses. The two main subclasses of neurons are inter neurons (local interconnections between neurons) and projection neurons. Among the non-neuronal cells are the endothelial cells lining blood vessels, ependymal cells lining the ventricular walls and glial cells. Glial cells are oligodendrocytes (insulating neuronal axons for faster signal transmission), microglia (the brain macrophage with a hematopoietic origin) and astrocytes which are involved in numerous functions such as blood brain barrier, homeostasis, neuronal growth and neurotransmitter recycling.

The overview and preserved orientation has enabled us to annotate cell classes (ependymal, endothelial, neuron or glia) and subpopulations of cells (microglia, oligodendrocytes and astrocytes) as well as subcellular locations (axons, dendrites, synapsse and glia endfeet) in both human and mouse brain.

Figure 1. The different types of neurological cell classes (ependymal cells, purple and endothelial cells, red), subpopulations (A=astrocytes, blue; M=microglia, brown; N=neuron, green; O=oligodendrocytes, orange), and subcellular locations (axon, dendrite, synapse, and glia endfeet).

Proteins specifically expressed in different cells of the brain

Examples showing protein located in different types of cells in the brain, both mouse and human.

GFAP - astrocyte


GFAP - astrocyte

MBP - oligodendrocyte


MBP - oligodendrocyte

SLC2A1 - endothelia


SLC2A1 - endothelia

RGS10 - microglia


RGS10 - microglia

LIAS - ependymal cells

ependymal cells

SPAG6 - ependymal cells

RBFOX3 - neuronal soma

neuronal soma

ELAVL3 - neuronal soma

ZNF3 - neuronal nucleus

neuronal nucleus

CBFA2T2 - neuronal nucleus

CAMK2B - neuronal dendrite

neuronal dendrite

ARHGEF33 - neuronal dendrite

SLC6A4 - neuronal axon

neuronal axon

SPTBN4 - neuronal axon

SYNJ2BP - neuronal synapse

neuronal synapse

SYP - neuronal synapse

3D imaging of the cells in the brain

By studying the cells in 3D, using light sheet microscopy and immunostaining it is possible to study the cells, their connections and processes in detail. This move briefly shows how the protein GPR151 is detected in neurons of the mouse thalamus with processes into other brain regions. The movie also includes detection of endothelial cells (PECAM1) and astrocytes (GFAP) in the mouse hippocampus. Extended version of the movie with more information about the orphan receptor GPR151 and the blood brain barrier is found here.