Electron Micrographs of the Neuropil: Basic Literacy¶

NEU466G, Dr. Harris · Class documents

Overview¶

Neuropil is any area of the nervous system made up mostly of unmyelinated axons, dendrites, and glial cell processes. It is dense with synapses and has relatively few cell bodies. When you look at electron micrographs (EMs) of the neuropil, you should be able to recognize dendrites, axons, and glia. You should also recognize their organelles and other structures inside them, such as the postsynaptic density (PSD), mitochondria, smooth endoplasmic reticulum (SER), spine apparatus, polyribosomes, and microtubules.

This video will help you get to know these structures: Cruise through the Hippocampal Neuropil: Brain Cells Visualized. This tutorial gives more information about synapses: Structure of Chemical Synapses.

This page is adapted from a handout by Patrick Parker, Kristen Harris Lab (2020).

Each Figure box below links a figure from the sources under References; open them while you read. The EM images on this page come from the class series.

Dendrites¶

The main features of a dendrite are:

Spines that stick out from the dendrite and form synapses with axons. (Some dendrites have no spines; their synapses are on the dendritic shaft.)
Organelles such as mitochondria and SER.

Figure: spiny dendrite, with a thin spine (S) and its synapse

Atlas Fig. 1.4.1.02. D is the dendritic shaft. You can spot the synapse by the dark postsynaptic density (PSD) in the spine head and the vesicles next to it in the axon. Scale = 250 nm. (Rat, hippocampus.) Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

Section 83 without traces: a spine head cut across, with a dark PSD along its top edge and a bouton with round vesicles above it — A dendritic spine of the class series (d03sp28_branched) with its PSD (d03c28b) on section 83, without traces (left) and with them (right). The bouton above the PSD holds round vesicles. The view is about 1.5 µm across.

Section 83 with spine d03sp28_branched in yellow and its PSD c-trace d03c28b in red — A dendritic spine of the class series (d03sp28_branched) with its PSD (d03c28b) on section 83, without traces (left) and with them (right). The bouton above the PSD holds round vesicles. The view is about 1.5 µm across.

Figure: mushroom-shaped spine (s) with a spine apparatus (arrow) in its head

Atlas Fig. 1.4.1.03. D is the dendritic shaft. Scale = 300 nm. (Rat, hippocampus.) Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

Figure: 3D reconstruction of a dendrite segment (D) with spines and synapses

Atlas Fig. 1.4.1.17. T marks thin spines with macular synapses; M marks a mushroom-shaped spine with a perforated synapse. (Rat, hippocampus.) Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

3D reconstruction of the class dendrite d03 in translucent yellow, with yellow spines along one part of it and red PSDs on the spine heads — The class dendrite d03 in 3D (opacity 0.4) with spines d03sp01 to d03sp29 and their PSDs (red), seen from the side.

Figure: nonspiny dendrite

Atlas Fig. 1.4.06. D is the dendritic shaft, S marks shaft synapses, and the shaft holds 4 mitochondria. Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

Axons¶

The main features of an axon are:

Many round vesicles in the bouton.
Boutons that form synapses with dendrites.
Mitochondria.

Figure: an axon swollen into an en passant bouton (B) that makes a synapse with a small spine (asterisk)

Atlas Fig. 1.5.02. Arrows mark microtubules cut along their length. Scale = 300 nm. (Rat, hippocampus.) Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

Section 84 without traces: an axonal bouton with round vesicles above a spine head — The bouton across from PSD d03c28b on section 84: the profile full of round vesicles, above the PSD. No axons are traced in the class series, so only the spine (yellow) and the PSD (red) are marked. The view is about 1.2 µm across.

Section 84 with spine d03sp28_branched in yellow and its PSD c-trace d03c28b in red — The bouton across from PSD d03c28b on section 84: the profile full of round vesicles, above the PSD. No axons are traced in the class series, so only the spine (yellow) and the PSD (red) are marked. The view is about 1.2 µm across.

Glia¶

The main features of glia are:

Pale cytoplasm.
Dark, round glycogen granules.
Processes that weave in among everything else: one astrocyte can fill the whole series.

Figure: astrocyte process (A) with many glycogen granules, wrapping the dendritic spines (S)

Atlas Fig. 2.1.12. The main features of the astrocyte are its pale cytoplasm, glycogen granules, and processes that weave among its neighbors. Scale = 400 nm. (Rabbit, cerebellar cortex.) Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

Section 100 without traces: a pale, angular process holding a few dark round glycogen granules, squeezed between a bouton full of vesicles and other profiles — A likely astroglial process in the class series, section 100: the pale profile in the middle with dark round glycogen granules, just above spine d03sp24 (yellow, right). No glia is traced in the series. The view is about 2 µm across.

The same view with spine d03sp24 traced in yellow just below the process — A likely astroglial process in the class series, section 100: the pale profile in the middle with dark round glycogen granules, just above spine d03sp24 (yellow, right). No glia is traced in the series. The view is about 2 µm across.

Figure: 3D reconstruction of an astrocyte

Atlas Fig. 2.1.36. Direct contacts with synaptic clefts are red. Scale = 1 µm. (Rat, hippocampus.) Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

Organelles¶

Mitochondria¶

Mitochondria are large organelles that are easy to spot in dendrites and axons. A mitochondrion often runs along the length of a dendrite, and mitochondria sometimes branch.

Figure: mitochondrion in a cerebellar granule cell, cut along its length

Atlas Fig. 1.1.4.01. Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

Section 93 without traces: a dendrite cut across, with a round mitochondrion with cristae at its upper right — A mitochondrion in the shaft of the class dendrite d03 on section 93, cut across so its cristae show as stripes. Without traces (left) and with d03 (right). The view is about 2 µm across.

The same view with the dendrite d03 outlined and filled in yellow — A mitochondrion in the shaft of the class dendrite d03 on section 93, cut across so its cristae show as stripes. Without traces (left) and with d03 (right). The view is about 2 µm across.

Smooth endoplasmic reticulum (SER)¶

Figure: SER in a dendrite (arrowhead)

Spacek & Harris, 1997, Fig. 1. Open the paper.

Section 15 without traces — SER in spine d03sp05 of the class series on section 15, without traces (left) and with d03sp05 and the SER stamp d03sern05 (right). The view is about 1.3 µm across.

Section 15 with spine d03sp05 in yellow and the SER stamp d03sern05, a yellow cross — SER in spine d03sp05 of the class series on section 15, without traces (left) and with d03sp05 and the SER stamp d03sern05 (right). The view is about 1.3 µm across.

Figure: 3D reconstruction of SER in a dendrite

Atlas Fig. 1.1.2.14. (Rat, hippocampal stratum radiatum.) Spacek, Atlas of Ultrastructural Neurocytology. Open the figure.

Spine apparatus¶

Figure: spine apparatus cut across, with six flat cisternae and five dense plates between them

Fig. 2 of the SynapseWeb Spine Apparatus tutorial. Open the tutorial.

Section 70 without traces — Spine apparatus in the head of spine d03sp19 of the class series on section 70, without traces (left) and with d03sp19 and the SA stamp d03sah19 (right). The view is about 1.6 µm across.

Section 70 with spine d03sp19 in yellow and the SA stamp d03sah19, a red cross — Spine apparatus in the head of spine d03sp19 of the class series on section 70, without traces (left) and with d03sp19 and the SA stamp d03sah19 (right). The view is about 1.6 µm across.

Figure: 3D reconstruction of a spine from hippocampal stratum radiatum

Fig. 6 of the SynapseWeb Spine Apparatus tutorial. A perforated excitatory synapse (red) and a macular inhibitory synapse (blue) sit on the spine head. The spine apparatus (yellow) sits in the head and neck of the spine. Open the tutorial.

References¶

Spacek J. Atlas of Ultrastructural Neurocytology. SynapseWeb. synapseweb.clm.utexas.edu/atlas
SynapseWeb anatomy tutorials. synapseweb.clm.utexas.edu/tutorials
Harris KM, Spacek J (2016). Dendrite structure. In: Stuart G, Spruston N, Häusser M (Eds.), Dendrites, 3rd edition. Oxford University Press. doi:10.1093/acprof:oso/9780198745273.003.0001
Spacek J, Harris KM (1997). Three-dimensional organization of smooth endoplasmic reticulum in hippocampal CA1 dendrites and dendritic spines of the immature and mature rat. Journal of Neuroscience 17:190-203. doi:10.1523/JNEUROSCI.17-01-00190.1997