Limits...
A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development.

Harris KM, Spacek J, Bell ME, Parker PH, Lindsey LF, Baden AD, Vogelstein JT, Burns R - Sci Data (2015)

Bottom Line: All axons, dendrites, glia, and synapses were reconstructed in a cube (~10 μm(3)) surrounding a large dendritic spine, a cylinder (~43 μm(3)) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm(3)) surrounding an apical dendritic segment (4.9 μm long).Representative synapses are quantified from varying section planes, and microtubules, polyribosomes, smooth endoplasmic reticulum, and endosomes are identified and reconstructed in a subset of dendrites.The original images, traces, and Reconstruct software and files are freely available and visualized at the Open Connectome Project (Data Citation 1).

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA.

ABSTRACT
Resurgent interest in synaptic circuitry and plasticity has emphasized the importance of 3D reconstruction from serial section electron microscopy (3DEM). Three volumes of hippocampal CA1 neuropil from adult rat were imaged at X-Y resolution of ~2 nm on serial sections of ~50-60 nm thickness. These are the first densely reconstructed hippocampal volumes. All axons, dendrites, glia, and synapses were reconstructed in a cube (~10 μm(3)) surrounding a large dendritic spine, a cylinder (~43 μm(3)) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm(3)) surrounding an apical dendritic segment (4.9 μm long). The data provide standards for identifying ultrastructural objects in 3DEM, realistic reconstructions for modeling biophysical properties of synaptic transmission, and a test bed for enhancing reconstruction tools. Representative synapses are quantified from varying section planes, and microtubules, polyribosomes, smooth endoplasmic reticulum, and endosomes are identified and reconstructed in a subset of dendrites. The original images, traces, and Reconstruct software and files are freely available and visualized at the Open Connectome Project (Data Citation 1).

Show MeSH

Related in: MedlinePlus

EM and 3D reconstructions from the volume that surrounds a large dendritic spine with the synapse (named d01c01Ax54e).(a) Sample EM illustrating a single section plane with spiny dendrites (yellow), excitatory axons (green), synapses (red), astroglial processes (light blue), and a myelinated axon (red center axon surrounded by purple sheath). (b) 3D reconstructions of all objects traced in the spine volume. (c) 3D of a dendritic spine protruding from the portion of the dendritic shaft (yellow) contained in this volume. The synapse on the head of this large spine has an irregularly shaped, perforated PSD (red). (d) 3Ds of all unmyelinated excitatory axons (green), an unmyelinated inhibitory axon (pink), and a myelinated axon (dark red) that entered this volume. (e) 3Ds of all dendritic segments (yellow) and (f) all excitatory synapses in the volume. (g) 3Ds of an astroglial process (light blue) and myelin (purple). The square outlined in (a) and the gray cubes in (b–g) are 2 μm per side, though the orientation foreshortens some of these edges in the 2D plane of this figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4555877&req=5

f2: EM and 3D reconstructions from the volume that surrounds a large dendritic spine with the synapse (named d01c01Ax54e).(a) Sample EM illustrating a single section plane with spiny dendrites (yellow), excitatory axons (green), synapses (red), astroglial processes (light blue), and a myelinated axon (red center axon surrounded by purple sheath). (b) 3D reconstructions of all objects traced in the spine volume. (c) 3D of a dendritic spine protruding from the portion of the dendritic shaft (yellow) contained in this volume. The synapse on the head of this large spine has an irregularly shaped, perforated PSD (red). (d) 3Ds of all unmyelinated excitatory axons (green), an unmyelinated inhibitory axon (pink), and a myelinated axon (dark red) that entered this volume. (e) 3Ds of all dendritic segments (yellow) and (f) all excitatory synapses in the volume. (g) 3Ds of an astroglial process (light blue) and myelin (purple). The square outlined in (a) and the gray cubes in (b–g) are 2 μm per side, though the orientation foreshortens some of these edges in the 2D plane of this figure.

Mentions: Three densely reconstructed regions (Fig. 1b) surrounded a dendritic spine (Fig. 2), an oblique dendrite (Fig. 3), and an apical dendrite (Fig. 4). For illustrative purposes, the traces were superimposed on a central EM image from each of the respective series (Figs 2,3,4a), followed by all of the reconstructed objects (Figs 2,3,4b) and the central spine or dendrite shown with its excitatory and inhibitory synapses (Figs 2,3,4c). The excitatory axons, inhibitory axons, and portions of a myelinated axon were reconstructed in 3DEM (Figs 2,3,4d). All of the other spiny dendrites were illustrated in 3DEM together (Figs 2,3,4e). There were only two nonspiny dendrites, which were presumably from interneurons, and both entered the volume surrounding the apical dendrite (Fig. 4e). Reconstruction of all of the excitatory and inhibitory synapses illustrated their distribution throughout the volumes (Figs 2,3,4f). Finally, the astroglia, myelin, and microglial processes were shown in 3DEM (Figs 2,3,4g). The overlap between astrocytic domains in the hippocampus occurs only at the borders of their processes, thus it is unlikely that the reconstructed astroglial processes in each volume arose from more than one astrocyte64,65. The number and identities of objects in each densely reconstructed volume are summarized in Table 2 (available online only) and in the figures described below.


A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development.

Harris KM, Spacek J, Bell ME, Parker PH, Lindsey LF, Baden AD, Vogelstein JT, Burns R - Sci Data (2015)

EM and 3D reconstructions from the volume that surrounds a large dendritic spine with the synapse (named d01c01Ax54e).(a) Sample EM illustrating a single section plane with spiny dendrites (yellow), excitatory axons (green), synapses (red), astroglial processes (light blue), and a myelinated axon (red center axon surrounded by purple sheath). (b) 3D reconstructions of all objects traced in the spine volume. (c) 3D of a dendritic spine protruding from the portion of the dendritic shaft (yellow) contained in this volume. The synapse on the head of this large spine has an irregularly shaped, perforated PSD (red). (d) 3Ds of all unmyelinated excitatory axons (green), an unmyelinated inhibitory axon (pink), and a myelinated axon (dark red) that entered this volume. (e) 3Ds of all dendritic segments (yellow) and (f) all excitatory synapses in the volume. (g) 3Ds of an astroglial process (light blue) and myelin (purple). The square outlined in (a) and the gray cubes in (b–g) are 2 μm per side, though the orientation foreshortens some of these edges in the 2D plane of this figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4555877&req=5

f2: EM and 3D reconstructions from the volume that surrounds a large dendritic spine with the synapse (named d01c01Ax54e).(a) Sample EM illustrating a single section plane with spiny dendrites (yellow), excitatory axons (green), synapses (red), astroglial processes (light blue), and a myelinated axon (red center axon surrounded by purple sheath). (b) 3D reconstructions of all objects traced in the spine volume. (c) 3D of a dendritic spine protruding from the portion of the dendritic shaft (yellow) contained in this volume. The synapse on the head of this large spine has an irregularly shaped, perforated PSD (red). (d) 3Ds of all unmyelinated excitatory axons (green), an unmyelinated inhibitory axon (pink), and a myelinated axon (dark red) that entered this volume. (e) 3Ds of all dendritic segments (yellow) and (f) all excitatory synapses in the volume. (g) 3Ds of an astroglial process (light blue) and myelin (purple). The square outlined in (a) and the gray cubes in (b–g) are 2 μm per side, though the orientation foreshortens some of these edges in the 2D plane of this figure.
Mentions: Three densely reconstructed regions (Fig. 1b) surrounded a dendritic spine (Fig. 2), an oblique dendrite (Fig. 3), and an apical dendrite (Fig. 4). For illustrative purposes, the traces were superimposed on a central EM image from each of the respective series (Figs 2,3,4a), followed by all of the reconstructed objects (Figs 2,3,4b) and the central spine or dendrite shown with its excitatory and inhibitory synapses (Figs 2,3,4c). The excitatory axons, inhibitory axons, and portions of a myelinated axon were reconstructed in 3DEM (Figs 2,3,4d). All of the other spiny dendrites were illustrated in 3DEM together (Figs 2,3,4e). There were only two nonspiny dendrites, which were presumably from interneurons, and both entered the volume surrounding the apical dendrite (Fig. 4e). Reconstruction of all of the excitatory and inhibitory synapses illustrated their distribution throughout the volumes (Figs 2,3,4f). Finally, the astroglia, myelin, and microglial processes were shown in 3DEM (Figs 2,3,4g). The overlap between astrocytic domains in the hippocampus occurs only at the borders of their processes, thus it is unlikely that the reconstructed astroglial processes in each volume arose from more than one astrocyte64,65. The number and identities of objects in each densely reconstructed volume are summarized in Table 2 (available online only) and in the figures described below.

Bottom Line: All axons, dendrites, glia, and synapses were reconstructed in a cube (~10 μm(3)) surrounding a large dendritic spine, a cylinder (~43 μm(3)) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm(3)) surrounding an apical dendritic segment (4.9 μm long).Representative synapses are quantified from varying section planes, and microtubules, polyribosomes, smooth endoplasmic reticulum, and endosomes are identified and reconstructed in a subset of dendrites.The original images, traces, and Reconstruct software and files are freely available and visualized at the Open Connectome Project (Data Citation 1).

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, Center for Learning and Memory, Institute for Neuroscience, University of Texas at Austin, 1 University Station C7000 , Austin, Texas 78712, USA.

ABSTRACT
Resurgent interest in synaptic circuitry and plasticity has emphasized the importance of 3D reconstruction from serial section electron microscopy (3DEM). Three volumes of hippocampal CA1 neuropil from adult rat were imaged at X-Y resolution of ~2 nm on serial sections of ~50-60 nm thickness. These are the first densely reconstructed hippocampal volumes. All axons, dendrites, glia, and synapses were reconstructed in a cube (~10 μm(3)) surrounding a large dendritic spine, a cylinder (~43 μm(3)) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm(3)) surrounding an apical dendritic segment (4.9 μm long). The data provide standards for identifying ultrastructural objects in 3DEM, realistic reconstructions for modeling biophysical properties of synaptic transmission, and a test bed for enhancing reconstruction tools. Representative synapses are quantified from varying section planes, and microtubules, polyribosomes, smooth endoplasmic reticulum, and endosomes are identified and reconstructed in a subset of dendrites. The original images, traces, and Reconstruct software and files are freely available and visualized at the Open Connectome Project (Data Citation 1).

Show MeSH
Related in: MedlinePlus