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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).

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Related in: MedlinePlus

EM and 3D reconstructions from the volume that surrounds an apical dendrite (named d000A).(a) Sample EM illustrating a single section plane through the apical dendrite volume with spiny dendrites (yellow), nonspiny dendrites (orange), excitatory axons (green), excitatory synapses (red), astroglia (light blue), microglia (dark brown), and colored stamp shapes identifying objects that entered the volume on other sections. (b) 3D reconstruction of all objects traced in the apical dendrite volume. Large microglial process (dark brown) and interneuron dendrite (orange) face outward. (c) 3D of the central apical dendrite (yellow, translucent) with all of its excitatory synapses (red) and its one inhibitory shaft synapse (blue). (d) 3Ds of all unmyelinated excitatory axons (green), unmyelinated inhibitory axons (pink), and the edge of a myelinated axon (purple) that entered this volume. (e) 3Ds of all spiny (yellow) and non-spiny (orange) dendritic segments. (f) All excitatory (red) and inhibitory (blue) synapses. (g) All astroglial processes (light blue), a microglial process (dark brown), and a myelinated axon (purple). Scale cube is 1 μm3.
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f4: EM and 3D reconstructions from the volume that surrounds an apical dendrite (named d000A).(a) Sample EM illustrating a single section plane through the apical dendrite volume with spiny dendrites (yellow), nonspiny dendrites (orange), excitatory axons (green), excitatory synapses (red), astroglia (light blue), microglia (dark brown), and colored stamp shapes identifying objects that entered the volume on other sections. (b) 3D reconstruction of all objects traced in the apical dendrite volume. Large microglial process (dark brown) and interneuron dendrite (orange) face outward. (c) 3D of the central apical dendrite (yellow, translucent) with all of its excitatory synapses (red) and its one inhibitory shaft synapse (blue). (d) 3Ds of all unmyelinated excitatory axons (green), unmyelinated inhibitory axons (pink), and the edge of a myelinated axon (purple) that entered this volume. (e) 3Ds of all spiny (yellow) and non-spiny (orange) dendritic segments. (f) All excitatory (red) and inhibitory (blue) synapses. (g) All astroglial processes (light blue), a microglial process (dark brown), and a myelinated axon (purple). Scale cube is 1 μm3.

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 an apical dendrite (named d000A).(a) Sample EM illustrating a single section plane through the apical dendrite volume with spiny dendrites (yellow), nonspiny dendrites (orange), excitatory axons (green), excitatory synapses (red), astroglia (light blue), microglia (dark brown), and colored stamp shapes identifying objects that entered the volume on other sections. (b) 3D reconstruction of all objects traced in the apical dendrite volume. Large microglial process (dark brown) and interneuron dendrite (orange) face outward. (c) 3D of the central apical dendrite (yellow, translucent) with all of its excitatory synapses (red) and its one inhibitory shaft synapse (blue). (d) 3Ds of all unmyelinated excitatory axons (green), unmyelinated inhibitory axons (pink), and the edge of a myelinated axon (purple) that entered this volume. (e) 3Ds of all spiny (yellow) and non-spiny (orange) dendritic segments. (f) All excitatory (red) and inhibitory (blue) synapses. (g) All astroglial processes (light blue), a microglial process (dark brown), and a myelinated axon (purple). Scale cube is 1 μm3.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: EM and 3D reconstructions from the volume that surrounds an apical dendrite (named d000A).(a) Sample EM illustrating a single section plane through the apical dendrite volume with spiny dendrites (yellow), nonspiny dendrites (orange), excitatory axons (green), excitatory synapses (red), astroglia (light blue), microglia (dark brown), and colored stamp shapes identifying objects that entered the volume on other sections. (b) 3D reconstruction of all objects traced in the apical dendrite volume. Large microglial process (dark brown) and interneuron dendrite (orange) face outward. (c) 3D of the central apical dendrite (yellow, translucent) with all of its excitatory synapses (red) and its one inhibitory shaft synapse (blue). (d) 3Ds of all unmyelinated excitatory axons (green), unmyelinated inhibitory axons (pink), and the edge of a myelinated axon (purple) that entered this volume. (e) 3Ds of all spiny (yellow) and non-spiny (orange) dendritic segments. (f) All excitatory (red) and inhibitory (blue) synapses. (g) All astroglial processes (light blue), a microglial process (dark brown), and a myelinated axon (purple). Scale cube is 1 μm3.
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