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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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Subcellular components in two dendrites in the apical dendrite volume visualized at OCP.(a) Web browser visualization of the apical volume using CATMAID with opacity controls for the Image data set at 100%. Each of the layers—Axon (green), Dendrite (yellow), Synapses (red), and Glia (blue)—are adjusted for translucent overlay on the Image. Controls for z-index (section number) and zoom-level (see text) are also available in the top menu bar. (b) Image data at 100% to illustrate d000A and d008, all other layers set to zero. (c) Image data at nearly 0% and all other sliders are set to maximum to illustrate various groups of subcellular components, including smooth endoplasmic reticulum (pink), polyribosomes (purple, PR—arrow), mitochondria and microtubules (turquoise), and endosomal compartments (peach).
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f8: Subcellular components in two dendrites in the apical dendrite volume visualized at OCP.(a) Web browser visualization of the apical volume using CATMAID with opacity controls for the Image data set at 100%. Each of the layers—Axon (green), Dendrite (yellow), Synapses (red), and Glia (blue)—are adjusted for translucent overlay on the Image. Controls for z-index (section number) and zoom-level (see text) are also available in the top menu bar. (b) Image data at 100% to illustrate d000A and d008, all other layers set to zero. (c) Image data at nearly 0% and all other sliders are set to maximum to illustrate various groups of subcellular components, including smooth endoplasmic reticulum (pink), polyribosomes (purple, PR—arrow), mitochondria and microtubules (turquoise), and endosomal compartments (peach).

Mentions: CATMAID enables interactive visualization through opacity, z-distance, zoom, and pan controls (Fig. 8a). Each slider on the left hand side controls the opacity of a layer of the 2D image where the first layer is the EM image and then each group of annotations is layered on top. Sliders control the opacity of annotation layers and allow users to hide or reveal the image or annotation layers completely, or as translucent overlays. By default, the EM Image slider is set to 100% opacity and the annotation layer sliders are set to 25% opacity. The menu bars at the top allow the user to manipulate position within the image stack (z-distance) and to zoom into or out of the current view. Each page through the z-distance corresponds to one section thickness. The z-index slider allows the user to jump to an arbitrary z-index (section) or click through z-indices (sections) sequentially with the up and down arrows to the right of the slider. Navigation through z-indices is also possible with the scroll wheel of a mouse or trackpad of a laptop computer. Users can also manually enter a z-index in the textbox between the slider and the arrows. Zoom level controls are located to the right of the z-index controls and operate identically. For these data sets, the image files and annotations have been scaled to three lower resolutions. Specific image sizes for each resolution are available at (Data Citation 1: http://w.ocp.me/datum:harris15#resolution_hierarchy). Integer zoom levels are native resolutions from the OCP database, and decimal zoom levels are a magnification of the image. In this way, as the user progresses to smaller zoom numbers, the resolution and magnification increase to allow objects to be scrutinized. Users can pan to different XY locations by adjusting the value in the X and Y box at the far left or by clicking the left mouse button and dragging the image.


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)

Subcellular components in two dendrites in the apical dendrite volume visualized at OCP.(a) Web browser visualization of the apical volume using CATMAID with opacity controls for the Image data set at 100%. Each of the layers—Axon (green), Dendrite (yellow), Synapses (red), and Glia (blue)—are adjusted for translucent overlay on the Image. Controls for z-index (section number) and zoom-level (see text) are also available in the top menu bar. (b) Image data at 100% to illustrate d000A and d008, all other layers set to zero. (c) Image data at nearly 0% and all other sliders are set to maximum to illustrate various groups of subcellular components, including smooth endoplasmic reticulum (pink), polyribosomes (purple, PR—arrow), mitochondria and microtubules (turquoise), and endosomal compartments (peach).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f8: Subcellular components in two dendrites in the apical dendrite volume visualized at OCP.(a) Web browser visualization of the apical volume using CATMAID with opacity controls for the Image data set at 100%. Each of the layers—Axon (green), Dendrite (yellow), Synapses (red), and Glia (blue)—are adjusted for translucent overlay on the Image. Controls for z-index (section number) and zoom-level (see text) are also available in the top menu bar. (b) Image data at 100% to illustrate d000A and d008, all other layers set to zero. (c) Image data at nearly 0% and all other sliders are set to maximum to illustrate various groups of subcellular components, including smooth endoplasmic reticulum (pink), polyribosomes (purple, PR—arrow), mitochondria and microtubules (turquoise), and endosomal compartments (peach).
Mentions: CATMAID enables interactive visualization through opacity, z-distance, zoom, and pan controls (Fig. 8a). Each slider on the left hand side controls the opacity of a layer of the 2D image where the first layer is the EM image and then each group of annotations is layered on top. Sliders control the opacity of annotation layers and allow users to hide or reveal the image or annotation layers completely, or as translucent overlays. By default, the EM Image slider is set to 100% opacity and the annotation layer sliders are set to 25% opacity. The menu bars at the top allow the user to manipulate position within the image stack (z-distance) and to zoom into or out of the current view. Each page through the z-distance corresponds to one section thickness. The z-index slider allows the user to jump to an arbitrary z-index (section) or click through z-indices (sections) sequentially with the up and down arrows to the right of the slider. Navigation through z-indices is also possible with the scroll wheel of a mouse or trackpad of a laptop computer. Users can also manually enter a z-index in the textbox between the slider and the arrows. Zoom level controls are located to the right of the z-index controls and operate identically. For these data sets, the image files and annotations have been scaled to three lower resolutions. Specific image sizes for each resolution are available at (Data Citation 1: http://w.ocp.me/datum:harris15#resolution_hierarchy). Integer zoom levels are native resolutions from the OCP database, and decimal zoom levels are a magnification of the image. In this way, as the user progresses to smaller zoom numbers, the resolution and magnification increase to allow objects to be scrutinized. Users can pan to different XY locations by adjusting the value in the X and Y box at the far left or by clicking the left mouse button and dragging the image.

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