Reconstruction


Reconstruction Data Files

Image, 512x512 image, Serial electron micrograph series through layers 1-4 of the primary visual cortex of the adult mouse. Reconstruction encompasses 450 X 350 X 52 um volume of tissue and contains ~ 1500 cell bodies. This same area of tissue was functionally characterized for orientation and direction selectivity using two photon calcium imaging.

The reconstruction is also available at: http://openconnectomeproject.org/Bock11/
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Animation video, Animation through the central core of serial electron micrograph series at full resolution (4 nm sampling) through layers 1-4 of the primary visual cortex of the adult mouse. Black images represent 'bookkeeping' sections inserted to maintain numbering alignment with the 1/8th resolution stack. The cropped full resolution volume used to create this animation is available for download through the "downsampled downloadable data file" link.
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Reconstruction Data Files, Downsampled version (1/8 resolution) of a 10 Tb serial section reconstruction of mouse primary visual cortex available as a series of TIFF files. Each file is an assembled mosaic of a single thin section. A 2K X 2K full resolution core is also available for download under the "downsampled downloadable file" link. Note: The full 10 TB data set is available but may not be downloaded via the CCDB. If you are interested in accessing these data, please contact webmaster@ccdb.ucsd.edu Voxel dimensions given above for reconstruction represent values for the downsampled reconstruction. The original voxel dimensions are available under Image 2D or Microscopy Product tables. Authors note that the range of section thicknesses varied from 40 nm to 50 nm. An average value of 45 nm (0.045 um) was chosen here.
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Licensing

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Description

Serial electron micrograph series through layers 1-4 of the primary visual cortex of the adult mouse. Reconstruction encompasses 450 X 350 X 52 um volume of tissue and contains ~ 1500 cell bodies. This same area of tissue was functionally characterized for orientation and direction selectivity using two photon calcium imaging. The reconstruction is also available at: http://openconnectomeproject.org/Bock11/ For more information see: Bock DD, Lee WC, Kerlin AM, Andermann ML, Hood G, Wetzel AW, Yurgenson S, Soucy ER, Kim HS, Reid RC. Network anatomy and in vivo physiology of visual cortical neurons. Nature. 2011 Mar 10;471(7337):177-82. PMID: 21390124. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.

Technical Details

The animal was perfused transcardially (2% paraformaldehyde/2.5% glutaraldehyde). Seven 300 um thick coronal vibratome sections were cut. The vibratome sections were post-fixed and stained with 1% osmium tetroxide/1.5% potassium ferrocyanide followed by 1% uranyl acetate, dehydrated with a graded ethanol series, and embedded in resin (TAAB 812 Epon, Canemco). Serial thin (<50 nm) sections were cut on a Leica U6 ultramicrotome, picked up on pioloform-coated slot grids, and then post-stained with uranyl acetate and lead citrate. Serial sections were imaged with a JEOL 1200EX, magnification, 2000.0 X, accelerating voltage, 120.0 kv, and compiled into a composite image.

Biological Sources

NCBI Organism Classification
Mus musculus
(house mouse)
Cell Type
pyramidal cell
stellate cell
astrocyte of the cerebral cortex
Cellular Component
cell body
neuronal cell body

Attribution

Name
R. Clay Reid
Link
CCDB 8448

Imaging

Image Type
recorded image
Imaging Mode
transmission electron microscopy (TEM)
Parameters Imaged
electron density
Visualization Methods
uranyl salt
Data Qualifiers
processed data

Sample Preparation

Methods
osmium tetroxide fixed tissue
glutaraldehyde fixed tissue
Relation To Intact Cell
microtome-sectioned tissue

Dimensions

Spatial Axis Image Size Pixel Size
X 512px ——

Detailed Project Information                           hide

Project ID: P2097
Leader: R. Clay Reid
Collaborators: Davi Bock, Wei-Chung Allen Lee, Aaron M. Kerlin, Mark L. Andermann, Greg Hood, Arthur W. Wetzel, Sergey Yurgenson, Edward R. Soucy, Hyon Suk Kim
Description: Large scale serial section electron microscopic reconstruction was used to reconstruct a portion of visual cortex in mouse that had been functionally characterized for preferred stimulus orientation using two photon calcium imaging. Reconstructions showed that that inhibitory interneurons receive convergent anatomical input from nearby excitatory neurons with a broad range of preferred orientations
Experimental purpose: To obtain structural characterization of neurons characterized by in vivo two photon calcium imaging.
Species: mouse
System: central nervous system
Organ: brain
Region: cerebral cortex
Structure: neuropil
Product type: confocal
Instrument: Biorad Radiance 2000 Confocal
Publications: Bock DD, Lee WC, Kerlin AM, Andermann ML, Hood G, Wetzel AW, Yurgenson S, Soucy ER, Kim HS, Reid RC. Network anatomy and in vivo physiology of visual cortical neurons. Nature. 2011 Mar 10;471(7337):177-82. PMID:21390124

Specimen Preparation                                     hide

Microscopy Product ID: 8448
Image Basename: PSC_final
Protocol Description: The animal was perfused transcardially (2% paraformaldehyde/2.5% glutaraldehyde). Seven 300 um thick coronal vibratome sections were cut. The vibratome sections were post-fixed and stained with 1% osmium tetroxide/1.5% potassium ferrocyanide followed by 1% uranyl acetate, dehydrated with a graded ethanol series, and embedded in resin (TAAB 812 Epon, Canemco). Serial thin (<50 nm) sections were cut on a Leica U6 ultramicrotome, picked up on pioloform-coated slot grids, and then post-stained with uranyl acetate and lead citrate.






Detailed Imaging Parameters                          hide

Electron microscopy product
Magnification: 2000.0
Recording medium: CCD
Accelerating voltage: 120.0 kv

Imaging Product Types                                    hide

Mosaic


Serial Section


*CIL – Cell Image Library accession number. Please use this to reference an image.