Alternate header for print version


Reconstruction
Display image 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/
Full resolution image description
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.
Downsampled image description
Cropped version (2048 X 2048) of 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. Some of the 2k x 2k images are pure black. This is not a mistake; they are 'bookkeeping' sections, to maintain numbering alignment with the 1/8th resolution stack. If you look at the equivalent 1/8th section you will see that these are sections that have information outside the field of view of the 2k x 2k image. (These are 'coming in' sections. They occur after pickup of a series of sections, when the ultramicrotome is restarted and only grazes a portion of the sample block face for a few sections.) Note that the voxel dimensions of the cropped version are 0.004 um X 0.004 um X 0.045 um.
File format
TIFF
Volume_dimension
16900, 14950, 1153
Volume scale
0.032, 0.032, 0.045
Animation description
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.

License
Attribution Only: This image is licensed under a Creative Commons Attribution License. View License Deed | View Legal Code

CCDB:8448*
Project: P2097
Project name
Large scale serial electron microscopic reconstruction of functionally characterized networks in mouse visual cortex
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
Funding agency
National Eye Institute
Leader(s)
R. Clay Reid
Collaborator(s)
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
Start date
unspecified
End date
unspecified
 
Experiment
Experiment ID
8442
Title
Serial section reconstruction of functionally characterized neurons
Purpose
To obtain structural characterization of neurons characterized by in vivo two photon calcium imaging.
Experimenter(s)
Davi Bock
Wei-Chung Allen Lee
Microscopy product
Microscopy product ID
8448
Instrument
JEOL 1200EX
Microscopy type
TEM
Product type
SERIAL SECTION
Image basename
PSC_final
Spatial Axis Image Size Pixel Size
X 11250px 0.04 um/pixels
Y 8750px 0.04 um/pixels
Y 1215px
Subject
Species
mouse
Scientific name
mus musculus
Strain
Thy1-YFP-H
Group by
Transgene
Treatment
Mouse expressing YFP under the control of neuron-specific elements from the thy1 gene (see Feng et al., Neuron. 2000 Oct;28(1):41-51, for details)
Age class
adult
Tissue section
Anatomical location
primary visual cortex
Microtome
Leica U6 ultramicrotome
Thickness
0.045 µm
Specimen description
Organ
brain
System
central nervous system
Structure
neuropil
Imaging parameters
Type
Electron microscopy product
Recording medium
CCD
Magification
2000
Accelerating voltage
120 kv
Specimen preparation
Protocol used
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.
Imaging product type
Type
Mosaic
Description
Each individual section in the reconstruction represents a mosaic
Imaging product type
Type
Serial section
Notes
Sections ranged in thickness from 40-45 um. Of the 4,150 serial sections obtained, 1,215 serial sections were targeted for imaging. Within this range, a total of 28 sections were lost: 2 during pickup, 16 during post-staining, 2 before imaging, and 8 during imaging. The final stitched and registered data set contains 1,153 sections.



Ascb_logo
Ccdb_logo_banner
Nif_button2
Dci_button
Labbyrcw