Alternate header for print version


Reconstruction
Display image description
Single slice through a serial section reconstruction of the optic nerve head in the area of transition between myelinated and unmyelinated axons the mouse obtained through serial section scanning electron microscopy. The location of the transition zone may be viewed on the image map (red box) associated with this data set.
Full resolution image description
Stitched, normalized reconstruction in IMOD format. Data set was normalized by computing the mean and standard deviation of the entire dataset then setting each plane to that mean and standard deviation by subtracting from each voxel the old mean (that is, the original mean of the plane), dividing by the old standard deviation, then multiplying by the new standard deviation and adding in the new mean. The location of the transition zone may be viewed on the image map (red box) associated with this data set. **Note: due to the size of the file (>200Gb), this data set is not available for automated download from the CCDB. A downsampled version (9Gb) may be downloaded. The full resolution data may be viewed through the WIB tool. If you would like the full resolution data file, please contact CCDB.
Downsampled image description
Binned version of the normalized volume in mrc format.
File format
MRC
Volume_dimension
10982, 15960, 750
Volume scale
0.013, 0.013, 0.07

Image 2D
Display image description
Single un-normalized mosaic slice from a serial section reconstruction of the optic nerve head of the mouse.
Full resolution image description
unstitched, not normalized raw data zipped.

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

CCDB:8093*  Cite 
Project: P2078
Project name
Morphology of Optic Nerve Head
Description
3D reconstruction using serial section scanning electron microscopy of the optic nerve head in mouse.
Funding agency
International Retina Research Foundation, and the Lasker Foundation
Leader(s)
Keun-Young Kim
Collaborator(s)
Eric Bushong
Mark Ellisman
Daniela Boassa
Masako Terada
Nicholas Marsh-Armstrong
Start date
07-19-2010
End date
unspecified
 
Experiment
Experiment ID
8087
Experiment date
07-19-2010
Title
Experiment 1
Purpose
purpose
Experimenter(s)
Keun-Young Kim
Microscopy product
Microscopy product ID
8093
Instrument
Gatan 3View system on FEI Quanta microscope
Microscopy type
Serial Block Face SEM
Product type
SERIAL SECTION
Image basename
ONH_wt_tz
Spatial Axis Image Size Pixel Size
X 6000px 13 nm/pixels
Y 6000px 13 nm/pixels
Y 750px
Subject
Species
Mouse
Scientific name
Mus musculus
Strain
C57BL/6
Age
9 months
Age class
Adult
Tissue section
Anatomical location
Eye (Optic Nerve Head)
Microtome
3-View ultramicrotome
Specimen description
System
central nervous system
Map location
View location
Imaging parameters
Type
Electron microscopy product
Recording medium
Gatan backscatter detector
Magification
1400
Accelerating voltage
2.5 kV
Notes
pixel dwell time = 8 usec chamber pressure = High Vacuum spot size = 3.0
Specimen preparation
Protocol used
The animal was perfused with Ringer's followed by 2% PFA / 2.5% glutaraldehyde. The tissue was postfixed in the same fixative for 2 hours on ice. The eye was enucleated and the optic nerve head was dissected for sagittal longitudinal section.The tissue was placed into solution containing 3% potassium dichromate and 2% osmium tetroxide in ddH2O. The samples were allowed to sit at room temp for 3 hours. The tissue washed with ddH2O at room temp 3x 5 minutes and placed in filtered thiocarbohydrazide(TCH) solution(0.1 g TCH in 10 mL ddH2O) for 30 minutes at room temp.The tissue washed with ddH2O at room temp 3x 5 minutes and placed in 2% osmium in ddH20 for an hour at room temp.The tissue washed with ddH2O at room temp 3x 5 minutes and placed in 1% aq. UA overnight in fridge.The next day, dissolve 0.066g of lead nitrate in 10 mL aspartic acid solution and adjust pH to 5.5 with 1N KOH. Place solution in 60 degree oven for 30 minutes. No precipitate should form.Take tissue from 1% UA and wash with ddH2O, 3x 5 minutes.Place tissue in the lead aspartate solution and leave in oven for 30 minutes. Wash tissue 3x 5 minutes with ddH2O and dehydrate and embed in Durcupan as described below.The tissue was dehydrated in EtOH (20, 50, 70, 90, 100, 100% for 10 minutes each) and then acetone (100% 3x 10 minutes). The tissue was placed into 50:50 Durcupan:acetone overnight. Tissue was placed in 100% Durcupan for 1 hour. Tissue was transferred to fresh Durcupan for 2 hours. Tissue was placed into 60 degree oven for 2 days and polymerized.
Imaging product type
Type
Mosaic
Description
mosaic with 6 sections
X position
2 tiles
Y position
3 tiles
Imaging product type
Type
Serial section
Cutting plane
longitudinal
Z resolution
70 nm/pixels
Notes
serial section series and mosaic