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Home • nmodel • Segmentation Information
Data Set Information
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  Specimen preparation
  Microscopy product
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  Imaging parameters

  2D image
  Reconstruction
  Segmentation

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Project Information
Microscopy product ID: 8244
Image basename: nmodel
Project information
Project
Experiment
Subject group
Subject
Organism
Tissue section or block

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Project (P2023)
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Experiment (8241)
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Subject group (8239)
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Subject (8240)
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Organism (8241)
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Tissue section or block (8242)
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Specimen Preparation Information
Microscopy product ID: 8244
Image basename: nmodel
Specimen Preparation
Tissue group type Golgi impregnation
Ext file name
Protocol used Perfused with 4% PFA, 0.1% glut. Postfixed 1 hour in same fix on ice. Left hemisphere cut into 2 mm thick coronal slabs. Tissue placed into 2.3% potassium dichromate / 0.4% OsO4 for 3 days at room temp. Tissue blotted with filter paper and then placed in 0.7% silver nitrate in dark for 3 days. Tissue was dehydrated, infiltrated and embedded in Durcupan in Beem capsules.




Microscopy Product Information
Microscopy product ID: 8244
Image basename: nmodel
Microscopy product
Microscopy product id 8244
Image basename nmodel
Instrument FEI Quanta 200 FEG SEM with Gatan 3 View
X Size 4096
Y Size 4096
Z Size 1570
X Resolution 47.0 nm/pixels
Y Resolution 47.0 nm/pixels
Z Resolution 60.0 nm/pixels
Create date 2009-09-03
PURL
Product type SERIAL SECTION
Microscope type Serial Block Face SEM
Session name
Grid box count
Grid info. N/A
Slide info.
Plane count 0
SRB ID 0
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Imaging Product Types
Microscopy product ID: 8244
Image basename: nmodel
Serial section
Description Serial block face imaging
Z resolution 60.0 nm
Cutting plane
Notes
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Specimen Description
Microscopy product ID: 8244
Image basename: nmodel
Specimen description (8244, nmodel)
System central nervous system
Tissue
Organ brain
Region neocortex
Subregions
Cell type neocortex pyramidal neuron
Cell id
Structure
Atlas coordinates
Atlas
Map location
Notes


Imaging Parameters
Microscopy product ID: 8244
Image basename: nmodel
Electron microscopy product
Magnification 600.0
EXT filename
Spot size
Recording medium
Accelerating voltage 2.0 kv
Energy filter type
Energy filter slit
Energy filter dispersion
Notes Beam energy: 2.0 kV Spot size: 2.5 Chamber pressure: 30 Pa Pixel dwell time: 18 usec
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2D Image Information
Microscopy product ID: 8244
Image basename: nmodel

Downloadable data file description
Full-resolution version Tar file containing raw data files in dm3 format
Down-sampled version N/A
Raw data info
Bit depth N/A
Digitized by N/A
Digitizing platform N/A


Animation
Slice by slice animation of Golgi-impregnated neurons from the mouse neocortex imaged using serial block face SEM. Contrast is reversed so that electron dense regions appear bright.
Data files
Action File type File size Description
Download 512x512 image Unknown Single slice through Golgi-impregnated neurons from the mouse neocortex imaged using serial block face SEM. Contrast is reversed so that electron dense regions appear bright.
Download Data file 49.15GB Tar file containing raw data files in dm3 format
Download Animation video 75.25MB Slice by slice animation of Golgi-impregnated neurons from the mouse neocortex imaged using serial block face SEM. Contrast is reversed so that electron dense regions appear bright.

Description: 
Single slice through Golgi-impregnated neurons from the mouse neocortex imaged using serial block face SEM. Contrast is reversed so that electron dense regions appear bright.

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Description: 
Single slice through Golgi-impregnated neurons from the mouse neocortex imaged using serial block face SEM. Contrast is reversed so that electron dense regions appear bright.


Reconstruction Information
Microscopy product ID: 8244
Image basename: nmodel

Reconstruction description
Reconstruction description The raw series had 1560 planes total, but there is no information available as to why some planes were left off the reconstruction.
Full-resolution reconstruction file Full resolution file in IMOD format. The raw series had 1560 planes total, but there is no information available as to why some planes were left off the reconstruction.
Down-sampled version of the reconstruction file Volume binned by a factor of 2 in the x, y and z planes: 2048 X 2048 X 632 slices
Image map file  
Reconstruction file format MRC
Volume dimension (4096.0, 4096.0, 1266.0) pixels
Voxel scale (0.047, 0.047, 0.06) µm
More details
Animation
Animation showing the segmentation of individual neurons from a reconstruction of Golgi-impregnated mouse neocortex using serial block face SEM. Segmentation files are available for download under the segmentation section.
Data files
Action File type File size Description
Download 512x512 image Unknown Golgi impregnated pyramidal neurons in the neocortex of an adult mouse. Contrast is reversed so that Golgi stain appears bright against the unstained background. A maximum intensity projection of the dataset is available in the thumbnail and by clicking the JPEG tab.
Download Reconstruction data file 19.78GB Full resolution file in IMOD format. The raw series had 1560 planes total, but there is no information available as to why some planes were left off the reconstruction.
Download Downsampled data file 2.47GB Volume binned by a factor of 2 in the x, y and z planes: 2048 X 2048 X 632 slices
Download Animation video 118.21MB Animation showing the segmentation of individual neurons from a reconstruction of Golgi-impregnated mouse neocortex using serial block face SEM. Segmentation files are available for download under the segmentation section.

Description: Golgi impregnated pyramidal neurons in the neocortex of an adult mouse. Contrast is reversed so that Golgi stain appears bright against the unstained background. A maximum intensity projection of the dataset is available in the thumbnail and by clicking the JPEG tab.

Launch WIB viewer (in a new window).

Description: Golgi impregnated pyramidal neurons in the neocortex of an adult mouse. Contrast is reversed so that Golgi stain appears bright against the unstained background. A maximum intensity projection of the dataset is available in the thumbnail and by clicking the JPEG tab.


Segmentation Information
Microscopy product ID: 8244
Image basename: nmodel

Segmentation description
Segmentation description Semi automated segmentation of Golgi stained pyramidal neurons in the cerebral cortex using Amira
Segmented by James Obayashi
Object type
Analysis description Used AMIRA semi-auto segmentation tool called "magic wand" to select stained neurons. Surface was generated from that trace in AMIRA.
Description for the downloadable segmentation data file
View list of segmented objects
Data files
Action File type File size Description
Download 512x512 image Unknown Semi automated segmentation of Golgi stained pyramidal neurons in the cerebral cortex using Amira
Download Segmentation data file 273.27MB Not available

Description: Surface reconstruction of a Golgi-stained pyramidal cell segmented from a serial block face SEM dataset from the neocortex of the adult mouse

Launch WIB viewer (in a new window).


Description: Surface reconstruction of a Golgi-stained pyramidal cell segmented from a serial block face SEM dataset from the neocortex of the adult mouse


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