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Home • ALZ301_4 • Segmentation Information
Data Set Information
Summary
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  Project
  Specimen preparation
  Microscopy product
  Imaging product type
  Specimen description
  Imaging parameters

  2D image
  Reconstruction
  Segmentation

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Project Information
Microscopy product ID: 6289
Image basename: ALZ301_4
Project information
Project
Experiment
Subject group
Subject
Organism
Tissue section or block

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Project (P1700)
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Experiment (188)
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Subject group (178)
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Subject (181)
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Organism (188)
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Tissue section or block (212)
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Specimen Preparation Information
Microscopy product ID: 6289
Image basename: ALZ301_4
Specimen Preparation
Tissue group type
Ext file name
Protocol used


Microscopy Product Information
Microscopy product ID: 6289
Image basename: ALZ301_4
Microscopy product
Microscopy product id 6289
Image basename ALZ301_4
Instrument JEOL100CX
X Size 0
Y Size 0
Z Size
X Resolution
Y Resolution
Z Resolution
Create date 1989-09-29
PURL
Product type SERIAL SECTION
Microscope type TEM
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: 6289
Image basename: ALZ301_4
Serial section
Description
Z resolution 0.25 um
Cutting plane
Notes
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Specimen Description
Microscopy product ID: 6289
Image basename: ALZ301_4
Specimen description (6289, ALZ301_4)
System central nervous system
Tissue
Organ brain
Region cerebral cortex
Subregions
Cell type Neocortex pyramidal cell
Cell id
Structure
Atlas coordinates
Atlas
Map location
Notes


Imaging Parameters
Microscopy product ID: 6289
Image basename: ALZ301_4
Electron microscopy product
Magnification 3300.0
EXT filename
Spot size
Recording medium film
Accelerating voltage 100.0 KeV
Energy filter type
Energy filter slit
Energy filter dispersion
Notes
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2D Image Information
Microscopy product ID: 6289
Image basename: ALZ301_4

Downloadable data file description
Full-resolution version Stack of Alzheimer neuronal images modified by IMOD using the newstack program.
Down-sampled version N/A
Raw data info
Bit depth 16.0 bit
Digitized by Brian Kang
Digitizing platform Flextight Precision II


Animation
No animation available. N/A
Data files
Action File type File size Description
Download 512x512 image Unknown Electron micrograph of the cell body of a 0.25 um thick section through a cortical pyramidal neuron from the brain of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago.
Download Data file 5.1GB Stack of Alzheimer neuronal images modified by IMOD using the newstack program.

Description: 
Electron micrograph of the cell body of a 0.25 um thick section through a cortical pyramidal neuron from the brain of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago.

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Description: 
Electron micrograph of the cell body of a 0.25 um thick section through a cortical pyramidal neuron from the brain of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago.


Reconstruction Information
Microscopy product ID: 6289
Image basename: ALZ301_4

Reconstruction description
Reconstruction description
Full-resolution reconstruction file Aligned serial section reconstruction in IMOD MRC format. Image stack that was aligned using Midas from the IMOD package to correct for non-linear distortions. The image stack was then binned down by 4x for both the X and Y axis.
Down-sampled version of the reconstruction file
Image map file  
Reconstruction file format MRC
Volume dimension
Voxel scale
More details
Animation
Data files
Action File type File size Description
Download 512x512 image Unknown Single aligned electron micrograph of a 0.25 um thick section from a serial section reconstruction of the cell body through a cortical pyramidal neuron from the brain of a patient with Alzheimer's disease.
Download Reconstruction data file 326.16MB Aligned serial section reconstruction in IMOD MRC format. Image stack that was aligned using Midas from the IMOD package to correct for non-linear distortions. The image stack was then binned down by 4x for both the X and Y axis.
Download Animation video 34.15MB Not available

Description: Single aligned electron micrograph of a 0.25 um thick section from a serial section reconstruction of the cell body through a cortical pyramidal neuron from the brain of a patient with Alzheimer's disease.

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Description: Single aligned electron micrograph of a 0.25 um thick section from a serial section reconstruction of the cell body through a cortical pyramidal neuron from the brain of a patient with Alzheimer's disease.


Segmentation Information
Microscopy product ID: 6289
Image basename: ALZ301_4

Segmentation description
Segmentation description
Segmented by
Object type
Analysis description
Description for the downloadable segmentation data file Trace of the reconstructed file using Jinx.
View list of segmented objects
Data files
Action File type File size Description
Download Segmentation data file 12.16KB Trace of the reconstructed file using Jinx.

Description: 



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