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Home • e17hpc1a • Segmentation Information

Data Set Information

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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: 5
Image basename: e17hpc1a

Project information
Project Experiment Subject group Subject Organism Tissue section or block View this project's published data sets View this project's tree structure

Project (P1123)
Project ID	P1123
Project name	CCDB rat test data
Project description	Confocal images
Leader	Maryann Martone (Other projects)
Funding agency	NIH
Project start date	2001-10-23
Project end date
Collaborators	Diana Price and Andrea Thor
Publications

Experiment (4)
Experiment title	Intracellular injection of hippocampal astrocyte
Experiment purpose	to obtain multi resolution data for CCDB
Experiment date	2002-02-27
Experimenter	Diana Price & Andrea Thor

Subject group (4)
Subject group name	control
Group by
Treatment

Subject (4)
Species	rat
Scientific name	rattus norvegicus
Strain	Sprague Dawley

Organism (4)
Age class	adult
Age	1.0 months
Sex	male
Weight	150.0 grams
Vendor
Cell Culture
Culture type
Date plated
Plating density
Number of passages
Media
Cultured by
Preparation
Cell type
Source
Tissue product storage
Cell line ID
Lot number
Notes

Tissue section or block (4)
Anatomical location	hippocampus
Tissue product storage
Microtome	vibratome
Thickness	100.0 um
Orientation	coronal

Specimen Preparation Information

Microscopy product ID: 5
Image basename: e17hpc1a

Specimen Preparation
Tissue group type
Ext file name
Protocol used

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Microscopy Product Information

Microscopy product ID: 5
Image basename: e17hpc1a

Microscopy product
Microscopy product id	5
Image basename	e17hpc1a
Instrument	Biorad Radiance 2000 Confocal
X Size	1024
Y Size	1024
Z Size
X Resolution	0.07 um/pixel
Y Resolution	0.07 um/pixel
Z Resolution
Create date	2002-03-13
PURL	NA
Product type	optical section series
Microscope type	confocal
Session name
Grid box count
Grid info.	N/A
Slide info.
Plane count	1
SRB ID	0

Imaging Product Types

Microscopy product ID: 5
Image basename: e17hpc1a

Optical section series
Optical PSF file
Descriptions
Optical Z resolution	0.3 um
Cutting plane

Specimen Description

Microscopy product ID: 5
Image basename: e17hpc1a

Specimen description (5, e17hpc1a)
System	central nervous system
Tissue
Organ	brain
Region	hippocampus
Subregions	CA1
Cell type	protoplasmic astrocyte
Cell id
Structure
Atlas coordinates	(1.5, -3.6, -2.9)
Atlas	Paxinos and Watson
Map location	Show map location
Notes

Imaging Parameters

Microscopy product ID: 5
Image basename: e17hpc1a

Light microscopy product (5, e17hpc1a)
Coverslip thickness	1.0 um
Lens
Lens magnification	60.0 X
Numerical aperture	1.4
Immersion medium	oil
Mounting medium	gelvatol
Refractive index

LM channels

All channels

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2D Image Information

Microscopy product ID: 5
Image basename: e17hpc1a

Downloadable data file description
Full-resolution version
Down-sampled version

Raw data info
Bit depth
Digitized by
Digitizing platform

Animation
No animation available.

Data files
Action	File type	File size	Description

WIB viewer
JPG view

Description:
No WIB image found.

Description:

id: 5 - Click to go back to the summary page

Reconstruction Information

Microscopy product ID: 5
Image basename: e17hpc1a

Reconstruction description
Reconstruction description
Full-resolution reconstruction file
Down-sampled version of the reconstruction file
Image map file
Reconstruction file format
Volume dimension	(1024.0, 1024.0, 58.0) pixels
Voxel scale	(0.07, 0.07, 0.3) µm

More details

Animation
Play/Download	Rotation loop of a maximum intensity projection of a filled astroctye in hippocampal area CA1

Data files
Action	File type	File size	Description
Download	512x512 image	Unknown	Protoplasmic astrocyte from rat hippocampal area CA1 injected with Alexa 488
Download	Reconstruction data file	58.0MB	Not available
Download	Animation video	9.74MB	Rotation loop of a maximum intensity projection of a filled astroctye in hippocampal area CA1

WIB viewer
JPG view

Description: Protoplasmic astrocyte from rat hippocampal area CA1 injected with Alexa 488

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Description: Protoplasmic astrocyte from rat hippocampal area CA1 injected with Alexa 488

Segmentation Information

Microscopy product ID: 5
Image basename: e17hpc1a

Segmentation description
Segmentation description
Segmented by
Object type
Analysis description
Description for the downloadable segmentation data file

View list of segmented objects

Data files
Action	File type	File size	Description
Download	512x512 image	Unknown	Not available
Download	Atlas location	101.51KB	Map of specimen indicating the position of the object of interest in a larger context.

JPG view

Description: