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Home • caulo_double1 • Segmentation Information

Data Set Information

Summary

Details
  All information
  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: 3628
Image basename: caulo_double1

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 (P1220)
Project ID	P1220
Project name	Caulobacter
Project description	Tomography of Caulobacter crescentus
Leader	Lucy Shapiro, Harley McAdams (Other projects)
Funding agency	Department of Energy
Project start date	2003-07-01
Project end date
Collaborators	Patrick H. Viollier, Tom Deerinck, Mason Mackey, John Crum, Mark Ellisman
Publications

Experiment (112)
Experiment title	Tomographic reconstruction of caulobacter
Experiment purpose	Produce a series of tomographic data of the normal morphology of Caulobacter Crescentus using rapid freezing methods.
Experiment date	2004-05-12
Experimenter	Patrick Viollier, Tom Deerinck

Subject group (88)
Subject group name	N/A
Group by
Treatment	None

Subject (105)
Species	Caulobacter
Scientific name	Caulobacter crescentus
Strain	3724

Organism (112)
Age class	not applicable
Age	days
Sex	unspecified
Weight	grams
Vendor
Cell Culture
Culture type	Cell Line
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 (123)
Anatomical location
Tissue product storage
Microtome
Thickness	um
Orientation

Specimen Preparation Information

Microscopy product ID: 3628
Image basename: caulo_double1

Specimen Preparation
Tissue group type	HPF
Ext file name
Protocol used	High Pressure Freezing (HPF): completed on January 26th, 2006 using Balzers HPM 010 in 100 micron deep gold plated copper planchettes. Bacteria was centrifuged decanted and paced applied to planchettes. Free Substitution: Started Friday January 26th. 1. Cocktail - 2% Osmium tetroxide, 0.5% urynal acetate in anhydrous acetone 2. Time - T1: -90 Celsius for 72 hours S1: 2 Celsius per hour for 15 hours T2: -60 Celsius per hour for 12 hours S2: 5 Celsius per hour for 12 hours T3: 0 Celsius Hold Leica FSU

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Microscopy Product Information

Microscopy product ID: 3628
Image basename: caulo_double1

Microscopy product
Microscopy product id	3628
Image basename	caulo_double1
Instrument	JEOL 4000
X Size	2242
Y Size	3340
Z Size
X Resolution	1.0 nm/pixels
Y Resolution	1.0 nm/pixels
Z Resolution
Create date	2006-10-17
PURL
Product type	DOUBLE TILT
Microscope type	IVEM
Session name
Grid box count	a3
Grid info.	N/A
Slide info.
Plane count	67
SRB ID	0

Imaging Product Types

Microscopy product ID: 3628
Image basename: caulo_double1

Double tilt
Description	Caulobacter Crescentus, 0.5 um thick, 400kv
Range min X	-66.0 degrees
Range max X	66.0 degrees
Tilt increment X	2.0 degrees
Range min Y	-66.0 degrees
Range max Y	64.0 degrees
Tilt increment Y	2.0 degrees

Specimen Description

Microscopy product ID: 3628
Image basename: caulo_double1

Specimen description (3628, caulo_double1)
System
Tissue
Organ
Region
Subregions
Cell type	Caulobacter crescentus
Cell id
Structure
Atlas coordinates
Atlas
Map location
Notes	Caulobacter Crescentus bacteria

Imaging Parameters

Microscopy product ID: 3628
Image basename: caulo_double1

Electron microscopy product
Magnification	30000.0
EXT filename
Spot size
Recording medium	film
Accelerating voltage	400.0 kV
Energy filter type
Energy filter slit
Energy filter dispersion
Notes

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2D Image Information

Microscopy product ID: 3628
Image basename: caulo_double1

Downloadable data file description
Full-resolution version	Files that are needed / used for a TxBR reconstruction. Included with the files are the .preali file, the .rawtlt file, .fid file and all processing files.
Down-sampled version	N/A

Raw data info
Bit depth	16.0 bits
Digitized by	James Obayashi
Digitizing platform	N/A

Animation
Play/Download	Tilt series of both the "A" and "B" stacks. The animation first shows the tilt series of A and then switches to the tilt series of stack B.

Data files
Action	File type	File size	Description
Download	512x512 image	Unknown	Image from the 0 degree tilt angle of image set "A" from the double tilt data series.
Download	Data file	1.99GB	Files that are needed / used for a TxBR reconstruction. Included with the files are the .preali file, the .rawtlt file, .fid file and all processing files.
Download	Animation video	56.78MB	Tilt series of both the "A" and "B" stacks. The animation first shows the tilt series of A and then switches to the tilt series of stack B.

WIB viewer
JPG view

Description:
Image from the 0 degree tilt angle of image set "A" from the double tilt data series.

Launch WIB viewer (in a new window).

Description:
Image from the 0 degree tilt angle of image set "A" from the double tilt data series.

id: 3628 - Click to go back to the summary page

Reconstruction Information

Microscopy product ID: 3628
Image basename: caulo_double1

Reconstruction description
Reconstruction description
Full-resolution reconstruction file	Includes only the final double tilt reconstruction in byte mode. This reconstruction has been saved as a .mrc file format.
Down-sampled version of the reconstruction file
Image map file
Reconstruction file format
Volume dimension	(2242.0, 3340.0, 261.0) pixels
Voxel scale	(0.0010, 0.0010, 0.0010) µm

More details

Animation
Play/Download	a .mpg movie of the slice by slice reconstruction made from a double tilt series of a Caulobacter Crescentus specimen

Data files
Action	File type	File size	Description
Download	512x512 image	Unknown	An image from the slice by slice reconstruction of a double tilt series for the Caulobacter Crescentus specimen
Download	Reconstruction data file	1.82GB	Includes only the final double tilt reconstruction in byte mode. This reconstruction has been saved as a .mrc file format.
Download	Animation video	95.09MB	a .mpg movie of the slice by slice reconstruction made from a double tilt series of a Caulobacter Crescentus specimen

WIB viewer
JPG view

Description: An image from the slice by slice reconstruction of a double tilt series for the Caulobacter Crescentus specimen

Launch WIB viewer (in a new window).

Description: An image from the slice by slice reconstruction of a double tilt series for the Caulobacter Crescentus specimen

Segmentation Information

Microscopy product ID: 3628
Image basename: caulo_double1

Message

No segmentation data is available for this data set yet.