Summary of 1-Bao-WormEmbryo

SSBD:database
SSBD:database URL
Title
-
Description
-
Relase date
2013-10-03
Updated date
2018-11-15
License
CC BY-NC-SA
Kind
Quantitative data based on Experiment
Number of Datasets
1 ( Image datasets: 0, Quantitative data datasets: 1 )
Size of Datasets
22.9 MB ( Image datasets: 0 bytes, Quantitative data datasets: 22.9 MB )

Organism(s)
C. elegans
Gene symbol(s)
NA
Protein name(s)
NA

Datatype
nuclear division dynamics
Molecular Function (MF)
Biological Process (BP)
embryo development
Cellular Component (CC)
nucleus
Biological Imaging Method
-
XYZ Scale
XY: 0.09 micrometer/pixel, Z: 1.0 micrometer/slice
T scale
1.0 minute for each time interval

Image Acquisition
Experiment type
-
Microscope type
-
Acquisition mode
-
Contrast method
Fluorescence
Microscope model
-
Detector model
-
Objective model
-
Filter set
-

Related paper(s)

Zhirong Bao, John I Murray, Thomas Boyle, Siew Loon Ooi, Matthew J Sandel, Robert H Waterston (2006) Automated cell lineage tracing in Caenorhabditis elegans., Proceedings of the National Academy of Sciences of the United States of America, Volume 103, Number 8, pp. 2707-12

Published in 2006 Feb 21 (Electronic publication in Feb. 13, 2006, midnight )

(Abstract) The invariant cell lineage and cell fate of Caenorhabditis elegans provide a unique opportunity to decode the molecular mechanisms of animal development. To exploit this opportunity, we have developed a system for automated cell lineage tracing during C. elegans embryogenesis, based on 3D, time-lapse imaging and automated image analysis. Using ubiquitously expressed histone-GFP fusion protein to label cells/nuclei and a confocal microscope, the imaging protocol captures embryogenesis at high spatial (31 planes at 1 microm apart) and temporal (every minute) resolution without apparent effects on development. A set of image analysis algorithms then automatically recognizes cells at each time point, tracks cell movements, divisions and deaths over time and assigns cell identities based on the canonical naming scheme. Starting from the four-cell stage (or earlier), our software, named starrynite, can trace the lineage up to the 350-cell stage in 25 min on a desktop computer. The few errors of automated lineaging can then be corrected in a few hours with a graphic interface that allows easy navigation of the images and the reported lineage tree. The system can be used to characterize lineage phenotypes of genes and/or extended to determine gene expression patterns in a living embryo at the single-cell level. We envision that this automation will make it practical to systematically decipher the developmental genes and pathways encoded in the genome of C. elegans.
(MeSH Terms)

Contact
Robert H. Waterston , University of Washington , Department of Genome Sciences
Contributors
Zhirong Bao, John I. Murray, Thomas Boyle, Siew Loon Ooi, Matthew J. Sandel, Robert H. Waterston


Dataset List of 1-Bao-WormEmbryo

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
Download BDML
Download Images
# 1
Datast ID 081505_L1
Dataset Kind Quantitative data
Dataset Size 22.9 MB
4D view
SSBD:OMERO
Download BDML
Download Image data