Header

UZH-Logo

Maintenance Infos

ASSET: A Robust Algorithm for the Automated Segmentation and Standardization of Early Caenorhabditis elegans Embryos


Blanchoud, Simon; Budirahardja, Yemima; Naef, Felix; Gönczy, Pierre (2010). ASSET: A Robust Algorithm for the Automated Segmentation and Standardization of Early Caenorhabditis elegans Embryos. Developmental Dynamics, 239:3285-3296.

Abstract

The early Caenorhabditis elegans embryo is an attractive model to investigate evolutionarily conserved cellular mechanisms. However, there is a paucity of automated methods to gather quantitative information with subcellular precision in this system. We developed ASSET (Algorithm for the Segmentation and the Standardization of C. elegans Time-lapse recordings) to fill this need. ASSET automatically detects theeggshell and the cell cortex from DIC time-lapse recordings of live one-cell-stage embryos and can also track subcellular structures using fluorescent time-lapse microscopy. Importantly, ASSET standardizes the data into an absolute coordinate system to allow robust quantitative comparisons between embryos. We illustrate how ASSET can efficiently gather quantitative data on the motion of centrosomes and precisely track cortical invaginations, revealing hitherto unnoticed differences between wild-type and saps-1(RNAi) embryos. In summary, we establish ASSET as a novel tool for the efficient quantification and standardization of images from early C. elegans embryos.

Abstract

The early Caenorhabditis elegans embryo is an attractive model to investigate evolutionarily conserved cellular mechanisms. However, there is a paucity of automated methods to gather quantitative information with subcellular precision in this system. We developed ASSET (Algorithm for the Segmentation and the Standardization of C. elegans Time-lapse recordings) to fill this need. ASSET automatically detects theeggshell and the cell cortex from DIC time-lapse recordings of live one-cell-stage embryos and can also track subcellular structures using fluorescent time-lapse microscopy. Importantly, ASSET standardizes the data into an absolute coordinate system to allow robust quantitative comparisons between embryos. We illustrate how ASSET can efficiently gather quantitative data on the motion of centrosomes and precisely track cortical invaginations, revealing hitherto unnoticed differences between wild-type and saps-1(RNAi) embryos. In summary, we establish ASSET as a novel tool for the efficient quantification and standardization of images from early C. elegans embryos.

Statistics

Citations

4 citations in Web of Science®
4 citations in Scopus®
Google Scholar™

Altmetrics

Downloads

64 downloads since deposited on 22 Jun 2013
23 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Interdisciplinary PhD Projects
Special Collections > SystemsX.ch > Interdisciplinary Pilot Projects
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:December 2010
Deposited On:22 Jun 2013 16:29
Last Modified:05 Apr 2016 16:49
Publisher:Wiley-Blackwell
ISSN:1058-8388
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1002/dvdy.22486

Download

Preview Icon on Download
Preview
Filetype: PDF
Size: 408kB
View at publisher