Quick Search:

uzh logo
Browse by:

Zurich Open Repository and Archive

Maintenance: Tuesday, July the 26th 2016, 07:00-10:00

ZORA's new graphical user interface will be relaunched (For further infos watch out slideshow ZORA: Neues Look & Feel). There will be short interrupts on ZORA Service between 07:00am and 10:00 am. Please be patient.

Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-26879

Zeder, M; Van den Wyngaert, S; Köster, O; Felder, K M; Pernthaler, J (2010). Automated quantification and sizing of unbranched filamentous cyanobacteria by model based object oriented image analysis. Applied and Environmental Microbiology, 76(5):1615-1622.

Accepted Version
View at publisher


The quantification and sizing of filamentous cyanobacteria in environmental samples or cultures is a time consuming process often performed by manual or semi-automated microscopic analysis. Automation by conventional image analysis is difficult because filaments may exhibit large variation in length and patchy autofluorescence. Moreover, individual filaments frequently cross each other on microscopic preparations, as can be deduced by modelling. This study presents a novel approach based on object oriented image analysis to simultaneously retrieve (a) filament number, (b) individual filament lengths, and (c) cumulative filament length of unbranched cyanobacterial morphotypes on fluorescence microscopic images in a fully automated high-throughput manner. Special emphasis was put on the correct detection of overlapping objects by image analysis and on the appropriate coverage of filament length distribution by using large composite images. The method was validated on a dataset of Planktothrix rubescens from field samples and compared with manual filament tracing, the line intercept method, and the Utermöhl counting approach. The described computer program features batch processing of large images from any appropriate source and annotation of detected filaments. It requires no user interaction, is freely available and might thus be a useful tool for basic research and drinking water quality control.


6 citations in Web of Science®
7 citations in Scopus®
Google Scholar™



133 downloads since deposited on 24 Jan 2010
13 downloads since 12 months

Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:05 Vetsuisse Faculty > Institute of Veterinary Bacteriology
07 Faculty of Science > Department of Plant and Microbial Biology
Dewey Decimal Classification:570 Life sciences; biology
580 Plants (Botany)
Date:March 2010
Deposited On:24 Jan 2010 12:00
Last Modified:05 Apr 2016 13:43
Publisher:American Society for Microbiology
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:10.1128/AEM.02232-09
PubMed ID:20048059

Users (please log in): suggest update or correction for this item

Repository Staff Only: item control page