Email updates

Keep up to date with the latest news and content from BMC Biotechnology and BioMed Central.

Open Access Open Badges Methodology article

A simple viability analysis for unicellular cyanobacteria using a new autofluorescence assay, automated microscopy, and ImageJ

Katja Schulze12*, Diana A López1, Ulrich M Tillich1 and Marcus Frohme1

Author Affiliations

1 Molecular Biology and Functional Genomics, TH Wildau, Bahnhofstr. 1, 15745 Wildau, Germany

2 Bioinformatics, University of Wuerzburg, Biocenter, Am Hubland, 97074 Wuerzburg, Germany

For all author emails, please log on.

BMC Biotechnology 2011, 11:118  doi:10.1186/1472-6750-11-118

Published: 30 November 2011



Currently established methods to identify viable and non-viable cells of cyanobacteria are either time-consuming (eg. plating) or preparation-intensive (eg. fluorescent staining). In this paper we present a new and fast viability assay for unicellular cyanobacteria, which uses red chlorophyll fluorescence and an unspecific green autofluorescence for the differentiation of viable and non-viable cells without the need of sample preparation.


The viability assay for unicellular cyanobacteria using red and green autofluorescence was established and validated for the model organism Synechocystis sp. PCC 6803. Both autofluorescence signals could be observed simultaneously allowing a direct classification of viable and non-viable cells. The results were confirmed by plating/colony count, absorption spectra and chlorophyll measurements. The use of an automated fluorescence microscope and a novel ImageJ based image analysis plugin allow a semi-automated analysis.


The new method simplifies the process of viability analysis and allows a quick and accurate analysis. Furthermore results indicate that a combination of the new assay with absorption spectra or chlorophyll concentration measurements allows the estimation of the vitality of cells.