KNAW Repository

Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP

Müller, L.N. and Brouwer de, J.F.C. and Almeida, J.S. and Stal, L.J. and Xavier, J.B. (2006) Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP. BMC Ecology, 6, 1 [1-15]. ISSN 1472-6785.

[img]
Preview
PDF - Published Version
974Kb

Official URL: http://dx.doi.org/10.1186/1472-6785-6-1

Abstract

Background Confocal laser scanning microscopy (CLSM) is the method of choice to study interfacial biofilms and acquires time-resolved three-dimensional data of the biofilm structure. CLSM can be used in a multi-channel modus where the different channels map individual biofilm components. This communication presents a novel image quantification tool, PHLIP, for the quantitative analysis of large amounts of multi-channel CLSM data in an automated way. PHLIP can be freely downloaded from http://phlip.sourcefo Results PHLIP is an open source public license Matlab toolbox that includes functions for CLSM imaging data handling and ten image analysis operations describing various aspects of biofilm morphology. The use of PHLIP is here demonstrated by a study of the development of a natural marine phototrophic biofilm. It is shown how the examination of the individual biofilm components using the multi-channel capability of PHLIP allowed the description of the dynamic spatial and temporal separation of diatoms, b Conclusions The presented case study reveals new insight into the temporal development of a phototrophic biofilm where multi-channel imaging allowed to parallel monitor the dynamics of the individual biofilm components over time. This application of PHLIP presents the power of biofilm image analysis by multi-channel CLSM software and demonstrates the importance of PHLIP for the scientific community as a flexible and extendable image analysis platform for automated image processing.

Item Type:Article
Institutes:Nederlands Instituut voor Ecologie (NIOO)
ID Code:11998
Deposited On:23 Nov 2011 01:00
Last Modified:16 Jul 2013 10:42

Repository Staff Only: item control page