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Biological Procedures Online

Open Access

The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the calgary biofilm device

  • Joe J. Harrison1,
  • Howard Ceri1,
  • Jerome Yerly2,
  • Carol A. Stremick1,
  • Yaoping Hu2,
  • Robert Martinuzzi3 and
  • Raymond J. Turner4Email author
Biological Procedures Online8:81194

Received: 6 September 2006

Accepted: 28 October 2006


Microbes frequently live within multicellular, solid surface-attached assemblages termed biofilms. These microbial communities have architectural features that contribute to population heterogeneity and consequently to emergent cell functions. Therefore, three-dimensional (3D) features of biofilm structure are important for understanding the physiology and ecology of these microbial systems. This paper details several protocols for scanning electron microscopy and confocal laser scanning microscopy (CLSM) of biofilms grown on polystyrene pegs in the Calgary Biofilm Device (CBD). Furthermore, a procedure is described for image processing of CLSM data stacks using amira™, a virtual reality tool, to create surface and/or volume rendered 3D visualizations of biofilm microorganisms. The combination of microscopy with microbial cultivation in the CBD — an apparatus that was designed for highthroughput susceptibility testing — allows for structure-function analysis of biofilms under multivariate growth and exposure conditions.

Indexing terms

BiofilmsImaging, Three-Dimensional