NSCPHD1006 Advanced Biofilm Course (ABC)

Volume 2015/2016



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In 2005 the idea came up to offer a course with theoretical and practical basics in biofilm research comprising an innovative approach.

The aim of the course is to explore a given biofilm with advanced standard methods applied to gain information about the structure and function of biofilms. This included so far microsensor measurements, fluorescence and confocal laser scanning microscopy as well as modeling of the data acquired. As optical coherence tomography is an emerging imaging technique for biofilms, the Advanced Biofilm Course 2012 will introduce this method to explore the mesoscale of biofilms.

The course is intended for PhD students and Post-Doctoral researchers in microbiology, environmental technology, bioengineering and related areas, who are going to use this combined and sophisticated approach for characterisation of their own microbial biofilms.

The course is a hands-on course. Attendees should feel free to communicate to the organisers whether their personal samples could be analysed or not.

Please bring your own computer (windows operating system).

Scope and Key Issues

The course aims to teach the major tools used in biofilm research:

  • biofilm imaging at the micro- and mesoscale
  • microelectrode technique
  • mathematical modeling

Topics in Detail

Cultivation of Biofilms

  • growth devices and reactors
  • processes (e.g. substrate metabolism)
  • development (e.g. growth and decay)


  • substrate gradients, diffusion and kinetics
  • theoretical and practical aspects of micro- environmental analyses


Biofilm Imaging

  • microscopic imaging with fluorescence microscopy
  • theory and application of optical sectioning at
  • the microscale by means of confocal laser scanning microscopy (CLSM)
  • theory and application of optical sectioning at the mesoscale by means of optical coherence tomography (OCT)


Digital Image Analysis and Quantification of 3-d Imaging Data Sets

Theory and Practice of Biofilm Modeling

  • biofilm modeling principles, building blocks and applications
  • computer practicals with 1-d, 2-d and 3-d models
Hands-on, exploration
  • Category
  • Hours
  • Class Instruction
  • 50
  • Practical exercises
  • 33
  • Total
  • 83
Type of assessment
Course participation
The course concludes with a presentation by the students of the results of their exercises.