Educational Workshop, 23 June, 9.00-16.00
Growth and imaging techniques for laboratory and clinical biofilm research
Directors: Paul Stoodley, (USA) Kasper Nørskov Kragh (Denmark) & Claus Sternberg, (Denmark)
Biofilm laboratory growth systems - an overview
Paul Stoodley, (The Ohio State University, Department of Microbial Infection and Immunity,
Columbus, OH, USA)
Working with clinical specimens
Kasper Nørskov Kragh (University of Copenhagen, Department of Immunology and Microbiology,
Copenhagen, Denmark)
You will get an introduction to working with clinical specimens. How to preserve them, stain them
and do microscopy on them. We will talk about experimental design and what to be aware of with
different types of specimens.
Biofilm flow cells - principles and assembly (lecture and hands on) Paul Stoodley, (USA).
This section will include setting up various types of biofilm reactors and flow cell systems. Training
microscopes will be available to demonstrate how biofilms are imaged during flow. BioSurface
Technologies will provided parallel plate flow cells and CDC reactors. We will also demonstrate how
to use home-made flow cells.
Staining biofilms for imaging - live/dead, PNA FISH (lecture and hands on and mock demo)
Kasper Nørskov Kragh (Denmark)
You will get some tips about different staining methods and staining dos and don’ts. We will go
through the work flow of live/dead staining and PNA FISH staining with a mock demo.
Rendering confocal biofilm images (Imaris - lecture and hands on)
Claus Sternberg, (Technical University of Denmark, Department of Systems Biology Lyngby,
Denmark)
Here you will get an introduction to one of the most popular commercial image presentation
programs for biofilms. The section will demonstrate some of the basic techniques for making
beautiful images out of your confocal files without manipulating the data. You will get a chance of
using your own data to make a 3D image if you bring your own confocal image files.
Techniques for quantifying biofilm for confocal images (COMSTAT - lecture and hands on)
Claus Sternberg (Denmark)
Comstat has become the de facto standard for quantifying biofilm images. This section will take you
through the use of the program and you will learn the strengths and limitations. In the practical
session you will analyze a test sample and if time allows you can use your own data for analysis.
Panel Discussion
Participants will learn the principles behind the use of various experimental systems to grow and
image biofilms as well as techniques to image biofilms on clinical and ex vivo animal samples. There
will be hands on demonstrations of how to assemble a basic flow cell system, perform PNA FISH and
live / dead viability staining and how to best present and quantify your confocal images using Imaris
and COMSTAT imaging software. There will be plenty of opportunity for interactive discussion
between participants and workshop faculty during the workshop.
The Imaris and Comstat2 programs will be provided free of charge (Imaris as an expiring demo
license) to the workshop participants prior to the session. Preferably, you should bring a laptop with
the installed programs (optional, of course). At the workshop we will have access to a very limited
number of workstations.
The link and password to the supporting web site will be e-mailed to all registered participants
directly.