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This is the homepage for 27820 - Ph.D course in Medical Biofilm Techniques.

Note: This page will be continuously updated and you should not expect all manuals to be here before a few days before the course starts.

Here you can find the general description of the course: DTU Course base


General information

The course will start August 13th 2013 at 9.00 am in room 056 (ground floor) at DTU, Building 301. For directions, please follow this link.

Click here for the General time table in short, version 1.20 Subject to changes. (PRINTED)

Please note:

  • Some files require a password to download. This should have been provided to you along with the link to this page. If for some reason you have not received the password, please e-mail Claus Sternberg.
  • Manuals and other materials marked with "(PRINTED)" will be given in hard copy at course start

FACEBOOK: We have a Facebook group for present and past participants and instructors/speakers which you can join if you like. Go here: and apply for membership. Note: The group is not terribly active, but who knows, perhaps someone will make it more interesting some time... :-)


Here we will keep you updated on changes of schedule, and other things you need to know (e.g. where to find result data files)

11-08-2013. Participant list uploaded.

14-08-2013. Participant List updated.

16-08-2013. Added motility assay protocol and speaker presentations.

18-08-2013. The title of the talk of Søren Molin will be: "Pseudomonas aeruginosa biofilms in CF airways – the role of adaptive mutations".

19-08-2013. The talks will start at 10.30. Supervisors (Janus and Claus) will be around from 9.00

Thank you to all the students of 27820 PhD course 2013. It was a great pleasure having you here!

Class of 2013


Here we will put changes and errors we detect in the documentation. This document will be updated as the course is progressing (latest update date is shown.

Participant List

Download the 2013 participant List.

Course manuals

Manuals for the excersises


Biofilm System 1
E.coli development: Download (updated Aug 7) (PRINTED)
Biofilm System 2
P. aeruginosa: FISH and Cell counting: Download (PRINTED)
Biofilm System 3
P. aeruginosa: Differentiation and colistin tolerance: Download (PRINTED)
Biofilm System 4
Monitoring gene expression in microbial biofilms: Download (PRINTED)
Biofilm System 5
Free exercise: Download
Microbial Diagnostics
Chip technlology and antibiotics screening (Exercise 6): Download (PRINTED)
Presentation of results (Exercise 7)
How to present on the last day: Download

Supplementary manuals and recipes

  • Biofilm Media Download
  • Biofilm general manual Download
  • FISH Manual Download
  • Embedding and FISH on flow chamber biofilms Download
  • Adhesion Microtiter Tray Assay (Crystal Violet) Download
  • Quorum Sensing assays (from course 27254) Download
  • LIVE/DEAD kit manual Download
  • Motility assay Download
  • Cheat sheet for making Motility assay plates (Excel sheet) Download
Diagnostic Excersise
Manuals for the BIOLOG machine
  • OmniLog ID User Guide Download (See pages 42-44)
  • OmniLog PM User Guide Download
  • GEN III Database List and Characteristics Download
  • MicroStation System Version 4.2 User Guide Download

Papers of relevance

Scientific Papers

Note: These papers are also included in the zipped package which you can download below.

Supplementary Papers

(The papers are in a zip file on our secure server. Password protected)

Result Data Files

Your own presentations!

  • Download all the presentations from 2013 here

Data files

Biofilm System 1

Biofilm System 2

Biofilm System 3

Biofilm System 4

Biofilm System 5

Diagnostic Exercise

List of Speakers and Notes

Powerpoint notes will be placed here as they become available

Speakers and teachers

Course mediators

  • Claus Sternberg
Practical information slides
Comstat 2 introduction
FISH slides
Presentation of the results
  • Janus Haagensen
Biofilms and Tools
  • Lea Madsen
  • Fatima Yousef

Other Speakers

  • Lars Jelsbak
Pseudomonas in CF patients
  • Søren Molin
Diversity Switching in P.aeruginosa in CF patients
  • Anders Folkesson
Biofilm Formation and antibiotics. Also includes intro to BF system 4
  • Claus Moser
Animal Models of Biofilm Infections
  • Lars Behrend
Microsensors in the Environment
  • Klaus Kirketerp-Møller
Biofilms in chronic wounds
  • Thomas Bjarnsholt
Biofilms in chronic bacterial infections and Quorum sensing

Download Software

Comstat 2

First - go to and get all nessesary support files. Please read the instructions in the HOW-TO-INSTALL document.

When all that has been done, get the comstat2 program file (Comstat2_.jar): here .

Note: When you download the comstat2 program file we imply that you accept the license conditions which are set out on, namely:

  • That you will not distribute the program to others, but refer them to where they can obtain a copy for free
  • That you will acknowledge the use of Comstat2 in any publication that will be written using Comstat2 generated data in any form.

Imaris 7.6

Download the program file appropriate for your system:

Install the program file. Save the license file somewhere on your computer and when you start Imaris, use the browse button in the license dialog box shown to point to the demo license file. The demo license is valid until the end of August 2013. If you need testing after that, please contact Bitplane.
See also: Installation Instructions on

In order to enable Imaris to communicate with MATLAB, ImageJ and Java, you need to download and install these two helper programs:
Note: In this course it is unlikely that you will need the MATLAB/Java functionality of Imaris. But in case you want to check it out we include the links.

and the MATLAB Compiler Runtime (MCR). Please download the MCR version appropriate for your system:

You may also want to download SceneViewer which allows you to show Imaris stacks without a full license. You will, however, need to obtain a permanent license directly from Bitplane, Inc. The program will show how to get that when the demo license has expired.

Brochures for Imaris:

Zeiss ZEN File Viewer

You can download the viewer program for native Zeiss confocal image stacks here

Leica LAF Viewer

You can download the viewer program for native Leica confocal image stacks here

Analysis of AT chip Images

A plugin for ImageJ have been developed to analyse the images from the AT Reader. The plugin evaluate the pattern and produce the corresponding "bar code". The plugin can be downloaded by clicking here (AT Chip Analyzer Plugin, and a manual is provided by clicking here (plugin manual).

In short: First install ImageJ ( Then place the plugin in the plugin folder of ImageJ. And you are then able to run the plugin from ImageJ's plugin menu.

Video files

The flow cell assembly and flow system setup has been documented in JoVE (Journal of Visualized Experiments).
We have made this paper freely accessible without subscription:

Web links

Personal tools