Welcome to the Comstat 2 homepage.

From this page you can sign up to receive the software, read the license conditions and find out
how to reference the use of Comstat 2 correctly.
What is Comstat2?

Comstat is a program that analyzes image stacks of biofilms recorded by confocal microscopes. It can extract a number of quantitative parameters from biomass to fractal dimensions. The program does not contain any statistical calculation methods.

Comstat was developed by Arne Heydorn and Prof. Bjarne Ersbøll in 2000 [1] as a MATLAB© script and has for many years been one of the preferred tools for biofilm quantification. In 2008 Martin Vorregaard ported and expanded the software [2] so it would run independently from MATLAB© but instead to utilize the public domain software Java© and the Image processing environment ImageJ (http://imagej.nih.gov/ij/) with the add-on package LOCI Tools (http://loci.wisc.edu/software/bio-formats). Comstat v. 2.1 is the latest build of this ImageJ plugin and this version was compiled and released July 1st 2015.

How to get Comstat2

Please follow this link to go to the sign up page. What you will have to do is to read the conditions, then add your name to the mailing list (you can unsubscribe at any time), confirm your e-mail addres and then download the software.
Main control panel

How to correctly cite the use of Comstat2

When publishing work which includes analyses made by Comstat2 we request that you will use these three references:
  • Heydorn, A., et al., Quantification of biofilm structures by the novel computer program COMSTAT. Microbiology, 2000. 146 ( Pt 10): p. 2395-407.
  • Vorregaard, M., Comstat2 - a modern 3D image analysis environment for biofilms, in Informatics and Mathematical Modelling. 2008, Technical University of Denmark: Kongens Lyngby, Denmark
  • www.comstat.dk
We are in the process of making a paper about Comstat2 which will replace these. When that happens the information on this page will be updated and a news bulletin will be sent to the mailing list.

License terms

Comstat2 remains the property of the Technical University of Denmark. You can use the software for free by obeying the the license terms below:
  • You may use Comstat2 for free for any non-commercial work related to biofilm analysis
  • You may use Comstat2 on as many computers you like
  • You must use the three references above in any publication you make using Comstat2 *
  • You may NOT pass on Comstat2 to someone else (they can get their own copy here for free)
  • You may NOT sell or lease Comstat2 or in any other way make a financial benefit from the use of Comstat2
* The required references will change when out paper on Comstat2 is published - so please check back here before you submit your manuscript.


This software is provided "as is" and any expressed or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the regents or contributors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.


You can contact us at comstat@comstat.dk


If you prefer COMSTAT1 which runs as a MATLAB© script, please go to www.imageanalysis.dk
MATLAB© is a trademark of The Matworks Inc., Natick, MA