Description: splash1


Welcome to the home of COMSTAT 2




COMSTAT 2 is a development of our original Comstat version 1 which was depending on the MATLAB software package.   Our new version has several improvements, apart from being independent of third-party commercial software. Now it is menu-driven and can analyze more native confocal image formats, notably the Zeiss LSM format and the Leica LIFF formats (see also latest news).


Comstat2 runs as a Java program under the ImageJ shell, using a bioformat reader plug-in, LOCI tools (Please do not download LOCI tools from this link  but use the version we direct you to (see the blog), or Comstat may not work as expected). Being a Java program, Comstat2 should be able to run on any platform that supports Java i.e. Microsoft Windows, Apple MacOS, Linux etc.


Comstat2 code is based on Comstat1 and most algorithms are derived from the original MATLAB script. Some functions have been rewritten, and some new has been added. Comstat 1 is still available, see below.


Project Status


We have now a nearly finished version. We have not fully debugged it yet but it is more or less ready, so you can try it out if you like.


See also our blog which contains latest news and bug lists etc: Click here



Getting Comstat2


We are taking requests for the program. It will still be considered beta software until the program has been fine polished. However we can not currently find the resources to do so. Also we are unable to provide technical support. If this is acceptable for you, you can mail us and we will send you the Comstat program when it is ready. Send mail to Comstat (at) with your request. In the mail you must indicate that:


·       You will not redistribute the program to others, but refer new users to this site ( where they can obtain a copy for free.


·       You will acknowledge the use of Comstat2 in any publication that will be written using Comstat2 generated data in any form. The proper reference can be found in the readme file that accompanies the program.


·       Also please indicate your affiliation and preferred contact e-mail address (for our records and so we can notify you of updates)


Expect up to one week before you get the program by mail.


Please note that although Comstat2 is public domain (not open source) we ask you to respect the above conditions.



Getting Comstat 1 for MATLAB


If you need Comstat 1 for MATLAB, please contact Arne Heydorn:

Email: aheydorn1 (at)

Comstat1 has a dedicated website with further information:


Comstat 2 tasks not yet ready


·       User manual

·       Sample test data

·       Description of how to make you own Comstat2 plugins

·       List of frequently asked questions

·       Submission of the manuscript describing Comstat2

·       Link collection for Comstat users

·       Publication list (uses of Comstat1 and Comstat2)



Further information


If you want to know what Comstat can do (version 1), please see these papers:


Heydorn, A., Nielsen, A.T., Hentzer, M., Sternberg, C., Givskov, M., Ersbøll, B.K., Molin, S. (2000) Quantification of biofilm structures by the novel computer program COMSTAT. Microbiology 146(10): 2395-407


Heydorn, A., Ersbøll, B.K., Hentzer, M., Parsek, M.R., Givskov, M., and Molin, S. (2000) Experimental Reproducibility in Flow-Chamber Biofilms. Microbiology 146(10): 2409-15


Latest news


2014: Currently the program is not further developed. This may happen in future, but at the moment we do not have the resources (economic or human) to do this. If we are making a new version it will be announced on this web site.


The blog has opened. Here you can find latest news and bug lists etc. Click here.


Development Team


Martin Vorregaard (Java programming, v2)

Arne Heydorn (MATLAB programming, v1)

Janus Haagensen

Liang Yang

Alex Toftgaard Nielsen

Morten Hentzer

Michael Givskov

Matt Parsek


Bjarne Kjær Ersbøll

Sren Molin

Claus Sternberg




Description: DTU_logo

Technical University of Denmark

Department of Systems Biology

Center for Systems Microbiology

Building 301

DK-2800 Lyngby


Claus Sternberg, Assoc. Prof.

E-mail: cst (at)


(note: do not use this e-mail to request Comstat  use Comstat (at)


Last update April 11 2014