Welcome to the BiofilmQ documentation!

BiofilmQ is an advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and time. It can work with many different kinds of 3D biofilm images, including flow-chamber biofilms, colonies on agar, pellicles, and aggregates.

BiofilmQ is based on a graphical user interface and does not require programming expertise or prior knowledge of image analysis.

BiofilmQ has a unique approach to quantifying biofilm properties in space and time: BiofilmQ does not require the optical resolution of single cells. Instead, BiofilmQ uses a different segmentation approach, based on dividing the biofilm biovolume obtained by threshold-based 3D segmentation into cubic pseudo-cells. Each cube is treated as a single cell, for which fluorescence, architectural, spatial, and many more properties are measured. By using this cube-based approach, it is possible to perform biofilm image cytometry (analogious to flow cytometry, but with spatial features), based on the quantification of many parameters for pseudo-cells.

BiofilmQ provides a powerful analysis and plotting functionality for presenting the data from each pseudo-cell cube. It is possible, e.g. to generate biofilm kymographs, demographs, and to generate flow-cytometry-like datasets, including population gating, which include not just fluorescence and structural properties of cells, but also spatial properties within the biofilm.

The easy-to-use analysis and visualization features enable you to generate high-quality data figures without any programming skills.

For advanced users with programming expertise, all features are fully scriptable (in MATLAB) for batch processing of large datasets.

Example image from BiofilmQ


Video tutorials

Join the forum!

We actively answer questions in the image.sc forum. If you have technical questions about BiofilmQ or find bugs, please use the image.sc forum.

More information

About us

BiofilmQ was developed by Raimo Hartmann, Hannah Jeckel, Eric Jelli, and Knut Drescher at the Max Planck Institute for Terrestrial Microbiology and the Department of Physics of the Philipps-Universität Marburg. For non-technical questions you can reach us at biofilmQ@gmail.com. For technical questions, problems, suggestions for improvements please use the image.sc forum.

How to cite

Please use the following reference for citing this software after you have used it:

Quantitative image analysis of microbial communities with BiofilmQ.
Raimo Hartmann*, Hannah Jeckel*, Eric Jelli*, Praveen K. Singh, Sanika Vaidya, Miriam Bayer, Daniel K.H. Rode, Lucia Vidakovic, Francisco Díaz-Pascual, Jiunn C.N. Fong, Anna Dragoš, Olga Besharova, Janne G. Thöming, Niklas Netter, Susanne Häussler, Carey D. Nadell, Victor Sourjik, Ákos T. Kovács, Fitnat H. Yildiz, Knut Drescher.
(* equal contributions)
Nature Microbiology (2021). https://doi.org/10.1038/s41564-020-00817-4


We would like to acknowledge the authors of the following MATLAB File Exchange contributions: