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.