Extended Data Fig. 1: Workflow of the BiofilmQ graphical user interface for image processing and parameter quantification.
From: Quantitative image analysis of microbial communities with BiofilmQ
a, First, images have to be imported; a wide range of formats are supported, including 3D image formats, and TIF image sequences, based on the Bio-Formats toolbox36. b, Next, optional pre-processing steps including image time series registration, filtering for noise reduction, and colony separation can be performed to improve the segmentation results. c, Biomass must be distinguished from background, which can be performed automatically using different thresholding algorithms, or semi-manually, or by importing a segmented binary image from other image analysis tools. After the segmentation of the biofilm volume, the biofilm can be dissected into cubes of a user-defined size, or a single-cell segmentation can be imported. d, Quantitative characterization of the biofilm is achieved via the parameter calculation for the biofilm as a whole, and for each cube in the biofilm. e, Parameter quantifications and biofilm structural analysis can be exported either as spreadsheets, flow-cytometry data format, graphs, or as input data for a 3D rendering software. f, The extensive data visualization capabilities that are built into BiofilmQ are described in Extended Data Fig. 2. Key steps in the BiofilmQ workflow are further described in Supplementary Note 1.
