Imaging biofilms in three dimensions: modalities, quantitative readouts, and the path to four-dimensional measurement

Abstract

Biofilms are spatially structured microbial communities whose architecture, chemistry, mechanics, and cellular states evolve over time. Bulk assays and two-dimensional projections remain useful, but cannot alone resolve how these properties vary with depth or change during growth, treatment, dispersal, and regrowth. Imaging provides complementary routes to three-dimensional measurement: fluorescence microscopy supplies molecular, taxonomic, and functional specificity; optical coherence tomography resolves mesoscale architecture and dynamics; quantitative phase imaging and holotomography report refractive index and biomass-related changes; Raman methods provide chemical and metabolic contrast; and Brillouin microscopy probes mechanical response. We compare these modalities using four independent descriptors-contrast provenance, live volumetric capability, perturbation, and demonstrated biofilm use-and connect their signals to quantitative biological readouts. No single modality simultaneously maximizes spatial coverage, resolution, acquisition speed, molecular specificity, and low perturbation. Implementations from any contrast class can serve as a longitudinal backbone when perturbation is empirically controlled at the relevant spatial and temporal scale, while molecularly specific measurements remain indispensable for identifying species, molecules, and functional states. We therefore frame four-dimensional biofilm measurement as a validated measurement architecture that integrates a low-perturbation volumetric backbone with spatially registered, molecularly specific measurements acquired continuously or at predefined validation points. Achieving this integration will require compatible cultivation formats, controlled imaging dose, shared quantitative parameters, and robust cross-modality registration.