Just as the phenotypically different cells that make up multicellular organisms are distributed in tissues with structures that embody specific functions, microbial cells with different metabolic functions form unique spatial structures and coordinate their activities as multicellular units, e.g. biofilms. Fundamentally, microbial communities differ from eukaryotic tissues because their cellular constituents may be genetically distinct; in fact, up to hundreds of different species may be present in a single biofilm. Any number of probes may be designed to identify the different species present in a community; however, the ability to unambiguously distinguish more than a few different labels in a single fluorescence image has been severely hampered by the excitation cross-talk and signal bleed-through of fluorophores with highly overlapping excitation and emission spectra.
I am interested in visualizing the systems-level structure of complex microbial communities associated with the human body. To achieve this goal, I am developing spectral imaging techniques and computational algorithms to greatly expand the number of distinguishable fluorophores in a single image of labeled microbes.