MRI: Development of high-throughput light sheet fluorescence microscopy

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An award is made to the University of Oregon to develop an instrument capable of three-dimensional imaging of large numbers of living multicellular specimens, especially embryos and larvae of zebrafish that serve as models for the study of many biological processes. Observation of cellular interactions during early development, wound healing, disease progression, and many other events has been enormously beneficial to our understanding of both normal and aberrant biological function. We have lacked methods, however, to apply recently developed advanced three-dimensional imaging techniques to large numbers of specimens, limiting both the rate of experiments and the statistical robustness of results. This project addresses this challenge through the development of new instrumentation. Implementing this research will provide valuable cross-disciplinary training for graduate students and undergraduates, as it fosters the development of skills in optics, device control, computational data analysis, microbiology, and developmental biology. In addition to research, the instrument will be used in activities related to summer undergraduate research internships and a day camp that the PI has co-organized for several years that exposes socioeconomically disadvantaged high school students to science. More broadly, the instrumentation developed by this project will provide previously unseen views of cells, tissues, and organs in living animals that can underpin new perspectives on health and disease.In recent years, advanced three-dimensional imaging methods have provided deep insights into the spatial and temporal arrangements of cells. A high-resolution, three-dimensional microscopy method known as light sheet fluorescence microscopy has proven itself to be particularly powerful for imaging living specimens over many-hour or several-day durations. This and similar methods, however, have suffered the limitation of very limited throughput, capable of imaging one or at most a few specimens during an experimental run. It is increasingly apparent that the high variability of developing organisms, and the subtleties of mechanisms governing them, call for studies that can apply high-precision imaging to much larger numbers of specimens. This motivates the instrument we will design and build, which integrates high-throughput specimen handling and real-time computational image analysis with light sheet fluorescence microscopy. Specific imaging targets that we will design our instrument to be capable of imaging and analyzing include the gut microbiota, immune system, and groups of neurons. Beyond this, there is a large list of systems for which long-duration three-dimensional imaging with high statistical power would be useful, implying a sizeable impact for our instrumentation.