The tools required for comprehensive and quantitative studies of development and nervous system function in vertebrate and higher invertebrate species have become available only recently. Key technologies are high-speed light sheet-based fluorescence microscopes and automated approaches to computer vision.
We design and apply new light-sheet microscopes, such as our SiMView and hs-SiMView microscopes for simultaneous multi-view imaging (Tomer et al. 2012, Nature Methods; Lemon et al. 2015, Nature Communications) as well as our IsoView microscope for spatially isotropic high-speed imaging (Chhetri et al. 2015, Nature Methods), to record entire zebrafish, mouse and fruit fly embryos in vivo and with subcellular resolution. The light sheet concept employed in such microscopes provides fast three-dimensional imaging of large specimens at high spatial resolution and with an excellent signal-to-noise ratio, while keeping photo-bleaching and photo-toxic effects at a minimum. Owing to this combination of imaging capabilities, we can take full advantage of advanced fluorescent marker strategies and simultaneously visualize cell movements, cell divisions, cell shape dynamics, and gene expression patterns in entire living embryos for up to several days of continuous high-speed imaging. Our imaging methods furthermore allow us to study the emergence of patterned activity in the nervous system and measure whole-brain neural activity at the single-cell level (Ahrens et al. 2013, Nature Methods; Lemon et al. 2015, Nature Communications).