Fully automated cellular-resolution vertebrate screening platform with parallel animal processing

The zebrafish larva is an optically-transparent vertebrate model with complex organs that is widely used to study genetics, developmental biology, and to model various human diseases. In this article, we present a set of novel technologies that significantly increase the throughput and capabilities of our previously described vertebrate automated screening technology (VAST). We developed a robust multi-thread system that can simultaneously process multiple animals. System throughput is limited only by the image acquisition speed rather than by the fluidic or mechanical processes. We developed image recognition algorithms that fully automate manipulation of animals, including orienting and positioning regions of interest within the microscope's field of view. We also identified the optimal capillary materials for high-resolution, distortion-free, low-background imaging of zebrafish larvae.National Institutes of Health (U.S.) (Director's New Innovator Award DP2 OD002989)National Institutes of Health (U.S.) (Transformative Research Award R01 NS073127)David & Lucile Packard Foundation (Award in Science and Engineering)Broad Institute of MIT and Harvard (SPARC Award)Foxconn International Holdings Ltd.Athinoula A. Martinos Center for Biomedical Imaging (Training Grant

High-throughput hyperdimensional vertebrate phenotyping

Most gene mutations and biologically active molecules cause complex responses in animals that cannot be predicted by cell culture models. Yet animal studies remain too slow and their analyses are often limited to only a few readouts. Here we demonstrate high-throughput optical projection tomography with micrometre resolution and hyperdimensional screening of entire vertebrates in tens of seconds using a simple fluidic system. Hundreds of independent morphological features and complex phenotypes are automatically captured in three dimensions with unprecedented speed and detail in semitransparent zebrafish larvae. By clustering quantitative phenotypic signatures, we can detect and classify even subtle alterations in many biological processes simultaneously. We term our approach hyperdimensional in vivo phenotyping. To illustrate the power of hyperdimensional in vivo phenotyping, we have analysed the effects of several classes of teratogens on cartilage formation using 200 independent morphological measurements, and identified similarities and differences that correlate well with their known mechanisms of actions in mammals.National Institutes of Health (U.S.) (NIH Transformative Research Award (R01 NS073127))National Institutes of Health (U.S.) (NIH (R01 GM095672)National Institutes of Health (U.S.) (NIH Director’s New Innovator award (1-DP2-OD002989))Howard Hughes Medical Institute (International Student Fellowship)Broad Institute of MIT and Harvard (SPARC grant)David & Lucile Packard Foundation (Award in Science and Engineering