Imaging deep-tissue morphogenesis at whole-organism scales

Project Summary/Abstract Morphogenesis of biological tissue is a rich and complex process in which coordinated interplay between molecular and mechanical stimuli progressively shapes an organism. Successful orchestration of this process enables an organism to develop from a single cell into complex arrangements of tissues and organs comprising up to trillions of cells. Optical

imaging has emerged as a tool of fundamental importance in studying morphogenesis. Compared to other imaging techniques used to study morphogenesis, such as X-ray or magnetic-resonance imaging, optical imaging enables non-

ionized live imaging of biological samples with sub-micron resolutions, morphological and molecular-specific contrast, and

high-speed data capture. Unfortunately, optical imaging within biological tissue is limited by optical scattering. Classical microscopes form images by focusing unscattered light, and achieve imaging depths up to hundreds of microns in tissue. Confocal and multiphoton microscopes achieve longer imaging depths by selectively illuminating and/or detecting only

with the unscattered component of the total light, which is detectable up to ~1 mm within biological tissue. Unfortunately, light from longer depths is dominated by scattering, which scrambles sample-specific information and is generally considered unusable. This is a major obstacle for imaging tissue morphogenesis within developing

organisms, many of which reach sizes up to multiple millimeters during their developmental cycle. Recent optical imaging technologies such as adaptive optics have demonstrated promising results in correcting for tissue scattering to achieve

enhanced imaging depths – however, they are still limited to small fields-of-view and are generally not suitable for imaging 3D morphogenesis across whole organisms composed with dense heterogenous tissue. We aim to establish a research program that develops computational microscopy technologies that overcome the

challenge of tissue scattering, to achieve large-scale 3D imaging of tissue morphogenesis. To accomplish this, our major

research thrusts will be to (1) develop computational scattering models that describes how light travels through scattering

tissue. These models will be used with gradient-based inverse-solvers to reconstruct the scattering sample’s 3D refractive- index and fluorescent distributions, enabling joint morphological and molecular imaging, respectively; (2) design multimodal optical hardware systems that combine refractive-index tomography with wavefront-shaped fluorescent

scattering tomography, to enable 3D co-registered morphological and molecular imaging. These systems will be designed to achieve millimeter-scale fields-of-view with micron-scale resolution, to enable visualization of entire embryos with subcellular resolution; and (3) apply our computational imaging developments to study in-vivo deep-tissue morphogenetic

processes. Specifically, we will quantitatively and at whole-organism scales study the interplay between collective cell movements and the planar cell polarity signaling pathway in early-stage Zebrafish and Xenopus embryos, which is recognized to be significant, but remains poorly understood.