Imaging deep-tissue morphogenesis at… (R35GM155424) – Project Grant to University Of Texas At Austin

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.

Action	Obligated	Date
Amendment	$369,346	Aug 13, 2026
Amendment	$337,554	Jul 29, 2025
Original award	$337,326	Sep 18, 2024

Imaging deep-tissue morphogenesis at whole-organism scales

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