UQ-bio Summer School

Prof. Doug Shepherd

Prof. Doug Shepherd 

Department: Physics

University: Arizona State University

Lecture: Single-Particle Tracking (Scalable, high-speed 3D imaging of molecular biology in action)

Date: Friday June 3 @ 09:00 – 10:00

Abstract: Continued advancements in biomedical optical microscopy and fluorescent labeling techniques have enabled multi-dimensional visualization of biology in action at the single-molecule level.  Many of these imaging experiments across these efforts rely on multiplexed fluorescence molecular imaging. The quality and confidence of biological knowledge extracted from the resulting digital images depend on the molecular labeling strategy, the optical microscope’s design, and detector choices. Compromises are often necessary to achieve the required volume, imaging speed, number of molecules, samples, or other biologically driven experimental design criteria. Such compromises inevitably increase uncertainty when quantifying molecular identity and dynamics. I will discuss the foundations of quantitative 3D molecular imaging and our recent efforts to improve the optical methods and computational tools used for high-speed, high-resolution, multiplexed, and volumetric imaging.

Links to codes or supplemental information:

Presenter Biosketch: Douglas Shepherd was born in Albuquerque, NM and went to the University of California Santa Barbara as a undergraduate where he studied physics. After a break from academia, he pursued his doctorate in single-molecule physics at Colorado State University under the direction of Profs. Alan Van Orden (Chemistry) and Martin Gelfand (Physics). He went onto a postdoctoral fellowship in the Center for Integrated Nanotechnologies (CINT) and Center for Nonlinear Studies (CNLS) at Los Alamos National Laboratory. Working with Drs. James Werner (CINT) and Brian Munsky (CNLS), he built new tools to measure and model gene regulation in pathogenic bacteria.

Shepherd directs the Quantitative Imaging and Inference (QI2) lab, which he formed at the University of Colorado Denver Anschutz Medical Campus in 2013. In 2019, Shepherd and the QI2 lab relocated to the Center for Biological Physics and Department of Physics at ASU. The QI2 lab develops, adapts, and uses high-throughput fluorescence imaging methods and statistical inference tools to build a quantitative understanding of how cells organize into tissue and organs. The QI2 lab is a contributing member of the Chan Zuckerberg Initiative Human Cell Atlas, with a particular interest in highly-multiplexed single-molecule mapping of gene expression to infer cell type throughout the human lung.

Presenter Website: Shepherd Laboratory

Presenter Email: douglas.shepherd@asu.edu

[Link to Slides]