Shaoying (Kathy) Lu
Project Scientist of Bioengineering and Institute of Engineering in Medicine
University of California, San Diego
Seminar Information
Investigation of dynamic molecular activities in live cells often requires the visualization and quantitation of fluorescent ratio image sequences with subcellular resolution and in high throughput. Here we describe a convenient, accurate, and efficient open-source software package, Fluocell, to visualize pixelwise ratiometric images and calculate ratio time courses in high throughput fashion at subcellular resolutions. Fluocell also provides group statistics and kinetic analysis functions for the quantified time course, as well as 3D structure and function visualization for ratio images. The application of Fluocell is demonstrated by the ratiometric analysis of intensity images for several Förster (or fluorescence) resonance energy transfer (FRET)-based biosensors, allowing efficient quantification of dynamic molecular activities in a heterogeneous population of single-live cells. Meanwhile, spatiotemporal molecular transport, interaction, and activity are of fundamental importance in biology and medicine. To construct subcellular diffusion maps based on bio-imaging data, we develop and characterize a general optimization framework with diffusion equation constraints (OPT-PDE). We demonstrate the general usability of the solver in recovering spatially heterogeneous and anisotropic diffusion maps with computer-simulated bio-images. The results indicate that the solver can accurately recover piecewise-constant isotropic and anisotropic diffusion coefficients, with efficient and robust convergence. Taken together, our work highlights the power of computational analysis in quantitatively evaluating the biochemical and biophysical signals in single live cells, with important applications in biomedical sciences.
Dr. Lu is currently a Project Scientist in Department of Bioengineering at University of California, San Diego. Dr. Lu received a Ph. D. in computational mathematics from UCSD (2004). She was a postdoctoral fellow working in the Departments of Bioengineering and Mathematics. Later she worked at University of Illinois Urbana-Champaign as a research assistant professor (2005-2013). She is a recipient of DMS/NIHGMS initiative award at the interface of mathematics and biology. Dr. Lu works in the areas of image-driven mathematical and systems biology. She develops computational algorithms and statistical inference methods for the high throughput analysis of biological imaging data, with applications in T cell immunology and cancer cell drug resistance.