Short Course 2014

Second Annual National Short Course in Computational Biophotonics, 4-8 August 2014

Each day of the short course is structured around a biomedical “theme”; together these themes span a broad range of current biomedical research activity. Morning sessions will feature two lectures, the first providing biomedical context for the daily theme and the second describing models and computational approaches keyed to the theme. Afternoons will be devoted to demonstrations of the daily biomedical technology, hands-on computational laboratories using the unique Virtual Tissue Simulator computational platform, trainee presentations, and moderated discussions. The second Short Course builds upon the success of annual Virtual Photonics Workshops and the inaugural short course held at UC Irvine.

VTS GUI Application

The version of the GUI used in the short course can be accessed here (Note: This is a Silverlight application which may no longer work in your browser, the labs can be completed using our current software from GitHub but be aware that the instructions may differ slightly).


The Short Course Flyer can be found here

The complete Short Course Schedule can be found here

A list of Short Course References can be found here

The complete list of Short Course Videos and Lecture Materials will be available here after the event.

List of Short Course participants

Day 1 -- Monday, 4 August 2014

Interaction of Light with Biological Systems

Lecture 1: Radiative Transport Fundamentals, Professor Vasan Venugopalan pdf » view online video

Lecture 2: Stochastic Solvers for Radiative Transport, Professor Jerry Spanier pdf » view online video

Tutorial: Use of the Virtual Tissue Simulator System, Ms. Lisa Malenfant and Dr. Carole Hayakawa pdf

Laboratory A: Tissue Absorption and Scattering Spectra

Laboratory B: Monte Carlo Simulations of Radiative Transport

Day 2 -- Tuesday, 5 August 2014

Biological Microscopy

Lecture 3: Optical Microscopy in Cells and Tissues, Professor Eric Potma pdf » view online video

Lecture 4: Modeling Focused Beam Propagation in Scattering Media, Dr. Janaka Ranasinghesagara pdf » view online video

Laboratory C: Mie Scattering and Analysis of Focused Beam Propagation

Day 3 -- Wednesday, 6 August 2014

Optical Dosimetry and Determination of Ex Vivo Tissue Properties

Lecture 5: Light Fields Generated by Collimated Beams, Professor Vasan Venugopalan pdf » view online video

Lecture 6: Inverse Adding Doubling for Recovery of Ex Vivo Tissue Properties, Dr. Rolf Saager pdf » view online video

Laboratory D: Inverse Adding Doubling Data Analysis

Day 4 -- Thursday, 7 August 2014

Diffuse Optics Using Steady Illumination

Lecture 7: NIR Endogenous Wide-Field Imaging for the Clinic, Professor Sylvain Gioux pdf » view online video

Lecture 8: Determination of Tissue Properties from Optical Signals, Dr. Carole Hayakawa pdf » view online video

Laboratory E: Analysis of Spatially Resolved and Spatial Frequency Domain Signals

Day 5 -- Friday, 8 August 2014

Diffuse Optics Using Time-Varying Illumination

Lecture 9: Biomedical Appplications of Diffuse Optics, Professor Bruce Tromberg pdf » view online video

Lecture 10: Analysis of Diffuse Optical Signals, Dr. Albert Cerussi pdf » view online video

Laboratory F: Analysis of Temporally Resolved and Temporal Frequency Domain Signals