Short Course 2016

Fourth Annual National Short Course in Computational Biophotonics, 1-5 August 2016

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 fourth Short Course builds upon the success of annual Virtual Photonics Workshops and the previous Short Courses 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, 1 August 2016

Course Intro and Scattering Fundamentals

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

Lecture 2: Optical Coherence Tomography & Scattering Contrast, Dr. Joseph Jing pdf » view online video

Laboratory A: Tissue Absorption and Scattering Spectra

Lecture 3: Modeling Focused Beam Propagation in Scattering Media, Dr. Janaka Ranasinghesagara pdf » view online video

Laboratory B: Mie Scattering and Analysis of Focused Beam Propagation

Day 2 -- Tuesday, 2 August 2016

Monte Carlo Methods

Lecture 4: Monte Carlo Fundamentals, Professor Jerry Spanier pdf » view online video

Lecture 5: Monte Carlo Extensions and Application, Dr. Carole Hayakawa pdf » view online video

Tutorial: Use of the Virtual Tissue Simulator System, Ms. Lisa Malenfant pdf 

Laboratory C: Monte Carlo Simulations: Error Analysis

Laboratory D: Monte Carlo Simulations: Spatial and Angular Distributions

Evening Presentation: “Biophotonics in Action: African Scientists Initiatives to Fight Against Malaria”, Jeremie Zoueu pdf and Aboma Merdasa pdf

Day 3 -- Wednesday, 3 August 2016

Optical Dosimetry and Determination of Ex Vivo Tissue Properties

Lecture 6: Light Fields Generated by Collimated Beams, Professor Vasan Venugopalan pdf » view online video

Lecture 7: Inverse Adding Doubling for Recovery of Ex Vivo Tissue Properties, Dr. Rolf Saager pdf » view online video

Laboratory E: Analysis of Integrating Sphere Data

Day 4 -- Thursday, 4 August 2016

Diffuse Optics Using Steady Illumination

Lecture 8: Spatially-Resolved and Spatial Frequency Domain Methods and their Biomedical Application, Dr. David Cuccia pdf » view online video

Lecture 9: Determination of Tissue Properties from Optical Signals, Dr. Carole Hayakawa pdf 

Laboratory F: Recovery of Tissue Properties from Spatially-Resolved and Spatial Frequency Domain Reflectance Measurements

Day 5 -- Friday, 5 August 2016

Diffuse Optics Using Time-Varying Illumination

Lecture 10: Biomedical Appplications of Diffuse Optics, Professor Bruce Tromberg pdf page1-38 and pdf page 39-64 » view online video

Lecture 11: Analysis of Diffuse Optical Signals, Professor Vasan Venugopalan pdf

Laboratory G: Recovery of Tissue Properties from Time-Resolved and Temporal Frequency-Domain Reflectance Measurements