# Scientific Software Projects

I am a Professor in Physics, and a Canada Research Chair in Biophotonics, member of the Centre d'Optique Photonique et Laser. I am based at the Centre de Recherche Universite Laval Robert Giffard where I focus on live animal imaging for neuroscience pathologies such as multiple sclerosis, chronic pain and nerve injuries.

Group web site: http://www.dcclab.ca/

Before that, I worked as a post-doctoral research fellow at the Wellman Centre for Photomedicine (Massachusetts General Hospital, Harvard Medical School) in Boston with Dr Charles Lin. I also trained as a post-docotoral fellow at the Ontario Cancer Institute in Toronto with I.A. Vitkin and Dr. B. C. Wilson. I originally graduated in laser and condensed matter physics from the University of Toronto. Over the years, I have written software to make my life easier in my research. This web site is here for mostly historical reasons, since a few publications refer to it, and other pages also link to it. It may eventually get folded back into www.dcclab.ca.

**Polarized light propagation in tissue with Monte Carlo**

Here you will find a discussion, an article and a computer implementation of the Monte Carlo algorithm for polarized light propagation in tissues.

**THz propagation article and computer code**

I recently wrote an article in the*Journal of the Optical Society of America*describing a simple plane wave decomposition technique for THz propagation that leads to analytical expressions for describing**real-life, experimental**THz pulses both in the near- and far-field, including the effects of dispersion, interfaces, diffraction, and that is valid for any radiation source (optical rectification or antennas). The publication might appear daunting at first, but the end result is a few equations that can be computed easily, without any finite difference methods (i.e. it is just a 1D integral and a Fourier transform). You can get the preprint and the computer code here. Feel free to contact me for questions at dccote@novajo.ca.

**ABCD**

A Macintosh program to propagate gaussian laser beams through standard optics based on the ray matrix formalism (also known as ABCD matrices). Register online with Kagi.

**BiblioTeX**

Database for managing BibTeX references. Register online with Kagi.

**Data Reader**

Tired of reading data off a graph with a ruler and a pen ? You have better things to do (so do I). This is why Data Reader was written: it allows you to obtain the data from a graph by clicking on the points and save it into an ASCII file for use in a fitting program, spreadsheet or plotting package. Register online with Kagi.

**Commented Fast Fourier Transform algorithm:**

How does the FFT algorithm actually work ? You have read it over and over, but you can't understand the FFT algorithm implementation. You looked at Numerical Recipes (available online by the way) but since it is a port of the Fortran-style routine, you get confused with the C indices (or vice-versa). You can download the source file fourier.cp as well as the header file fourier.h of a commented FFT routine in C++.