A list of some useful links to other resources.

Affilliations

• Laboratory for Optical and Computational Instrumentation
• McPherson Eye Research Institute

Collaborators

• Alf Dubra at Stanford University
• Joe Carroll at Medical College of Wisconsin
• Gill McLellan Lab at UW-Madison
• Kevin Elicieri (LOCI) at UW-Madison
• Paul Campagnola Lab at UW-Madison
• Vadim Backman Biophotonics Lab at Northwestern University

Code and software

• List of Optical Design Software: http://www.optenso.com/links/links.html
• Code for Monte Carlo, Mie scattering, and inverse scattering: http://omlc.ogi.edu/software/
• Andrew Radosevich's homepage with matlab tools and opensource Monte Carlo for simulating or processing EBS data

Writing

• Latex for NIH grants: http://www.cs.duke.edu/brd/NIH/tips/
• Latex for NSF grants: https://math.mit.edu/services/grants/index.php

• Bibtex entries from ISBN numer: http://manas.tungare.name/software/isbn-to-bibtex/
• Bibtex entries (or Endnote, Refman, Refworks, etc) can be generated by http://scholar.google.com by editing preferences

Code

Code, programs, tools, etc. written by J.D. Rogers

All code on this page is Copyright J.D. Rogers. Please use, copy, modify and redistribute anything you find here, but please give credit where due. I prefer to keep a running list of authors in the top of the code, so add your name, write some code, and have fun.

Programs

Some instructions on how to write:

• Parallel Monte Carlo using MPI to easily distribute MC loops across multiple cores, processors, or nodes.
• Signal handling to make Interruptible MC that can be stopped without loosing simulation data making it possible to run MC for a specified time rather than for a specified number of rays.

MCML_mpi

MCML for parallel processing, for example on clusters or multiprocessor workstations.

MCML is a multi-layered Monte Carlo simulation for studying light transport in random media. It was written by Steve Jacques and Lihong Wang for light scattering in biological tissue (or other random media). This version is the minimal modification to the original that adds MPI support. Message Passing Interface (MPI) allows the code to be run in parallel across many processors (or cores) such as clusters, multi-processors workstations, etc. You will need a working installation of MPI such as open-mpi.

• README
• tarball
• zip file
• Patch file

nscat_MCML

MCML modified to track and bin the number of scattering events, and other parameters.

It also uses a more general 3-parameter phase function based on the Whittle-Matern correlation function. The phase function includes exponential, stretched-exponential, Henyey-Greenstein and mass-fractal type scattering functions.

Code snippets, matlab functions, etc

Matlab functions

• findpeak.m
• rotavg.m