Resources
Lab resources
GIT: http:gitlab.com/rogerslab
Old website: http://loci.wisc.edu/rogers
A list of some useful links to other resources.
Affilliations
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.