Resources

Software

Monte Carlo packages:

Monte Carlo multi-layered (MCML) modeling: Modeling of photon transport in multi-layered tissues in ANSI C

tMCimg: Modeling the transport of photons through 3D highly volumes in Monte Carlo algorithm in Linux

Molecular optical simulation environment (MOSE): Simulation of light propagation both in tissues with complicated shapes and in free-space

Others: Collections of Monte Carlo simulations

Mie approximation:

MieTab: Window-based program for Mie scattering calculation

Online Mie calculator: Calculation of scattering phase functions and optical properties of absorbing and non-absorbing spheres base on Mie theory

Discrete dipole approximation (DDA):

Amsterdam discrete dipole approximation (ADDA): Calculation of scattering and absorption of electromagnetic waves for particles of arbitrary geometry using the DDA (Written in C)

DDSCAT: Calculation for scattering and absorption of light by irregular particles based on DDA written in FORTRAN 90

Finite-difference time-domain:

3D Finite-difference time-domain simulation: Electrodynamic modeling of 3-dimensional space by solving Maxwell equations in the time domain (Written in C)

Hardware

Charge coupled device (CCD) vs complementary metal oxide semiconductor (CMOS) features and performance --- Comparison by DALSA

Guide to detector selection: photomultiplier tubes (PMTs), silicon photomultipliers (SiPMs), avalanche photodiodes (APDs), and silicon photodiodes, by Hamamatsu Photonics --- Technical notes of products from Hamamatsu

Introduction to various photoreceivers --- Types of Photoreceivers from Newport

Spectrograph and monochromators --- Resources from Princeton Instruments

Optical filters offered by Semrock and lens including cleaning tips from Edmund Optics

Light sources --- Technical references by Newport

Fibers and fiber-optic probes basic concepts by fiber 101

Tutorial in the Optics of Spectroscopy at Horiba

Nice websites

Biomedical optics Fundamentals from Oregon Medical Laser Center

Microscopy Fundamentals from Nikon

Useful microscopy links from Duke University

Optics fundamentals from "Handbook of optics, volume I", Edited by Michael Bass, Casimer DeCusatis et al. 2009 (requiring XMU proxy login)

Handbook of Coherent-Domain Optical Methods Edited by Valery Tuchin, 2013 (requiring XMU proxy login)