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1. Crystal/Phantom Hits
2. Rayleigh scatter and Optical Absorption
3. Boundary processes – dielectric-metal surface – detection of optical photons
4. Rayleigh scattering length of water
5. Rayleigh/Mie scattering regimes
6. Comparison between Gate and MCML
7. Fluorescence process (implementation in Gate)
8. Gate: cuda code implementation
9. Validation GPU vs. GATEG4
10. Optical Imaging: publication
11. Fluorescence validation data versus simulation
12. Heat diffusion

Gate Optical Imaging Module Progress
  • hGATE Meeting (Dec. 16th 2011 – first report: root output file for optical photons, few validation plots, plan) [here]
  • Seminar SHFJ 24 Jan. 2012 [here]
  • Weekly Meetings @ IMNC (Jan. 27th – Feb. 17th 2012: Biomimic benchmark and first tests, Comparison Gate/MCML, Absorbance, Transmitance, Reflectance – with/without surface effects.) [here]
  • Weekly Meeting @ IMNC (Feb. 24th 2012 – Smooth/rough surface study (micro-facets angle distribution), cuda code description, GPU-tests at CCRT) [here]
  • Weekly Meeting @ IMNC (Mar. 9th 2012 – Fluorescence and GFP Simulation using Gate) [here]
  • Weekly Meeting @ IMNC (Mar. 16th 2012 – Optical imaging benchmark, voxelized phantom moby) [here]
  • hGATE Meeting (Mar. 27th 2012 – Comparison Gate/MCML, WLS code, first test of the hgate cuda code, plan for the GPU: Mie and surface effects) [here]
  • Weekly Meeting @ IMNC (April 20th 2012 – Mie scattering – cuda implementation and validation process) [here]
  • hGATE Meeting (May 22th 2012 – status report: two abstracts for IEEE) [here]
  • Weekly Meeting @ IMNC (June 1st 2012 – Comparison between GATE Fluorescence and “MCMLFluo”) [here]
  • Weekly Meeting @ IMNC (June 8th 2012 – Looking at SHFJ Fluo Data and GATE simulation tests) [here]
  • Weekly Meeting @ IMNC (June 22nd 2012 – Looking at IMNC Fluo Data) [here]
  • hGATE Meeting (July 1st 2012 – status report) [here] [PPT here]
  • Monthly Work Report (July 2012 – Gatev6.2 optical imaging developments, GPU Mie scattering LogLog interpolation, 2 materials phantom, Fresnel reflectance and processes cuda-implementation) [here]
  • hGATE Meeting (September 25th 2012) [here]
  • Bioluminescence Experiment (October 2012) [here]

GATE Gmane archives
Geant4 Cross Referencer (Code browser)
Geant4 General Particle Source Users Manual: primary source particle definition
Ecole Geant4 2008
Geant4 HEP Units and Physical constants
C++ hash Table
Diffusion du rayonnement (Rayleigh) [avec figures interessantes et animations]
Table of RINDEX
Imagej documentation

Optical Imaging Documentation
Optical Photon Processes

With the optical imaging, we will get the distribution of optical properties inside biological tissues. The difficulty in this approach is that photons from the visible and near IR (1 to 5 eV) which are involved in the optical imaging interact a lot with biological tissues and are partially absorbed but mostly scattered. We are interested in a photon source that would cover the visible and near IR region of the electromagnetic spectra. Photons from that spectra range have an energy of 1eV to 5eV.
E = hPlanck x ν = h x c/λ
Optical photons of energy [1eV to 5eV] have a wavelength of [1 μm = near IR to 0.25 μm = visible]. We use: 1eV/c2=1.783×10-36kg – hPlanck=6.626×10-34m2kg/s – c=3×108m/s. [400nm optical photon have an energy of ~3eV]

Rayleigh scattering
The photon is scattered in a new direction that is required to be perpendicular to the photon’s new polarization in such a way that the final direction, initial and final polarizations are all in one plane. This process thus depends on the particle’s polarization. A photon which is not assigned a polarization at production may not be Rayleigh scattered.
The process requires the Material Properties filled by the user with Rayleigh scattering attenuation length (average distance traveled by a photon before it is Rayleigh scattered in the medium).
The G4OpRayleigh class provides a RayleighAttenuationLengthGenerator method which calculates the attenuation coefficient of WATER ONLY following the Einstein-Smoluchowski formula. N.B: For Water where no Rayleigh scattering attenutation length is specified, the program automatically calls the RayleighAttenuationLengthGenerator which calculates it for 10 degrees Celsius liquid water.

Mie Scattering
Mie Scattering is an analytical solution of Maxwell’s equations for scattering of optical photons by spherical particles. It is significant only when the radius of the scattering object is of order of the wave length.The analytical expressions for Mie Scattering are very complicated since they are a series sum of Bessel functions.One common approximation made is call Henyey-Greenstein (HG). The implementation in Geant4 follows the HGapproximation (for details see the Physics Reference Manual) and the treatment of polarization and momentum are similar to that of Rayleigh scattering. We require the final polarization direction to be perpendicular to the momentum direction. We also require the final momentum, initial polarization and final polarization to be in the same plane.The process requires a G4MaterialPropertiesTable to be filled by the user with Mie scattering length data(MIEHG) analogous to Rayleigh scattering. The Mie scattering attenuation length is the average distance traveled by a photon before it is Mie scattered in the medium and it is the distance returned by the GetMeanFreePath method. In practice, the user not only needs to provide the attenuation length of Mie scattering, but also needs to provide the constant parameters of the approximation: MIEHG_FORWARD, MIEHG_BACKWARD, and MIEHG_FORWARD_RATIO.
Mie regime ==> the medium scattering particles should have ~ 1μm diameter. Using the Mie scattering calculator, we obtain the corresponding scattering coefficient (μs) for that particular medium. The scattering length = 1/μ (see Relation between the scattering coefficient and the scattering length)

This process kills the particle.
It requires the Material properties filled by the user with the Absorption length (average distance traveled by a photon before being absorbed by the medium). The GetMeanFreePath method calculates it.

Boundary Processes
When the surface concept is not needed, and a perfectly smooth surface exists between two dielectric materials, the only relevant property is the index of refraction, a quantity stored with the material. In all other cases, the optical boundary process design relies on the concept of surfaces: physical properties of the surface itself (stored in Materials.xml) and characteristics of the surface specifying the two ordered pairs of physical volumes touching at the surface (Surface.xml).
The user can choose different optical properties for photons arriving from the reverse side of the same interface.
The physical surface object also specifies which model the boundary process should use to simulate interactions with that surface. Combinations of surface finish properties, such as polished or ground and front painted or back painted, enumerate the different situations which can be simulated.
When a photon arrives at a medium boundary its behavior depends on the nature of the two materials that join at that boundary.
In the case of two dielectric materials, the photon can undergo total internal reflection, refraction or reflection, depending on the photon’s wavelength, angle of incidence, and the refractive in on both sides of the boundary. In the case of an interface between a dielectric and a metal, the photon can be absorbed by the metal or reflected back into the dielectric.

[More details can be found here]