MCCL: Calculation of reflectance and transmittance of media containing fluorescence and non fluorescence particles

[Bhrigu Rishi Mishra]

Hii,

Does MCCL have the option to calculate reflectance and transmittance of a heterogeneous media containing fluorescent and non-fluorescent (scattering/absorbing) particles?

Thank you

WIth regards

Bhrigu

[Carole Hayakawa]

Hi Bhrigu,

Thanks for your interest in our software.  Yes!  We have the capability to generate fluorescent results.  The basic concept is this:

1)  Define an excitation source and tissue and run an excitation simulation generating an absorbed energy result.  If you download our MCCL software and generated sample infiles as described here: https://github.com/VirtualPhotonics/Vts.MonteCarlo/wiki/MCCL-Getting-Started-on-Windows (we have other pages for Linux and Mac OS), there is an example infile infile_infinite_cylinder_AOfXAndYAndZ.txt which generates an absorbed energy map in Cartesian coordinates generated by a directional point source.

2) After that simulation has been run, the results will be in an output folder infinite_cylinder_AOfXAndYAndZ.  Using the example infile infile_fluorescence_emission_AOfXAndYAndZ_source_infinite_cylinder, a fluorescence simulation will be run that uses the absorbed energy from the first simulation as a fluorescent internal source for the second simulation.  The "SourceInput" in the infile designates which folder to find absorbed energy results, what tissue region index should be considered the fluorescent region, and which sampling method to use.  Currently, the "SamplingMethod" of "CDF" is specified if you have a multi-voxel fluorescent source. 

This is a very brief overview.  Take a look at the software and let me know if you have questions.  Or tell me what you'd like to simulate and I can help with particulars.

Best,

Carole

[Bhrigu Rishi Mishra]

Hi Carol,

Thanks for the description.

Following is the description of what I want to simulate:

Three layers - air, tissue layer, air.

I know the scattering and absorption coefficient of the tissue layer. After parameter sweep, I will get wavelength-dependent reflectance and transmission of this system. Now, I want to add fluorescence particles in the tissue layer with known excitation and emission wavelength range, and also quantum yield of the fluorescence particles. And I want to simulate this modified system to know the total reflection and transmission. Basically, I want to know the contribution of the fluorescence particles in total reflection and transmission of the tissue layer. 

Could you please tell me how to simulate such kind of problem in MCCL? Please let me know if you have any questions.

Thank you

With regards

Bhrigu

--
You received this message because you are subscribed to a topic in the Google Groups "Virtual Photonics" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/virtual-photonics/785bX0gETvc/unsubscribe.
To unsubscribe from this group and all its topics, send an email to virtual-photon...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/virtual-photonics/b632acaf-add6-434e-9ab6-db9ead02d524n%40googlegroups.com.

[Carole Hayakawa]

Hi Bhrigu,

I have created infile templates for you.  The infile_singletissuelayer_AOfXAndYAndZ.txt defines a point source impinging upon a air-tissue-air system with tissue layer thickness of 100.0mm.  This layer optical properties are Mua=0.01/mm, Musp=1.0/mm, G=0.8, N=1.4.  Edit the thickness and optical properties per your system.  I ran 10K photons ("N"=10000), then edited load_results_script.m and replaced datanames with "singletissuelayer_AOfXAndYAndZ" and ran an obtain the absorbed energy plot excitation_absorbedenergy.jpg (this is taken at a y-axis slice of the 3D Cartesian map of absorbed energy).  Then I used the infile infile_fluorescence_emission_AOfXAndYAndZ_source_tissuelayer.txt to read these absorbed energy results and generate an isotopic source using the absorbed energy map created by the excitation simulation.  Note that the tissue thickness used in the excitation infile needs to match here, however you would define the emission optical properties for the tissue layer.  After running, again if I edit datanames in load_results_script.m with "fluorescence_emission_AOfXAndYAndZ_source_tissuelayer" and run the fluorescence_emission.jpg is produced (again at a y-axis slice).  The fluorescence spikes up at X= -10mm and 10mm because all fluorescence beyond those bins laterally are captured in those edge bins so that integrating the absorbed energy over all internal bins will give back total absorbed energy.

Let me know if you have questions.

Best,

Carole

[Carole Hayakawa]

I said something in error in last post.  The last sentence updated is: The fluorescence spikes up at X= -10mm and 10mm because all fluorescence beyond those bins laterally are captured in those edge bins so that integrating the reflectance over all surface bins will give back total diffuse reflectance.  Similarly for the absorbed energy plot, the edge bins spike because all absorbed energy beyond those bins are tallied to the edge bin so that integrating the absorbed energy over all internal bins gives back total absorbed energy.

Sorry about that!

Best,

Carole