Understanding fluence map output for modelling a source-detector separation problem

[Emillie Jo]

(Part of this question connects to my other post titled: Modelling an LED source vs laser - equivalent power, profile and unit conversion)

Hello,

I'm working on a source-detector separation problem for a non-invasive optical methodology where I need to detect light emerging from the epidermis (surface layer only). 

I have a couple of questions about how to interpret the data outputted in MCX's fluence map (.mc2 file) for this:

Photon Fluence Map:

• Does the fluence map (.mc2) file contain any information about the exit directionality (whether they are moving out of the tissue or deeper in)? 
• I'd like to detect photons leaving the tissue surface - is it possible to treat the fluence map of the epidermis layer (z=0) as representing outgoing photons? Or do I need to define a dedicated surface detector instead and analyse the .mch file?

i.e. -> would I be able to determine optimal detector placement on the surface of the epidermis (z=0) based on photon fluence in the first image attached?

Spherical Detector Issue: 

MCX studio only supports spherical detectors, is there a recommended workaround for modelling planar surface detection? So that I can detect the photons coming out of the entire epidermis surface and estimate realistic detector placement - the spherical detector is causing issues not covering the entire surface (see second image attached):

Essentially, I'm trying to determine whether the fluence map on the z=0 tissue surface is enough to estimate the detected returning signal - or if I need a dedicated .mch surface detector to isolate the exiting photons only.

Any help on this would be greatly appreciated :) 

Many thanks, 

Emillie 

[Qianqian Fang]

hi Emillie,

I suggest you first taking a look at this detailed reply I wrote on one of the Github tickets on several photon detection approaches using mcx

https://github.com/fangq/mcx/issues/102#issuecomment-682093350

then a few specific comments:

1. if you want to capture all exiting photons's information (position/direction/...) at the bottom of the bounding box, you will have to set the cfg.bc='______001000' in mcxlab or --bc ______001000 in mcx command line; mcxstudio GUI does not directly expose this bounding-box detector option, but you can expand the "Advanced settings", and find the "Additional parameters" field, and type "--bc ______001000"

2. if you want to capture the exiting directions of these photons, you should also set cfg.savedetflags to include letter 'v'. in mcxstudio, there is a checkbox under the "Save detected photon" box inside the Switches group.

3. no, fluence/volumetric output does not contain the existing direction; it is part of the detected photon data output

4. if you can ignore the photon exiting direction, and just want to accumulate the diffuse reflectance (dref), you can do this via the approach#3 in my above github post.

5. finally, I suggest you moving away from mcxstudio and start using mcxlab. the latter is much more "programmable" and flexible, and easier to debug and plot. mcxstudio GUI is extremely limited

here are a list of mcxlab examples that show you various aspect related to detection and dref output

https://github.com/fangq/mcx/blob/v2025.10/mcxlab/examples/demo_bc_det.m

https://github.com/fangq/mcx/blob/v2025.10/mcxlab/mcxlab.m#L411-L412

https://github.com/fangq/mcx/blob/v2025.10/mcxlab/examples/demo_colin27_atlas.m

Qianqian

On 10/22/25 16:31, Emillie Jo wrote:

You don't often get email from emyjoga...@gmail.com. Learn why this is important

(Part of this question connects to my other post titled: Modelling an LED source vs laser - equivalent power, profile and unit conversion)

Hello,

I'm working on a source-detector separation problem for a non-invasive optical methodology where I need to detect light emerging from the epidermis (surface layer only). 

I have a couple of questions about how to interpret the data outputted in MCX's fluence map (.mc2 file) for this:

Photon Fluence Map:

• Does the fluence map (.mc2) file contain any information about the exit directionality (whether they are moving out of the tissue or deeper in)? 
• I'd like to detect photons leaving the tissue surface - is it possible to treat the fluence map of the epidermis layer (z=0) as representing outgoing photons? Or do I need to define a dedicated surface detector instead and analyse the .mch file?

i.e. -> would I be able to determine optimal detector placement on the surface of the epidermis (z=0) based on photon fluence in the first image attached?

Spherical Detector Issue: 

MCX studio only supports spherical detectors, is there a recommended workaround for modelling planar surface detection? So that I can detect the photons coming out of the entire epidermis surface and estimate realistic detector placement - the spherical detector is causing issues not covering the entire surface (see second image attached):

Essentially, I'm trying to determine whether the fluence map on the z=0 tissue surface is enough to estimate the detected returning signal - or if I need a dedicated .mch surface detector to isolate the exiting photons only.

Any help on this would be greatly appreciated :) 

Many thanks, 

Emillie 

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[Emillie Jo]

Hi Qianqian,

 

Thank you so much for your detailed response and for the links to the Github examples - they've all been incredibly helpful!

 

I have moved from mcxstudio to mcxlab - thank you for suggesting that, it is much more flexible and easier to debug, and provides everything I need at the moment for graphical analysis of my simulation data.

 

Specific exit directions of the photons aren't a main focus at the moment - but it's great to have the option there for future work/ analysis - have been using the dref approach, #3 in the GitHub link, which has worked perfectly. I've used it to observe the reflectance across the entire epidermis surface then added targeted detectors in optimised regions.

 

Hope you have had a great week!

Emillie