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I'm quite new to photography, but was wondering what settings I should have in order to have a good approximation of the relative number of photons that creates each pixel?
i.e. best settings such that pixel intensity is roughly proportional to number of photons that created that pixel.
I'm worried that there are some settings on the camera that will skew the RGB pixel intensities for example like white balance.
The camera i'm using is Canon EOS 1100D.
Get an idea on the spectral sensitivity and quantum efficiency of your camera. The data are provided by the camera manufacturer and/or chip manufacturer. It's easier for monochrome cameras as there is no colour filter (bayer pattern) involved. They are also more light sensitive. CCDs are more sensitive than CMOS and CCD is also more linear. (Your Canon camera has a CMOS sensor). For colour cameras you'll get separate curves of quantum efficiency for each colour.
An important aspect is the colour spectrum you want to observe. Cameras and normal lenses are designed to detect visible light only. That is only an extremely small part of the electromagnetic spectrum.. Any camera, including the monochrome ones, do have an IR filter to disallow any light with wavelength longer than red to pass. These IR filters can be removed from some chips (there are offers for certain cameras). Yet even then, the material of the chips has a cut-off around 1.5µm.
If you are using some optics, get the spectral transmission curve for that as well. Different coatings block different wavelengths. Data are availble from manufacturers - usually they are designed for visible wavelength exclusively.
In order to get a rough estimate of your photon count you thus have to take the pixel value, de-convolve that with the quantum efficiency of the pixel (per colour if you use a colour camera) and de-convolve that with the transmission curve of your optics and then the spectral density of the light source you observe. You might want to make several measurements at different wavelength (small band pass filters) to get a better idea of the spectral content.
If you have a monochrome colour source with known intensity (i.e. laser), you can use that in order to calibrate your guestimate.
In any case: use raw images. Try to get a handle on the actual values per pixel without any colour corrections via white balance etc done.
There are no camera settings that will create pixel intensities that correspond linearly to the number of photons. The conversion from raw camera sensor data to an image is non-linear.
To get something proportional to photons, you will need to access the raw file directly. This is non-trivial, the file format is complicated, and some of the processing steps are still required for what you want.
You should get a device meant to do that. Cameras are sold as tools for making visual art. Since cameras meant to take photographs are optimized for that purpose, they do not make good scientific instruments.
I'm worried that there are some settings on the camera that will skew the RGB pixel intensities for example like white balance.
Oh, not just white balance. The translation from RAW to what you see on a preview is a proprietary translation utilizing more than a few unknown processes in tandem with user defined preferences (like vibrance, sharpness, contrast...).
I'm quite new to photography, but was wondering what settings I should have in order to have a good approximation of the relative number of photons that creates each pixel? i.e. best settings such that pixel intensity is roughly proportional to number of photons that created that pixel.
The absolute best setting that you can use to count photons is more of a process than a simple setting...but it goes like this:
