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:
It's definitely possible to determine the relationship between the value of a pixel in a RAW file (measured in analog-to-digital units) and the number of incident photons. Modern CCD and CMOS sensors are highly linear, so in theory there should just be some arbitrary conversion factor.
Actually doing so is a different matter. To understand why, we need to look at what happens between a photon striking the sensor until the final digital value of the pixel is determined. Here's a rough chronological outline:
The photon first encounters the color filter array, which may scatter the photon with a probability dependent on its wavelength.
The energy of the photon is converted to electron-hole pairs in the photosite; the rate of conversion is the quantum efficiency. For sensors manufactured in the past 10-20 years this value usually peaks at anywhere from 40%-90%.
At the end of the exposure, the accumulated charges are read out and digitized. The nature of this process is entirely different between CCD and CMOS sensors. Before digitization the analog signals may undergo amplification. The applied gain is determined by the camera's ISO setting.
A good approximation of gain (ADU per electron) can be made using some basic calculations on the statistics of dark noise. However, the uncertainties introduced by QE and color filter transmittance make translating this value from electrons to photons a fairly difficult task. I am not an expert in this field, but to my understanding you will probably need some sort of calibrated light source to determine these values for certain.
If your intent is to count individual photons, a consumer camera is not going to be a very good option, primarily because of unavoidable read noise. There are technologies built for this purpose like photomultiplier tubes (or EMCCDs if the photon counts must be spatially resolved).
Addressing the concern you expressed in your question:
I'm worried that there are some settings on the camera that will skew the RGB pixel intensities for example like white balance.
White balance settings usually do not affect the outputted data. However, many cameras are known to apply various adjustments to the raw data obtained from the sensor. Some common ones are channel scaling and various spatial filters to combat noise or hot pixels. Nikon's old "star eater" filter is a particularly notorious example. In some cases these adjustments may be disabled using unusual methods like firmware hacks. Check out Roger N. Clark's page on the subject for more info. (But frankly, these adjustments will be the least of your problems.)
