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I have a question regarding the units conversion from photon counts on a detector to Rayleighs. I am pretty new to the subject but I would like to know more.

The problem is the following :

I know that $1\, \mathrm{R} = 10^6\ \text{photon}\, {\rm s}^{-1}\, {\rm cm}^{-2}$, but that area should I use in order to obtain the rights conversion. I have an example in which the full area of the HST aperture is used (ish 2.4m in diameter) as a reference but what if I have some optical elements, like a slit for spectroscopic observations?

Should I still consider the same area? In specific I would be happy to have a systematic way of doing the conversion from counts to Rayleighs using the correct reference area.

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In case of light losses in your optical system you obviously have to correct for this. Anything attached in front of your detector could potentially reduce your photon count, so you may have to re-calibrate this to interpret your count rates correctly. You have to examine your setup and make either some theoretical or, if possible, experimental analysis of the effect.

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