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Dear Gabor, 
    you may find some information in Qiaole Zhang et al  published in J Biomed 
Opt "Photon budget analysis for fluorescence lifetime imaging microscopy"

As you said, a major impact is the NA of the objective. For single molecule 
detection using top end EM-CCD, you will not lose much at the camera. 

However, you will lose quite a bit into the filters and relay optics. I've written 
a short description about this in Suppoprting Text S1 here: 
http://www.plosone.org/article/info%3Adoi%2F10.1371%
2Fjournal.pone.0077392

Cheers, 

Alessandro

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>
>Dear All,
>
>I made a quick search but found nothing really useful. My question is the
>following: does anyone have some data/literature how efficient microscopes
>are in detecting the photons of a fluorescent sample? Obviously the NA and
>the QE of the camera (plus the performance filters/dichroics) are
>important factors but taken e.g. A single molecule experiment with a 1.49
>NA objective and a back-illuminated EM-CCD what ration of the emitted
>photons really reach the detector? Of course the transmission of the
>objectives and other lenses in the microscopes can vary but is there still
>an estimate?
>
>Thanks     Gabor