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 This is off-topic, but I suspect the same people who replied to this
thread could answer my question. Can someone describe the type of noise I
should expect with an Airyscan-style detector?

 I'm familiar with sCMOS and EMCCD cameras, but I have almost no experience
with megahertz few-pixel detectors. I assumed that the noise of each
'pixel' of the Airyscan detector would behave similarly to the pixels of a
sCMOS: Wavelength-dependent quantum efficiency above 50%, Poisson noise
that depends only on the number of photoelectrons generated by the signal
light, and additive Gaussian noise that depends only on the detector
settings. Is this true? Are there other important details I should know
about, like dynamic range, etc?

Thanks for the help!

-Andrew

On Wed, Feb 4, 2015 at 11:53 AM, James Pawley <[log in to unmask]> wrote:

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>
>> @Zdenek: A SNR of 3.5 or a little bit more might be enough for some
>> applications ... I was planning to measure the photon count per pixel
>> (using this method :
>> http://labrigger.com/blog/2010/07/30/measuring-the-gain-
>> of-your-imaging-system/ ), but I always was busy with other things, so I
>> cannot give you numbers for my imaging system.
>>
>
> Hi all,
>
> Thanks to Labrigger for working on this important topic.
>
> However, I have read his analysis and think that the assumption that one
> can use this procedure to measure the number of photoelectrons (PE: i.e.,
> detected photons) created at the photocathode (PC) of the PMT may be an
> over-simplification.
>
> The analysis depends on the assumption that the only source of noise in
> the data recorded in the "image" of a flat white field is Poisson Noise
> associated with the small number of PEs produced at the photocathode.  This
> might be true if PMTs were free from multiplicative noise but in fact
> Poisson Noise also affects every stage in the multiplication of a single PE
> after it leaves the PC. In the very unusual case that the voltage between
> the PC and the first dynode is 500-600 volts (and that this dynode has both
> the optimal shape and the best GaAs surface), the gain of this stage may be
> 25 +/-5 or 20% additional noise. More commonly, this gain will be closer
> to  4 +/-2 or 50% additional noise. More noise is added at each stage and
> even though these noise terms are not additive (they are combined as the
> sqrt of the sum of the squares), it is not at all uncommon for this process
> to double or even triple the variation present in the resulting signal
> beyond what one would expect from Poisson Noise applied only to the number
> of PE. Furthermore, this added noise will be somewhat larger if the system
> is working at a relatively high signal level because then the PMT will be
> turned down, the gain/stage correspondingly lower and the Poisson Noise
> proportionally higher.
>
> Offsetting this error to some extent is the finite bandwidth of the entire
> amplifier system (PMT plus the electronics between the final dynode and the
> ADC). This bandwidth is in general unknown but may be adjusted by the
> computer to more-or-less match what the computer estimates is needed to
> pass the finest optical details that the system can transmit on the basis
> of settings for wavelength, objective NA, zoom/pixel size, and even PMT
> setting (high PMT voltage implies a noisy signal that may benefit from the
> artificial, 1-dimensional smoothing that attends lower bandwidth).
>
> Clearly, because bandwidth limits the maximum excursion that can be
> transmitted between one pixel and its neighbour, it will tend to reduce the
> apparent noise present in the digitized signal. The magnitude of this
> clipping is unknown but may vary with the parameters mentioned above.
>
> This is relevant because, unlike the optical signal, the Poisson Noise
> signal that we are searching for shows no correlation between adjacent
> pixels. In particular, following the blog's suggestion of using a high zoom
> (to reduce fixed pattern noise) may cause the computer to limit the
> bandwidth more than using a lower zoom.
>
> Although, as noted above, because these two factors bias the results in
> opposite directions, their effects may cancel each other out to some
> extent. However, we need to know a lot more about how the components are
> actually operating before we can decide whether and to what extent this is
> true.
>
> The analysis also assumes that there is no fixed patterns noise in the
> image of a "flat white field" as might be caused, for instance, by field
> curvature, spherical aberration, vignetting, dust or other optical
> parameters that may change detected signal across the field of view.  I
> note that many of these sources of non-Poisson Noise can be substantially
> reduced by recording two sequential frames and obtaining a measure of the
> noise by subtracting one from the other.
>
> For the analysis to work, it is also important to set the brightness
> control (DC - offset) so that zero signal corresponds to closely to zero
> intensity in the image memory.
>
> I should note that multiplicative noise ceases to be a factor in systems
> employing either hybrid PMT (where the first stage gain is about 10,000) or
> effective photon-counting (i.e. a photon counting where the recorded peak
> pixel signal is at least 10x smaller than the saturation count rate of the
> system as set by pulse-pileup.).
>
> One can avoid multiplcative noise by recording the data using  a CCD (but
> NOT on an EM-CCD used with the electronic gain turned on) and the
> record-two-then-subtract approach can again be used to reduce inevitable
> fixed pattern noise.  However, this sensor will probably work best when
> recording a fairly large signal (at least 10% of peak?) so that read noise
> will be relatively insignificant. And as above, the results will again be
> limited by the finite bandwidth of the FET amplifier between the read-node
> and the ADC. Finally, when using a CCD for quantitative measurements, it is
> particularly important to remember that they are usually set up so that
> zero light corresponds to 20-50 computer intensity units.
>
> The noise performance of sCMOS detectors is both non-Gaussian and depends
> strongly on the extent to which the internal pixel-by-pixel variations in
> gain and offset are detected and corrected. This will make their use for
> this type of measurement somewhat more difficult unless the signal levels
> are well away from the noise floor.
>
> Bottom line: Although the procedure may indeed give a useful benchmark
> that we might call the "effective gain" of the signal path, the measurement
> is subject to influence by a number of imaging parameters and will not
> really allow one to measure how many recorded-signal-intensity-units
> correspond to one PE.
>
> Jim Pawley
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