AW: Readout noise in sCMOS cameras

Posted by Gerhard Holst on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Readout-noise-in-sCMOS-cameras-tp7588012p7588029.html

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Hi Zdenek,

now, I can only speak for our cameras, because I don't know what the others are doing. In general there are two classes of bad, defect or hot pixels.

Class "defect pixels":
they don't react to light or their dynamic is dramatically reduced (for example by having a pretty high start value), these pixels are replaced by a kind of neighborhood average value, always. They are known and stored in a defect or hot pixel list in the camera, and this list can be read out, and in case that the averaging operation has an unwanted impact on applied image processing algorithms, the averaging can be switched off by an SDK (software development kit) command.

Class "blinkers" or "higher noise" pixels (referring to the tail in the histogram:
They have higher pixel values in some images and in some images they behave normal, or some of the pixels show a larger noise. They are locally fixed, such they can be identified (which for example thermally or clock induce charges in emCCDs are not). For these pixels the camera manufacturers have installed a filter, which can remove them dynamically. Usually it is a kind of lowpass which takes the signal into account, which means in case a single pixel has a value that is more than x times sigma of the neighborhood average different, it is assumed not to contain information, and it is replaced by a weighted neighborhood average. But these are software filters, which can be switched off either by SDK or by the controlling camera application software.

Our storage or the list for defect pixel values can contain as max 4096 values, which are usually not filled, therefore I am surprised by your number of 11000 bad pixels, which to me appears to be too high, based on my experience. But maybe you had the software filter on, because as demonstrated by the noise histograms, there are still some "higher noise" pixels, which are not considered to be "defect".

Right now, I don't have enough statistical data to compare the new sCMOS image sensors to the former ones, but the current data support, that the new image sensors show a better noise behavior, which allows to use them as well without cooling.

with best regards,

Gerhard


Dr. Gerhard Holst
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Von: Confocal Microscopy List [mailto:[hidden email]] Im Auftrag von [hidden email]
Gesendet: Freitag, 9. März 2018 21:44
An: [hidden email]
Betreff: Re: Readout noise in sCMOS cameras

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Hi Listers,
I have a related question: since every pixel of a CMOS sensor behaves a bit differently, some of them are so much off the specs that they can be regarded as bad pixels (hot pixels, dead pixels, etc). For example one of our 4-megapixel front-illuminated sCMOS cameras has over 11000 bad pixels (they are easy to spot, as they are 'corrected' by averaging neighboring pixels, so their standard deviation is much lower that what is dictated by Poisson statistics).

What are the specifications for the number of bad pixels? I could not find any useful info on the websites of the camera vendors, nor the chip manufacturer. Does anyone know how the new back-illuminated sensors compare with the mainstream 4 megapixel CIS2020 (or SCI2020?) sensors in terms of bad pixels?


Thanks!

Best, zdenek
--
Zdenek Svindrych, Ph.D.
Research Associate - Imaging Specialist
Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth
email: [hidden email]


---------- Původní e-mail ----------
Od: JAMES B PAWLEY <[hidden email]>
Komu: [hidden email]
Datum: 6. 3. 2018 2:23:24
Předmět: Re: Readout noise in sCMOS cameras
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Dear Sripad,

In a CMOS chip, every pixel has its own read amp. All of these vary slightly
in gain and DC-offset. So the raw output from a a black (no light) image
would have a noise term related to how much the offsets of the pixel amps
varied and a uniform white image would have Poisson noise on the photo
charge plus a noise term mostly related to the variation in the gains of the
pixel amplifiers.
In an sCMOS chip to these uncertainties must be added variations in the gain
and offer of the 4,000-plus separate ADCs mounted at the edges of the chip.
An effort is made to correct for the multi-amplifier and multi-digitizer
noise by “flat fielding” the raw data from the chip using data from previous
“black” and “white” images, The system works quite well but as the white
image always involves a lot of charge, its Poisson noise (sqrt of n) is
large and this can skew the results. So can using the chip at a different
temperature, dwell time or pixel clock than was used for the “black” and “
white” images. Other sources on non-“Gaussian” noise include “hot pixels”
(perhaps leaky photodiodes that are sometimes flagged and removed by the
camera system software).

Indeed, the noise spectrum in these low-light systems is almost never “
Gaussian”. Even if the electronic noise (that signal variation which becomes
evident when reading the same pixel with no light signal) seems Gaussian, it
is usually caused by Poisson Noise (Or Johnson noise) affecting the small
number of electrons that constitute the (fairly table currents passing
through the elements of the charge amplifier. And of course, at signal
levels of more than a few dozen photoelectrons, Poisson Noise on the PE
number soon dominates most other noise sources (not hot pixels).

Gaussian noise is just easier to think about, and easier to model. We should
remember that in low-light photodetectors, it is almost never appropriate.
(Poisson Noise get bigger as the signal increases!).

Best,,

JP
James and Christine Pawley, 5446 Burley Place, Box 2348, Sechelt BC, Canada,
V0N3A0 [hidden email]<mailto:[hidden email]>, Phone [phone],
cell 1-604-989-6146



On Mar 5, 2018, at 9:54 AM, S Ram <[hidden email]<mailto:sripad.ram@
GMAIL.COM>> wrote:

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Hello Gerhard,
This is a slightly off-topic question in connection to your recent response
to the thread on the choice of sCMOS cameras.

You made a comment that the distribution of noise in sCMOS is not Gaussian.

Can you clarify whether you meant noise during the readout process (charge
to voltage conversion step)? If it is not Gaussian, what is the underlying
noise process? Is there any literature that you can point me to?

Thanks.

Sripad

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