http://confocal-microscopy-list.275.s1.nabble.com/sCMOS-salt-n-pepper-issues-tp7583323p7583332.html
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> Hi Neil,
> On 01/21/2015 04:24 AM, Neil Anthony wrote:
>>
>> On the first camera we saw a bright cluster of 4 pixels that are
>> between 2 and 10x greater than the surrounding pixels across nearly
>> all imaging conditions (not seen in the other three cameras).
>>
>
> We have an Andor Zyla 4.2 and I've tested a separate Zyla and the
> Flash 4.0 and I've never observed the clustering of hot spots.
>
>> Salt:
>> In images with low signal and longer exposure times we see speckled
>> bight pixels using both Volocity and ExCap/HDImage, with an intensity
>> approx twice that of the background signal.
>
> These hot spots I believe come from the "anonymously" noisy chip-level
> amplifiers. In an sCMOS camera, each pixel has its own amplifier and
> it seems that it's nearly impossible to ensure that all ~4 million
> pixels are defect free. In contrast, an EMCCD does not have
> pixel-dependent noise properties because the amplification is not
> pixel-dependent. Therefore, it seems like you have to accept hot spots
> by thinking of them as manufacturing defects that occur in making a
> large number of single pixels.
>
> We characterized our camera by measuring the pixel-dependent gain,
> noise variance, and hot spot locations according to the procedure in
> the supplement of this paper from the Bewersdorf lab:
>
http://www.ncbi.nlm.nih.gov/pubmed/23708387. We found that our
> characterization matched the hot pixel map provided by Andor exactly,
> so we know what the intensity statistics of those pixels are.
>
>> Pepper:
>> In almost the inverse situation, where we have higher signals with
>> lower exposure times were also seen on all sCMOS cameras (the first
>> camera with the clear hotspot had very bad 'peppering' compared to
>> the others).
>
> I'm not sure about this one. I haven't noticed the peppering. Is the
> hot spot correction algorithm on in this case?
>>
>> I know that the pco cameras used on the Deltavision OMX have
>> reference images applied to reduce the affects of these artifacts,
>> and I was wondering if that's something that can be applied
>> post-acquisition.
>
> We work in STORM/PALM microscopy and incorporate the hot spots into
> our noise model when performing the localization analysis, much like
> in the paper I cited above. We therefore do not use the manufactuer's
> algorithm for hot pixel smoothing.
>
> For "normal" imaging, I think you either have to use the hot spot
> correction algorithms to smooth over those pixels, or turn off the
> algorithm and post-process the hot spots yourself.
>
> I hope this helps!
>
> Kyle
>