Re: SNR estimation of a single image

Posted by Frederic V. Hessman on Jul 13, 2007; 4:07pm
URL: http://imagej.273.s1.nabble.com/SNR-estimation-of-a-single-image-tp3698855p3698857.html

Just be careful : Lidke et al. suggest (page 1238)

"A defocused object is an easy and suitable test image. A background  
dark level is measured and subtracted from the series. To rule out  
fluctuations of the light source, one normalizes every image by its  
integrated intensity. The mean intensity and variance is computed per  
pixel over the series. A plot of the variance versus intensity yields  
a line with slope equal to the gain..."

This is basically what I suggested, but DON'T normalize the images  
before calculating the mean intensity and variance: if you do, you'll  
mess up your result (I'm not sure what Lidke et al. originally meant  
by this).  You don't have to worry about "fluctuations of the light  
source" anyway, since if the level changes, so will the Poisson noise.

Rick


On 13 Jul 2007, at 4:07 pm, winnok ugent wrote:

> Dear all
>
> Thank you for your replies.
> I had also thought of using deconvolved images as noise free images  
> (estimation of original), but decided not to since the  
> deconvolution 'erodes' objects by the PSF, hence causing objects to  
> be smaller and have different intensities. It might be possible to  
> normalize the latter, but I fear the shape adjustment will cause a  
> bias in noise calculation.
> It seems the best way must be to use the relation of the detector  
> gain (CCD or PMT) with the photon flux.
> But as I want to compare with the synthetic images which are  
> independent of detector characteristics, I would prefer a way to  
> directly compare the images purely from image variables.
> A variance estimation over small neighbourhoods throughout the  
> image might roughly give an idea of noise, but then again might be  
> skewed by border regions?
>
> Winnok
>
>
> ______
> ir. Winnok De Vos
> Research Assistant
>
> dep. Molecular Biotechnology
> Faculty of Bioscience Engineering
> Ghent University
> Coupure links 653
> 9000 Ghent
> Belgium
>
> tel [phone]
> fax [phone]
> www.molecularbiotechnology.ugent.be
> ----- Original Message ----- From: "Alessandro Esposito"  
> <[hidden email]>
> To: <[hidden email]>
> Sent: Friday, July 13, 2007 11:05 AM
> Subject: Re: SNR estimation of a single image
>
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> It could be useful the following:
>
> "The Role of Photon Statistics in Fluorescence Anisotropy Imaging"  
> by Lidke
> et al.
>
> They use multiple images of the same object to compute a variance  
> from which
> you may infer the number of collected photons in the assumption  
> that only
> poissonian noise is present.
>
> Cheers,
>
> Alessandro
> --
> Dr. Alessandro Esposito
> Laser Analytics Group - Department of Chemical Engineering
> University Cambridge
> CV: home.quantitative-microscopy.org
> Web: wikiscope.org

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