How to estimate the signal to noise ratio?
It is good to read Set The Signal To Noise Ratio first.
Before going into details, the SNR number controls what you can think of as an artifact limiter. If you set it 'high', noise, if present, will be amplified. Also other distortions in the image formation might get amplified. A low SNR setting will attenuate these artifacts at the cost of the final resolution in your image.
In practice you start out with a SNR number derived either from an estimate of the number of photons in the image, or from rule of thumb reasoning. Subsequently you do a restoration run and inspect the result for artifacts and residue background. If you are confident all is fine you rerun the restoration with a higher SNR setting (say 30%-50%) and perhaps a higher background. The software will continue were you left off. After this run you compare the results, for instance using the undo function (in Huygens Pro). <br />
If you have done this a previous time for a similar image then of course you just use the values established then.
Images from widefield microscopes equipped with 12-bit CCD camaras usually have a SNR in the range of 40-60. This kind of images can also well be deconvolved with the very fast Quick-MLE algorithm for low noise images (Huygens Pro only).
In many confocal images the SNR in the image is due to photon noise. If you look into the background and it is largely zero with spikes here and there, then these spikes are probably single photon events. From the height of the average small spike you can roughly estimate how many gray levels correspond with one photon. If, for example, such a single photon event has an intensity value of 5, then the max in the image (255) corresponds with 51 photons. The SNR is the square_root(51)= 7. <br />
Some microscopes are equipped with photon counters like avalanche photo diodes. In this case the SNR is simply the square root of brightest part.
In a good confocal image, and using a 8-bit converter, you can easily get into a situation were one gray level corresponds with more than one photon. Now the procedure to determine SNR above fails, but you can start a run with SNR 20-30 and increase it later.
Keywords: estimate SNR MLE
Categories: Faq Deconvolution, Faq Microscopy, Huygens Faq, Imported Faqs
Platforms: Irix Linux Windows Mac AIX
Related products: Hu Ess Hu Pro
