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Determining the Signal-to-Noise Ratio and Optimal Photomultiplier gain setting in the GenePix 4000B

Siobhan Pickett, M.S., Sean Carriedo, Ph.D. and Chang Wang, Ph.D. Axon Instruments, Inc. 3280 Whipple Road, Union City, CA 94587

Last updated: September 13, 2001

Introduction
An important criterion for comparing the performance of array scanners is the quality of the images produced. One objective measure for evaluating image quality is the Signal-to-Noise ratio (SNR). The ability to distinguish a signal from the background image or the noise improves as the SNR increases. In addition to quantifying the quality of the scanned images, the SNR is used to define the detection limit and the optimal photomultiplier gain setting of a scanner.

Signal
The signal from the array scanner originates from photo-exciting a fluorophore . The photons emitted from the fluorophore are collected onto the surface of a photon-detecting device such as a photomultiplier tube (PMT)*. The signal (represented by S) generated by a photo-detecting device is a function of the number of emission photons (represented by N) contacting the detector and the detection systems quantum efficiency (represented by QE). Therefore, S = N x QE. It is important to remember that the quality of the signal depends on both biological and technical factors (based mainly upon the design considerations used in the array scanner). For instance, maximizing the collection of the emitted photons (N) is dependent upon designing efficient pathways not only for delivering the maximal amount of excitation light to the sample but also for directing the light emit
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