30
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Imaging System Hardware
anode. The amount of current that flows from the anode is directly
proportional to the amount of incident light at the photocathode.
The amount of amplification that a PMT can produce depends on the
number of dynodes in the PMT, and the voltage that is applied to the PMT.
With PMTs it is possible to achieve a gain of 10
7
. When you increase the
PMT voltage setting in the GenePix 4200AL software, you are increasing
the gain of the PMTs.
Note:
It is important to realize that when you increase the gain of the system,
you are also increasing the sensitivity to non-specific fluorescence, thus
increasing any electronic noise in the system. This increase in noise can often
be overcome by line averaging but the cost is decreased acquisition speed. In
general, the signal-to-noise ratio is not improved by increasing the PMT
voltage.
The PMTs in the GenePix scanner meet two essential criteria for high-
quality imaging. First, since different photocathodes have varying
sensitivities to specific wavelengths of light (quantum efficiency) , the
PMTs have been optimized for the typical wavelengths of fluorescence
emission light produced by microarrays. Second, the PMTs have been
further selected for their reliability and optimal signal-to-noise
performance.
Mechanical
The GenePix scanner is a mechanical device. Its laser-based scanning system uses
a patent-pending mechanical design. The GenePix scanner operates by slowly
scanning the slide in the
y
-direction, and rapidly scanning in the
x
-direction. The
design of the GenePix scanner allows scanning up to four wavelengths of a 25 mm
× 75 mm slide at 5-
µ
m resolution in about 30 minutes.
When using such a mechanical device, one must be able to monitor the variability
in the performance of its mechanical components. The GenePix scanner has been
designed with a number of optimizations to ensure that variability in the mechanical
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
