32
•
Imaging System Hardware
y
-direction scanning operates eight times faster, and only one eighth of the pixels in
the
x
-direction are used.
It is possible to change the resolution of Data Scans by changing the pixel size
setting in the Hardware Settings dialog of the GenePix Pro software. The scanner
implements changes in resolution by increasing the
y-
direction step size and
averaging the
x-
direction samples over multiples of 5-
µ
m spots. For example, to
change resolution from 5
µ
m to 10
µ
m the instrument scans only every second
x-
direction line (by increasing each
y-
direction step from 5 to 10 microns—and
consequently a 10-
µ
m scan is twice as fast as a scan at 5
µ
m) and outputs the
average of each adjacent pair of 5-
µ
m spots in the
x-
direction as the value of a
single 10-
µ
m ‘pixel’. Similarly, a scan at 20-
µ
m resolution is implemented by
scanning every fourth
x-
direction line (and so is four times faster than at 5
µ
m) and
using the average of four contiguous 5-
µ
m spots on each
x-
direction line as the
value of a 20-
µ
m ‘pixel’.
Changing the resolution of a Data Scan may often be useful if you have large
features and you do not need to scan at maximum resolution. As you decrease the
resolution, you will decrease the final image size (in megabytes). However, keep in
mind that you need to acquire enough pixels for each feature in order to make
accurate measurements. Note too that increasing the scan resolution increases the
signal-to-noise ratio (that is, improves it) by the square root of the number of pixels
averaged.
Dynamic Range and Detection Limit
The dynamic range of an instrument is the signal width that can be resolved above
the noise the instrument produces. The dynamic range depends on all the
components in a given system. For example, if you use a PMT with a dynamic
range of 10
6
but process the signals through a sub-standard 8-bit analog-to-digital
converter, you will end up with an instrument with a poor dynamic range.
Furthermore, while an instrument may have a large dynamic range, one may not be
able to use the whole range reliably if the response is non-linear. Therefore when
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
