5000450 D
29
B
Instrument Performance Factors
Spatial resolution, and dynamic range and detection limits are two key
principles of the GenePix
®
4000B Microarray Scanner operation.
Spatial Resolution
In the GenePix 4000B Microarray Scanner, a single beam of light is
rapidly scanned across the microarray, and a composite pixelated
image is created from the digitized signals from the PMT. The spatial
resolution of the system refers to the size of the pixel. It determines
the minimum distance that can be distinguished between two points of
light. In the GenePix 4000B Microarray Scanner, the smallest spatial
resolution is 5
μ
m.
It is possible to change the resolution of data scans by changing the
pixel size setting in the GenePix Pro Software. It is important to note
that this does not change the size of the scanning beam. The GenePix
4000B Microarray 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 the pixel
size from 5
μ
m to 10
μ
m, the instrument only scans every second
X-direction line (by increasing each Y-direction step from 5
μ
m to 10
μ
m). 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 pixel size 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.
Data scan pixel size can be increased beyond 20
μ
m in increments of
20
μ
m, but the scanning pattern (and therefore scan duration) remains
the same. Every fourth X-direction line is scanned, and the spots within
the larger pixel size are averaged. For example, a 60
μ
m data scan will
average the values of thirty-six 5
μ
m spots (three X-direction lines
contribute twelve 5
μ
m spots each) to calculate the value for each 60
μ
m pixel.
See
Figure B-1 Data scans on page 30
.
Changing the resolution of a data scan can often be useful if you have
large features and you do not need to scan at maximum resolution. As
the resolution is decreased, so is 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.
GenePix_4000B.book Page 29 Friday, October 22, 2010 3:07 PM
