Roche Nimblegen MS 200, Operator'S Manual

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NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 | 3
The amplification of the photon signal can be controlled by the voltage
applied to the tube. PMT voltages are adjustable in the PMT gain settings
for different channels to equalize intensity values on each slide.
To optimize and increase the dynamics of scanning, adjust the PMT setting
using the histogram mode to balance channel intensity. Balance the
histogram at all points above background across signal intensity. For more
information on histograms, refer to
Chapter C, Operation .
Histogram mode is not available for 2 μ m scans during the run but is
available post run.
Repeated use of high power settings for the lasers causes
photobleaching of the dye molecules and thus detrimentally affects
fluorescence intensity.
Read Speed
The Microarray Scanner can measure two fluorescent dyes simultaneously
(parallel mode) at increased overall scan speed. Alternatively, the dyes can
be read one at a time (sequential mode). In addition, two scanning velocities
are available: 16 lines per second (8Hz) and 24 lines per second (12Hz).
The overall processing time includes loading and unloading of a slide,
reading the barcode, performing the autofocus, autogain, and scanning
processes, and saving the image file. The file size of an image depends on the
resolution and size of the scanned area. Increasing the spatial pixel size is
accompanied with an increasing scan speed and decreasing amount of data.
The following table shows approximate file sizes and processing times for
the NimbleGen HD2 family of arrays (2.1M, 3x720K, and 12x135K probe
formats) using a speed of 24 lines per second, parallel mode, autogain
turned off, and scan length of 62mm. File size and processing time will vary
if a different scan speed or scan length is specified.