Roche Nimblegen MS 200, Operator'S Manual

Page: 13 / 104

A Overview
1. Introduction
The Microarray Scanner is a laser-scanning instrument dedicated to
acquiring fluorescent images on standard microarray slides (1 x 3 inch).
High resolution combined with high sensitivity as well as uniformity,
reproducibility, auto calibration, and a dynamic range are key characteristics
of the Microarray Scanner.
A slide magazine enables the automatic processing of up to 48 slides, which
can be scanned several times using different laser, filter, and photomultiplier
tubes (PMTs) gain settings with no further user intervention in a single
batch run.
Active air filtering reduces ozone concentration so that the slide processing
and storage area is protected from external high ozone concentrations
during operation.
The Microarray Scanner produces single- or multi-image Tagged Image File
Format files (TIFF, .tif) that can be read by software packages available from
Roche NimbleGen and other vendors.
Following is a description of the instrument’s key functionality and
components:
Autofocus Procedure
Microarray slides can have a variable surface planarity, which can affect the
focusing of the scanning laser and may cause problems with measuring
fluorescence intensities.
To counter this problem, the Microarray Scanner implements a dynamic
autofocus procedure that measures the surface contour (surface modeling)
before it scans a slide. During this procedure, the Microarray Scanner
performs a multi-line scan using different positions across the entire slide to
evaluate the surface. Then the contour of the slide is interpolated to correct
for focal distance and tilt while scanning.