Roche Nimblegen MS 200, Operator'S Manual

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NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 | 89
Scan area
Specifying a single scan area ...................................................................................................... 50
Specifying multiple scan areas................................................................................................... 52
Scan parameters
Assigning scan parameters using an existing file...................................................................... 44
Specifying scan parameters for multiple slides......................................................................... 44
Specifying scan parameters for one slide .................................................................................. 41
Scanned images.................................................................................................................See Images
Scanner experiment, typical steps ................................................................................................. 31
Scanning
Aborting a scan .......................................................................................................................... 60
Adjusting the PMT gain during a scan ..................................................................................... 60
Before you start the scan............................................................................................................ 58
Saving log files............................................................................................................................ 60
Starting a scan ............................................................................................................................ 58
Sensitivity test................................................................................................................................... 5
Session files
Creating, saving, and opening session files............................................................................... 36
Description of session files ........................................................................................................ 36
Relationship between session, parameter, and area files ......................................................... 36
Slide
Barcode dimensions............................................................................................................... 9, 80
Inserting the ILC slide into the slide magazine ........................................................................ 28
Recommendations for non-NimbleGen microarrays................................................................ 9
Slide dimensions .......................................................................................................................... 8
Slide mishandling/handling ...................................................................................................... 17
Specifying a single scan area ...................................................................................................... 50
Specifying multiple scan areas................................................................................................... 52
Specifying the autogain area...................................................................................................... 56
Specifying the barcode area ....................................................................................................... 55
Specifying the slide type for a scan............................................................................................ 42
Slide magazine
Components of the slide magazine........................................................................................... 13
Inserting or removing the slide magazine from the instrument ............................................. 16
Inserting slides into the slide magazine .................................................................................... 14
Slide magazine box......................................................................................................................... 14
Slide transport, removing slide from ............................................................................................ 77
Space requirements, instrument ................................................................................................... 19
Specifications, control unit.............................................................................................................. 8