Molecular Devices GenePix SL50 User manual

GenePix®SL50
Slide Loader
User Guide
5001410 B
February 2011
GenePix SL50.book Page 1 Tuesday, February 1, 2011 12:20 PM

This document is provided to customers who have purchased Molecular Devices, Inc.
(“Molecular Devices”) equipment, software, reagents, and consumables to use in the
operation of such Molecular Devices equipment, software, reagents, and
consumables. This document is copyright protected and any reproduction of this
document, in whole or any part, is strictly prohibited, except as Molecular Devices
may authorize in writing.
Software that may be described in this document is furnished under a license
agreement. It is against the law to copy, modify, or distribute the software on any
medium, except as specifically allowed in the license agreement. Furthermore, the
license agreement may prohibit the software from being disassembled, reverse
engineered, or decompiled for any purpose.
Portions of this document may make reference to other manufacturers and/or their
products, which may contain parts whose names are registered as trademarks and/or
function as trademarks of their respective owners. Any such usage is intended only
to designate those manufacturers' products as supplied by Molecular Devices for
incorporation into its equipment and does not imply any right and/or license to use
or permit others to use such manufacturers' and/or their product names as
trademarks.
Molecular Devices makes no warranties or representations as to the fitness of this
equipment for any particular purpose and assumes no responsibility or contingent
liability, including indirect or consequential damages, for any use to which the
purchaser may put the equipment described herein, or for any adverse circumstances
arising therefrom.
For research use only. Not for use in diagnostic procedures.
Product manufactured by Molecular Devices, Inc.
1311 Orleans Drive, Sunnyvale, California, United States of America 94089.
Molecular Devices, Inc. is ISO 9001 registered.
© 2011 Molecular Devices, Inc.
All rights reserved.
Printed in the USA.
The trademarks mentioned herein are the property of Molecular Devices, Inc. or their
respective owners. These trademarks may not be used in any type of promotion or
advertising without the prior written permission of Molecular Devices, Inc.
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GenePix SL50 Slide Loader User Guide
5001410 B 3
QUESTIONS? See Molecular Devices technical support:
http://support.moleculardevices.com
VERIFICATION
This slide loader is extensively tested and thoroughly calibrated before
leaving the factory. Nevertheless, researchers should independently
verify the basic accuracy of the slide loader using suitable test samples.
WARNING
If this equipment is used in a manner not specified by the
manufacturer, the protection provided by the equipment may be
impaired.
DISCLAIMER
This equipment is not intended to be used, and should not be used, in
human experimentation or applied to humans in any way.
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4 5001410 B
Licensing Notice
Molecular Devices is not licensed under any patents owned by Oxford
Gene Technology Limited (“OGT”), covering oligonucleotide arrays and
methods of using them to analyze polynucleotides. The purchase of
Molecular Devices products does not convey any license under any of
OGT’s patent rights, including any right to make or use oligonucleotide
arrays under OGT’s patents.
Customers may use Molecular Devices products to analyze
oligonucleotide arrays according to OGT’s patented methods if those
arrays have either been purchased from OGT’s licensed suppliers, or
have been made by the customer under a license from OGT.
Please contact OGT to enquire about a license under OGT’s patents at
[email protected].
USE OF THIS INSTRUMENT WITH MICROARRAYS MAY REQUIRE A
LICENSE FROM ONE OR MORE THIRD PARTIES THAT HAVE PATENTS
RELEVANT TO SUCH USE. MOLECULAR DEVICES DOES NOT SUGGEST
OR PROMOTE THE USE OF THIS INSTRUMENT IN A MANNER THAT
INFRINGES ON THE PATENT RIGHTS OF A THIRD PARTY. YOU ARE
ENCOURAGED TO EVALUATE WHETHER A LICENSE IS REQUIRED FOR
YOUR SPECIFIC APPLICATION OF THIS INSTRUMENT. COMPANIES
THAT HAVE INTELLECTUAL PROPERTY RIGHTS IN THE POTENTIAL
FIELD OF APPLICATION OF THIS INSTRUMENT INCLUDE WITHOUT
LIMITATION, AFFYMETRIX, INC. (“AFFYMETRIX”), AGILENT, AND
OXFORD GENE TECHNOLOGY. THIS INSTRUMENT HAS NOT BEEN
LICENSED OR APPROVED FOR DIAGNOSTIC APPLICATIONS.
THE USE OF THIS INSTRUMENT IN CONNECTION WITH MICROARRAYS
MAY BE WITHIN THE SCOPE OF PATENTS HELD BY AFFYMETRIX. TO
THE EXTENT THAT AFFYMETRIX PATENT RIGHTS ENCOMPASS THIS
INSTRUMENT OR ITS USE, AFFYMETRIX HAS GRANTED A LIMITED
PATENT LICENSE FOR RESEARCH USE ONLY AND NOT FOR USE IN
DIAGNOSTIC PROCEDURES. SUCH LICENSE, IF APPLICABLE, IS
LIMITED TO USE OF THIS INSTRUMENT WITH SPOTTED MICROARRAYS
SEPARATELY LICENSED BY AFFYMETRIX. NO LICENSE IS CONVEYED,
BY IMPLICATION, ESTOPPEL OR OTHERWISE, TO USE THIS
INSTRUMENT WITH MICROARRAYS MADE USING IN SITU OR
PHOTOLITHOGRAPHIC SYNTHESIS. NO OTHER LICENSE IS CONVEYED,
BY IMPLICATION, ESTOPPEL OR OTHERWISE, UNDER ANY AFFYMETRIX
PATENT OR OTHER INTELLECTUAL PROPERTY RIGHT.
This instrument is licensed by Affymetrix under the following patents:
U.S. Patent Nos. 5,578,832; 5,631,734; 5,834,758; 5,936,324;
5,981,956; 6,025,601; 6,141,096; 6,171,793; 6,185,030; 6,201,639;
6,207,960; 6,218,803; 6,225,625; 6,252,236; 6,262,838; 6,335,824;
6,403,320; 6,403,957, 6,407,858; 6,472,671; 6,490,533; 6,545,264;
6,597,000; 6,643,015; and 6,650,411.
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5001410 B 5
Contents
Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Who this manual is for . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Features of the GenePix SL50 Slide Loader . . . . . . . . . . . . 9
Applications of the GenePix SL50 Slide Loader. . . . . . . . . 10
Specifications of the GenePix SL50 Slide Loader
and GenePix 4300A/4400A Microarray Scanner . . . . . . . . 10
Safety and Regulatory Warnings and Markings . . . . . . . . 11
Electromagnetic Compatibility (EMC) . . . . . . . . . . . . . . . 13
Regulatory Information for Canada
(ICES/NMB-001:2006) . . . . . . . . . . . . . . . . . . . . . . . . 13
ISM Equipment Classification (Group 1, Class A) . . . . . . 13
Information to the User (FCC Notice) . . . . . . . . . . . . . . 13
Chapter 2 Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Operation Startup Procedure . . . . . . . . . . . . . . . . . . . . . 15
Turning on the control computer . . . . . . . . . . . . . . . . . . 15
Turning on the scanner. . . . . . . . . . . . . . . . . . . . . . . . . 15
Turning on the slide loader . . . . . . . . . . . . . . . . . . . . . . 16
Starting the GenePix Pro Software . . . . . . . . . . . . . . . . . 16
GenePix Pro Software icons . . . . . . . . . . . . . . . . . . . . . 16
Performing a Functional Checkout . . . . . . . . . . . . . . . . . 18
Manual Scanning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Batch Scanning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Stopping a Batch Scan . . . . . . . . . . . . . . . . . . . . . . . . 28
Setting PMT Gain Automatically . . . . . . . . . . . . . . . . . . 29
Performing a Batch Analysis . . . . . . . . . . . . . . . . . . . . 29
Reviewing the Batch Scan Log File . . . . . . . . . . . . . . . . 29
Shutting Down the Slide Loader. . . . . . . . . . . . . . . . . . . 30
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Contents
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Chapter 3 Routine Maintenance and
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Using Compatible Slides . . . . . . . . . . . . . . . . . . . . . . . . 31
Removing Particles from Equipment . . . . . . . . . . . . . . . . 32
Troubleshooting Fuse Errors . . . . . . . . . . . . . . . . . . . . . 32
Returning the Slide Loader to Home Position . . . . . . . . . . 33
Appendix A Warranty and Service . . . . . . . . . . . . . . . . . 35
Standard Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Out-of-Warranty Repair Service . . . . . . . . . . . . . . . . . . 35
Optional Service Agreement. . . . . . . . . . . . . . . . . . . . . 35
Technical Support. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
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5001410 B 7
Foreword
Who this manual is for
This manual is written for microarray service personnel and core lab
personnel using the GenePix®SL50 Slide Loader. It contains the
information required to load and operate the slide loader and perform
routine maintenance procedures.
Conventions
Within the scope of this manual, the following typographical
conventions are used:
CAUTION! Indicates an operation that may cause damage to the
instrument, device, or data, if the precautions are not followed.
Related documentation
The customer documentation for the GenePix SL50 Slide Loader
includes the GenePix®4300A/4400A User Guide, the GenePix®Pro 7
Software User Guide, and the GenePix®Pro online Help.
WARNING! Indicates an operation that may cause
personal injury if precautions are not followed.
Tip! Provides useful information that helps apply the techniques
and procedures in the text to your specific needs, and provides
shortcuts, but is not essential to the completion of a procedure.
Note: Provides essential information for the completion of a
procedure.
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Foreword
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5001410 B 9
1
Introduction
The GenePix®SL50 Slide Loader is a robotic slide loader system that
automates high-throughput operation of the GenePix 4300A and 4400A
Microarray Scanners.
The software user interface for the GenePix SL50 Slide Loader is
GenePix Pro 7.2 (and later) Software.
Features of the GenePix SL50 Slide Loader
The GenePix SL50 Slide Loader includes a wide range of features:
•Storage of up to 50 microarray slides
•A light-tight slide storage enclosure
•Removable slide cassettes
•Slide mapping
•Slide cassette detection
•Manual single-slide scanning capability, independent of the
automated mechanism
•3-axis robotic slide assembly, for moving slides from slide
storage to the scanner and back
•Support for Auto PMT on all scan areas for individual slides
•Accommodation of standard 1 inch by 3 inch (25 mm by 75 mm)
microscope slides
•Audible noise of less than 70 dB during operation
•Direct communication with the controlling PC using a USB
connection
•Diagnostics for calibration and for field support of robotics
•Full compatibility with GenePix 4300A and 4400A Microarray
Scanners
•Full integration with GenePix Pro 7.2 (and later) Software
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Introduction
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Applications of the GenePix SL50 Slide Loader
The GenePix SL50 Slide Loader can be used for numerous applications
related to the individual and batch processing of microarray slides,
including, but not limited to:
•Gene expression arrays
•Protein arrays
•Arrayed comparative genomic hybridization (aCGH) arrays
•Chromatin immunoprecipitation (ChIP) arrays
•DNA methylation arrays
•SNP genotyping arrays
•RNA interference (RNAi) arrays
•MicroRNA (miRNA) arrays
Specifications of the GenePix SL50 Slide Loader
and GenePix 4300A/4400A Microarray Scanner
Figure 1-1 GenePix SL50 Slide Loader and GenePix 4300A/4400A
Microarray Scanner Specifications
Specification Measurement
Weight (GenePix SL50 Slide Loader) 41 kg
Weight (GenePix 4300A/4400A scanner) 45 kg
Combined Weight 86 kg
Combined Height 620 mm
Combined Width 807 mm
Combined Depth 870 mm
Mains Power Input 100V - 240 VAC, 125W
Mains Voltage Fluctuations Not to exceed 10% of nominal
supply voltage
Equipment Class 1
Pollution Degree 2
Installation Category 2
Operating Environment Indoor Use Only
Altitude Not to exceed 2000 m
Operating Temperature 5 - 40 degrees C
Humidity < 80% RH at 40 degrees C
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GenePix SL50 Slide Loader User Guide
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Safety and Regulatory Warnings and Markings
Note the warnings and markings below as part of the preventative
maintenance of your slide loader.
WARNING! Biohazardous Material. It is your
responsibility to decontaminate the slide loader, as well
as any accessories, before requesting service from
technical support or before returning the slide loader or
any components to Molecular Devices.
WARNING! Biohazardous Material. Never perform any
maintenance procedures on the slide loader in an
environment where potentially damaging gases or
liquids are present.
WARNING! Shock Hazard. Do not remove the protective
enclosure or any covers marked with the high-voltage
warning symbol.
WARNING! Shock Hazard. Always turn the power switch
off and disconnect the main power cable before
performing any maintenance procedures.
WARNING! Shock Hazard. The GenePix SL50 Slide
Loader is an Equipment Class 1 product that relies on
protective earth grounding for safe operation. To avoid
potential injury, do not interrupt the protective earth
ground conductor (inside or outside the instrument) or
disconnect the protective earth ground terminal.
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Introduction
12 5001410 B
CAUTION! Do not touch or loosen any screws or parts other than those
specifically described in the maintenance procedures. Doing so may
cause misalignment and void the slide loader warranty.
CAUTION! Do not use the GenePix SL50 Slide Loader in a manner not
specified by Molecular Devices. Doing so may impair the protection
provided by the equipment and void the slide loader warranty.
WARNING! Pinching hazard. To avoid potential injury,
use caution when working near a potential pinch hazard
location.
WARNING! Lifting hazard. The slide loader weighs
approximately 90 pounds (41 kg) and is precisely
aligned to the scanner. To avoid potential injury and
potential damage to the alignment and equipment,
contact Molecular Devices if you need to move the slide
loader.
This symbol indicates that you must not discard this electrical or electronic
product in domestic household waste.
This symbol indicates the location of the Protective Earth Ground Terminal.
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GenePix SL50 Slide Loader User Guide
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Electromagnetic Compatibility (EMC)
Regulatory Information for Canada
(ICES/NMB-001:2006)
This ISM device complies with Canadian ICES-001.
Cet appareil ISM est conforme a la norme NMB-001 du Canada.
ISM Equipment Classification (Group 1, Class A)
This equipment is designated as scientific equipment for laboratory use
that intentionally generates or uses conductively coupled radio-
frequency energy for internal functioning, and is suitable for use in all
establishments, with the exception of domestic establishments and
those establishments directly connected to a low-voltage power supply
network which supplies buildings used for domestic purposes.
Information to the User (FCC Notice)
This equipment has been tested and found to comply with the limits for
non-consumer ISM equipment, pursuant to part 18 of the FCC Rules.
These limits are designed to provide reasonable protection against
harmful interference in a non-residential installation.
To maintain compliance with FCC regulations, shielded cables must be
used with this equipment. Operation with non-approved equipment or
unshielded cables can result in interference to radio and TV reception.
This equipment generates, uses, and can radiate radio frequency
energy and, if not installed and used in accordance with the
instructions, can cause harmful interference to radio communications.
There is no guarantee that interference will not occur in a particular
installation. If this equipment does cause harmful interference to radio
or television reception (determined by turning the equipment off and
on), the user is encouraged to try to correct the interference using one
or more of the following measures:
•Reorient or relocate the receiving antenna.
•Increase the physical separation between the equipment and
the receiver.
•Connect the equipment and the receiver into outlets on different
circuits.
•Consult the dealer or an experienced radio or television
technician for assistance.
The user is cautioned that changes and modifications made to the
equipment without the approval of Molecular Devices could void the
authority of the user to operate this equipment.
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Introduction
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5001410 B 15
2
Operation
The GenePix®SL50 Slide Loader should be in position on a flat level
surface before operating. Before using, make sure that qualified
Molecular Devices service personnel have installed and calibrated the
GenePix SL50 Slide Loader.
Operation Startup Procedure
The GenePix SL50 Slide Loader is designed to work with a GenePix
4300 Scanner or a GenePix 4400A Scanner. The startup procedure for
using the slide loader and scanner involves the following procedures:
•Turning on the control computer on page 15
•Turning on the scanner on page 15
•Turning on the slide loader on page 16
•Starting the GenePix Pro Software on page 16
Turning on the control computer
Molecular Devices service personnel will install and set up the slide
loader and scanner and connect them to a control computer where the
GenePix Pro Software is installed.
To turn on the control computer
•Turn on the control computer power switch.
Turning on the scanner
If this is the first time you are using the scanner, make sure you follow
the procedures in the user guide for the scanner before you start the
GenePix Pro Software.
To turn on the scanner
•Turn on the scanner power switch.
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Operation
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Turning on the slide loader
Initial startup of the GenePix SL50 Slide Loader includes a functional
check to confirm that the slide loader is performing according to the
specifications established by Molecular Devices.
To turn on the slide loader
1. Open the slide enclosure door of the slide loader and install both
the left and right slide cassettes. Go to To load the slide cassette
on page 24.
2. Close the slide enclosure door.
3. Turn on the slide loader power switch.
The power LED turns on. No movement occurs.
4. If this is the first time you are turning on the slide loader or if
you want to check the performance of the instrument, go to
Performing a Functional Checkout on page 18.
Starting the GenePix Pro Software
While it is recommended that you perform a functional checkout after
initial installation of the GenePix SL50 Slide Loader, this is not required
each time you start the GenePix Pro Software.
GenePix Pro Software icons
The icons shown in Table 2-1 on page 17 are used when operating the
GenePix SL50 Slide Loader.
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GenePix SL50 Slide Loader User Guide
5001410 B 17
Table 2-1 GenePix Pro Software icons
Icon Description
Scan Area Properties
Scanner Door is Open.
Click to Close Scanner Door.
Scanner Door is Closed.
Click to Open Scanner Door.
Hardware Settings
Preview Scan
Data Scan
Stop Scan
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Operation
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To start the GenePix Pro Software
1. Make sure that the slide loader and scanner are both free from
any obstructions.
2. On the control computer, click Start > Programs > Molecular
Devices > GenePix Pro 7 > GenePix Pro 7.
The slide loader moves to its starting position. If the scanner
door is open, the GenePix Pro Software closes the door before
performing calibration. The scanner is calibrated and the
GenePix Pro Software starts in Manual mode.
CAUTION! It is important to use slides that are compatible with the
GenePix SL50 Slide Loader microarray scanner. Using incompatible
slides can result in damage to the scanner or to the slides. For more
information, see Using Compatible Slides on page 31
CAUTION! It is important that you inspect the scanner’s slide holder, as
prompted by the software, and remove any slides that might be
remaining on the slide holder from a previous session. Failure to
remove slides can damage the slide, scanner, or slide loader.
3. If you are changing from Manual mode to Batch Scan mode and
the GenePix Pro Software prompts you to remove any slides in
the slide loader, click OK.
Performing a Functional Checkout
Use the Functional Checkout procedure to help you confirm that your
GenePix SL50 Slide Loader is performing according to factory
specifications. A similar, but much more detailed procedure, was
performed at the factory prior to shipping your unit.
The GenePix SL50 Slide Loader has been designed to provide robust
service for years of normal use. However, if you think there is a
problem with the slide loader, it is important to perform a functional
check before contacting Technical Support.
Note: For optimum performance, allow the GenePix
4300A/4400A Scanner to warm up for 15 minutes before
scanning slides with the GenePix Pro Software.
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GenePix SL50 Slide Loader User Guide
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We recommend that you perform a functional checkout once upon
receiving the instrument and then at any time you want to check the
performance of the instrument. The functional checkout procedure
checks that:
•the slide detection mechanism on the GenePix SL50 Slide
Loader is functioning correctly.
•the scanner and the slide loader are aligned correctly.
•the door of the scanner is opening and closing correctly and is
synchronized with the slide loader.
•the Data Scan feature of the scanner is functioning correctly.
Follow the To perform a Functional Checkout procedure to load four
compatible slides and configure and check the alignment and
movement of the slide loader and scanner.
To perform a Functional Checkout
1. Follow the startup procedure for using the slide loader and
scanner. See Operation Startup Procedure on page 15.
2. On the Batch Scan tab, in the Scan Type group, make sure
that Batch is the selected scan type.
If Manual is the selected scan type, click Select, select Batch,
remove any slides on the scanner’s slide holder, and click OK.
3. On the slide loader, open the slide enclosure door and remove
both the left and right slide cassettes.
4. Place four compatible slides in slide cassette positions 1, 25, 26,
and 50. For more information, see Using Compatible Slides on
page 31.
5. Return both the left and right slide cassettes into the slide
enclosure.
6. Close the slide enclosure door completely.
The Map Slides button on the Batch Scan tab is enabled. The
Scan Batch button remains disabled.
7. Click Map Slides.
The slide loader scans the two slide cassettes. When the scan is
complete, the Map window is updated to show the available
slides. The Scan Batch button is enabled.
8. On the Batch Scan tab, right-click on slides 1, 25, 26, and 50,
and then select Data Scan Only for all four slides.
9. Click Save loader settings.
Tip! Slide cassette positions 1, 25, 26, and 50 are equivalent to
positions 1 and 25 in each of the left and right slide cassettes.
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Operation
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10. On the Image tab, press Ctrl+N to create a New Settings file.
A scan area is created that matches the size of each slide. You
can reduce the amount of time for the scan by reducing the scan
area size.
11. Click Scan Area Properties.
12. Type the following values:
Left: 3500
Top: 5000
Width: 15000
Height: 3000
13. Click OK.
14. On the Batch Scan tab, click Scan Batch.
The batch scan begins and all four slides are loaded, scanned,
and unloaded, based on the defined settings.
The GenePix Pro Software automatically logs hardware
performance into the Hardware Diagnostics Report every two
hours during operation.
Manual Scanning
In Manual scan mode, the GenePix Pro Software operates the scanner
only, in a conventional way. You can open and close the motorized
scanner door, perform Preview Scans, Data Scans, adjust scanner
settings from the Hardware Settings dialog box, and stop and start
scans.
Any Global file options (Save locations, File name) set during a batch
scan apply when performing a manual scan.
Follow the instructions carefully when inserting a slide in the scanner
slide holder. The slide holder is a precision component designed to
ensure proper focusing and field uniformity. Improper handling may
damage the slide holder and affect imaging performance. In Manual
scan mode, the GenePix SL50 Slide Loader is inactive and will not
move.
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