iScan System

InstallationGuide

Document # 15020309 v03 ILLUMINA PROPRIETARY

March 2020 Internal Use Only
FOR RESEARCH USE ONLY
 Revision History
Revision History

Revision Date Description of Change

v03 March • Updated Logins and Passwords on page 4 to include System Computer.
2020 • Added note to Software Installation on page 18 to check ATS and ICS
software version on new instruments and spare PCs before installing.
• Added new section with Windows OS and iScan System Software Compatibility
on page 19.
• Added new section, API Key Installation on page 21.
• Updated last step in Final Installation Tasks on page 75.
• Added Manually Activate Windows 10 for Offline Instruments on page 73.
• In Install Accessory Equipment on page 77:
• Updated IQOQ reference to BeadLab Ancillary Equipment IQOQ
(Document # 1000000067830) for BeadLab accessories.
• Added photos of accessories.
• Added steps for Walton SD31 temperature controller in "Qualify the Heat
Block" section.
v02 April 2018 • Updated Perform the Functional Test on page 67.
• Removed Chapter 1 Safety; removed Electrical Safety, Laser Light Safety,
Moving Safety, Caution Markings, and Safety Interlocks and Defeats.
Moved General Safety to under Before You Begin.
• Added reference to iScan Safety and Compliance Guide under General
Safety.
• UpdatedSoftware Installation on page 18
• Updated Install ATS on page 20.
• Updated file name in Install iScan Control Software on page 22.
• Deleted last step in Install iScan Control Software on page 22.
• Changed value to 5.5 in NOTE in Verify Stage and Tray Function on page 34.
• Added to rows to If/Then table in Verify Stage and Tray Function on page 34.
• Updated Data CC Specs table in Verify Data CC on page 36.
• Added reference to Measure and Adjust XY Offsets on page 102 in Align the
BeadChip on page 44.
• Added new topic, Measure and Adjust XY Offsets on page 102.
• Updated If/Then table in Measure the Z-offset on page 55.
• Updated Tip Tilt and Chromatism Specs Table in Check Tip Tilt and
Chromatism on page 63.
• Deleted topic-Verify ICS Functionality.
• Changed Create New DataCC Folder to Create New DataCC Files on page
113.
• Updated screen shot in Measure the Green Laser Power on page 40.

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Revision Date Description of Change
v01 November • Corrected computer password (it is null) in Logins and Passwords on page 4.
2015 • Added Create New DataCC Files on page 113.
• Per C. Escano, removed the following items from on page 1 as they are
included in the iScan System Safety and Compliance Guide (15022905):
• “This is a Class 1 laser instrument as evaluated per IEC 60825-1:2007 (2nd
Edition) with consideration for IEC 60825-1:1993 + A1:1997 + A2:2001 and EN
60825-1:1994 + A2:2001 + A1:2002; CAN/CSA-E60825-1:R2007.”
• “Product Compliance” section.
• Incorporated feedback from Field Services in the Tilt Motor Adjustment on
page 109 to avoid crashing the slide holder into the objective (move tilt
motors 5.5 mm instead of 8 mm).
• Added Final Installation Tasks on page 75with instructions to complete iScan
System IQ/OQ (Document # 15021804) and upload to SFDC Field Asset page
per request from Field Services.
• Incorporated feedback from Product Support in Verify iScan Control Software
Functionality on page 1 to provide images for good BeadChip scans (step
13).
• Corrected Camera Barrel Mounting and Adjustment Screw Locations in
Camera Rotation Adjustment on page 105.
• Updated UPS information in Electrical on page 10.
B June 2013 • Incorporated feedback from subject matter experts throughout the guide
for clarity
• Reorganized the guide for logical flow
• Added “Manual Adjustments and Corrections” appendix which contains
procedure to address issues found during qualification
• Added the following sections:
• Install the Software
• Remove the Covers
• Load the BeadChip and Carrier
• Re-incorporated the following qualification procedures:
• Align the BeadChip
• Measure Adapter Tray Skew
• Measure the Z-offset
• Check Tip Tilt and Chromatism
• Replaced Camera Noise test with Verify Data CC test, which provides
additional data (viz. correction table test)
• Changed maximum Watts to 600 Watts
• Clarified the Verify Color Offset, X-Offset, and Camera Rotation on page 58
procedure and added Camera Rotation on page 61.
• Changed the green residual tip tilt spec to -0.75 to .75 µm.
• Changed red residual tip tilt spec to -1.5 to 1.5 µm.
• Changed chromatism spec to -0.75 to .75 µm.
• Changed Camera rotation spec to -4 to 4 pixels.

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 Revision History
Revision Date Description of Change
B June 2013 • Incorporated the following changes from C. Escano:
(continued) • Added UPS specs and updated part numbers
• Added air supply requirement (at least 35 psi required)
• Changed laser power exposure from 120mW to 110mW
• Changed Red Laser to wavelength 662nm, output power 110 mW
• Changed Green Laser to wavelength 532nm, Output power 50 mW
• For product compliance, added: IEC 61010-2-101: Safety Requirements for
Electrical Equipment for Measurement, Control, and Laboratory Use Part 2-
101: Particular Requirements for in Vitro Diagnostic (IVD) Medical
Equipment
• Changed the instrument and components weights to ~114 kg (~ 245 lbs)
• Added Isolation Platform Specifications
• For Laser Light Safety, added: This is a Class 1 laser instrument as evaluated
per IEC 60825-1:2007 (2nd Edition) with consideration for IEC 60825-1:1993 +
A1:1997 + A2:2001 and EN 60825-1:1994 + A2:2001 + A1:2002; CAN/CSA-
E60825-1:R2007. The iScan instrument also houses a Class 2 laser barcode
reader.
• Changed the psi spec for the Isolation Platform regulator to 25-35 from
30-35.
• Changes that occurred post-validation (VTS number VIR-2012-108):
• Corrected Hybex Heat Block, 115v part number. Changed to 11191471
• Removed the spare “S” suffix from all parts in table 8 and 9
• Changed X-offset spec to -8 pixels to 8 pixels between X coordinates
• Removed the “Color Balance the iScan System” section as this is now done
when measuring laser power
• Corrected ATS login and password information
• Added or changed solution paths for errors found during the following
qualification tests: Verify DataCC, Check Tip Tilt and Chromatism, and
Perform the Functional Test.
A July 2011 Initial publication

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 Table of Contents

Revision History 2
Table of Contents 5

Chapter 1 Before You Begin 1

General Safety 2
Intended Audience 3
Reference Documents 3
Installation Procedure Workflow 3
Logins and Passwords 4
Tools and Additional Equipment Required 5

Chapter 2 Preinstallation Procedures 7

Inspect the Laboratory 8
Box Dimensions and Contents 8
Laboratory Space Requirements 9
Instrument Dimensions 9
Laboratory Bench Guidelines 10
Isolation Platform Specifications 10
Electrical 10
Environmental Conditions 12
Network 12
Inventory the System Components 13
System Components 13

Chapter 3 iScan System Setup 15

Unpack and Install the Uninterruptible Power Supply (UPS) 16
Install the Computer and Monitor 17
Software Installation 18
Windows OS and iScan System Software Compatibility 19
Install ATS 20
API Key Installation 21
Install iScan Control Software 22
Unpack and Place the Isolation Platform 23
Qualify the Isolation Platform 24
Unpack and Connect the iScan System 25
Remove the Covers 26
Unlock the Z-Stage 28
Unlock the Optical Bench 29
Remove Optical Bench Foam 30
Turn on and Initialize the System 31

Chapter 4 Qualify the iScan System 33

Verify Stage and Tray Function 34
Verify Data CC 36
Measure the Laser Power at the Objective 38
Measure the Green Laser Power 40
Measure the Red Laser Power 41
Load the BeadChip and Carrier 42
Check the Barcode Reader 43
Align the BeadChip 44
Check the Laser Line Quality 46
Green Laser Line Quality 46
Red Laser Line Quality 50

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 Review the Results 50
Measure Adapter Tray Skew 51
Measure the Z-offset 55
Verify Color Offset, X-Offset, and Camera Rotation 58
Camera Rotation 61
Check Tip Tilt and Chromatism 63
Perform the Functional Test 67
Perform Functional Test at + 0.0015mm From Best Focus 70
Perform Functional Test at -0.0015mm From Best Focus 71
Interpreting Results 72
Manually Activate Windows 10 for Offline Instruments 73
Final Installation Tasks 75

Appendix A Install Accessory Equipment 77

Unpack and Install the Hybridization Oven 78
Qualify the Hybridization Oven 79
Unpack and Install the Heat Block 81
Qualify the Heat Block 82
Unpack and Install the Shaker 84
Qualify the Shaker 84
Unpack, Install, and Qualify the Heat Sealer 86

Appendix B Manual Adjustments and Corrections 87

Remove the Front-Door Latch 88
X-Soft Limit Adjustment 90
Verify the X-Soft Limits 90
Laser Power Adjustments 92
Line Centering Adjustment 93
Center Camera Line 93
Check and Correct Green Line Rotation 96
Adapter Plate De-Skew 97
Adjust Optical Bench Tilt 98
Chromatism Adjustment 100
Color Offset Adjustment 101
Measure and Adjust XY Offsets 102
X-offset Adjustment 104
Camera Rotation Adjustment 105
Z-Offsets Verification 106
Tilt Motor Adjustment 109
Create New DataCC Files 113

Index 119
Technical Assistance 121

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   Chapter 1  Before You Begin

Before You Begin

Chapter 1
General Safety 2
Intended Audience 3
Tools and Additional Equipment Required 5

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Before You Begin
General Safety
Before servicing the iScan System, review the safety information included in the iScan
System iScan System Safety and Compliance Guide (Document #15022905).
The following section describes general safety precautions when using the iScan System.
These include precautions for:
} General safety
} Electrical safety
} Laser light safety
} Moving safety

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 Intended Audience
Intended Audience
This guide is intended for qualified field service engineers (FSEs). Qualified engineers are
those who have received appropriate service training, and are authorized to carry out the
installation procedures described in this guide by appropriate managers within the
Customer Solutions organization.

Reference Documents
The following documents may contain useful or necessary information about the iScan
System, or may be referred to within this guide.
Table 1 Reference Documents
Document Number Title

15021804 iScan System IQ/OQ

11325281 iScan System Field Service Guide

11313555 iScan System System Quick Reference Card

Installation Procedure Workflow

The general workflow is illustrated in Figure 1.

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Before You Begin
Figure 1 Installation Workflow

Logins and Passwords

Table 2 Field service logins and passwords
Application Login Password

System Computer Illumina Contact Regional Product

Support
ATS — sandiego

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 Tools and Additional Equipment Required
Tools and Additional Equipment Required
To perform this installation, you need the following tools:
} Standard Field Service Engineer (FSE) Toolkit.
} Dyed bead standard slide (part # 15013953)
} ATS and iScan Control Software software applications
} Laser power meter
} Color balancing tool (part # 15020683S)
} Stroboscope
} Fluke Meter

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6 iScan System Installation Guide
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   Chapter 2  Preinstallation Procedures

Preinstallation Procedures

Chapter 2
Inspect the Laboratory 8
Inventory the System Components 13

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Preinstallation Procedures
Inspect the Laboratory
Ensure the laboratory meets minimum requirements that are described below.
The iScan System arrives in a blue corrugated plastic box with the computer and
accessories bundled on top, similar to the configuration shown below.
Figure 2 iScan System

WARNING
At least two people are required to lift the instrument to the lab bench top. The instrument
and components weighs ~114 kg (~245 lbs).

Box Dimensions and Contents

The components of the iScan System are shipped in four boxes. Use the following
dimensions to determine the minimum door width required to accommodate the shipping
boxes.
} Box #1 contains the iScan System instrument.
} Box #2 contains the workstation PC, keyboard, and accessories.
} Box #3 contains the workstation monitor.
} Box #4 contains the isolation platform.

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 Inspect the Laboratory
Table 3 Box Dimensions
Measurement Box #1 Box #2 Box #3 Box #4

Width 122 cm (48 in) 56 cm (22 in) 41 cm (16 in) 75 cm (30 in)

Height 74 cm (29 in) 36 cm (14 in) 23 cm (9 in) 19 cm (8 in)

Depth 71 cm (28 in) 56 cm (22 in) 48 cm (19 in) 66 cm (26 in)

Shipping Weight 90 kg (198 lbs) 31 kg (67 lbs) 18 kg (40 lbs)

Instrument
Alone: 71 kg
(157 lbs)

Laboratory Space Requirements

The bench must be capable of safely supporting the weight of the iScan System, isolation
platform, and dedicated workstation, approximately 111 kg (245 lbs).
} Make sure that the iScan System is accessible from all sides.
} Allow for an additional 15.5 cm (6 in) behind the instrument.
} Position the iScan System so that personnel can quickly disconnect the power cord
from the outlet.
} The Lab Bench surface must be level (within ± 2 degrees) and be non-vibrational.
} The iScan System must be located away from other machinery that generates any
vibration.
} The iScan System loaded on the isolation platform requires 42 cm (17 in) above it to
take off the exterior panels during installation and maintenance. The height dimension
listed in the following table includes this required overhead space.
The dual-scanner configuration, consisting of two iScan System instruments and a Robot.
easily fits on a typical bench.
Figure 3 Dual-Configuration Setup

Instrument Dimensions
The iScan System, isolation platform, and dedicated workstation have the following
dimensions upon installation:

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Preinstallation Procedures
Table 4 Instrument dimensions
iScan Computer, Keyboard, and Isolation
Dimensions
System  Monitor Platform

Width 52 cm 21.6 cm (8.5 in.) 69 cm (27 in.)

(20.4 in.)

Height 46 cm (18 in.) 57 cm (22.3 in.) 6 cm (2 in.)

Depth 66 cm (26 in.) 55.4 cm (21.8 in.) 61 cm (24 in.)
Weight 65 kg 34 kg (75 lbs.) 12 kg (26.5 lbs.)
(143 lbs.)

Laboratory Bench Guidelines

Illumina recommends placing the instrument on a mobile lab bench with locking casters.
The bench must be capable of supporting the weight of the instrument and workstation.
Table 5 Lab Bench Guidelines
Width Height Depth

52.4 cm (60 in) 76.2–91.4 cm (30–36 in) 76.2 cm (30 in)

For North American customers, Illumina recommends the following mobile lab bench:
Bench-Craft (www.bench-craft.com), part # HS-30-60-30P2 with casters
} HS indicates standard bench
} 30-60-30 indicates 30 inches wide × 60 inches, long × 30 inches high
} P2 indicates outlets on rear of bench

Isolation Platform Specifications

The isolation platform that the iScan System sits on helps isolate the instrument from
vibrations produced by the surrounding environment. The isolation platform is placed
between the iScan System and the laboratory bench top and is hooked up to a regulator
connected to the house air line.
The isolation platform pressure should be set to a nominal value of 25 psi and should not
exceed 40 psi. The maximum pressure from the house line to the air regulator should not
exceed 80 psi.
NOTE
The iScan System is very sensitive to vibrations. Because of this, the isolation platform is
mandatory.

Electrical
The power consumption of the iScan System and its components are shown below. The
instrument operating specifications are:
} 100V–240V
} 50/60 Hz
} 600W
} Fuse: T10A, 250VAC (Slow Blow)

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 Inspect the Laboratory
Table 6 iScan System Electrical Requirements
Equipment Description

iScan System The building should be wired with the following receptacles:
• 100–120 volts AC: A 20-amp grounded, dedicated line with proper
voltage and electrical ground is required.
North America and Japan—receptacle: NEMA 5-20
Interpower Corp. receptacle, part # 88030080 (or equivalent)
• 200–240 volts AC: A 10-amp grounded line with proper voltage and
electrical ground is required.

Power Line If the voltage fluctuates more than 10%, a power line regulator is
Regulator required.

Uninterruptible Shipped with the instrument. See Table 7.

Power Supply

Table 7 iScan SystemUninterruptible Power Supply (UPS)

Specificatio
North American International Japan
n

Model ABCE80 ABCE80 ABCE80 ABCE80 ABCE80 ABCE80

Number 0-11B 2-11B 0-22B 2-22B 0-11B 2-11B

MFG PN 54080- 50080- 55080- 55080- 54080- 50080-

96R 96R 70R 70R 95R 95R

Max Watts 560 Watt 720 Watt 560 Watt 720 Watt 560 Watt 600 Watt

s s s s s s

VA Rating 800 VA 800 VA 800 VA 800 VA 660 VA 670 VA

Input 120 VAC 120 VAC 230 VAC 230 VAC 100 VAC 100 VAC

Voltage (96–151 60 HZ (181–290 50/60 HZ 60 HZ 50/60 HZ
(Nominal) VAC (96–144 VAC (185–276 (80–
without VAC without VAC 120 VAC
using without using without without
batteries) using batteries) using using
batteries) batteries) batteries

Input NEMA 5- NEMA 5- IEC 320 IEC 320 NEMA 5- NEMA 5-

Connection 15P 15P Inlet Inlet 15P 15P
Module Module
with with
input line input line
cord cord
provided provided

Typical 9–13 9–13 9–13 9–13 9–13 9–13

Run Time minutes minutes minutes minutes minutes minutes
(50% load)*

Typical 4–6 4–6 4–6 4–6 4–6 4–6

Run Time minutes minutes minutes minutes minutes minutes
(100%
load)*

*    Back-up runtime information is based on estimates. Actual runtime may vary depending upon the
loads and power factors of the protected equipment and the condition of the UPS batteries.

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Preinstallation Procedures

Environmental Conditions
The lab should maintain a temperature between 15–30° C ± 2° C (59–86° F ±36° F) with the
relative non-condensing humidity kept between 20 to 80%.

Network
Illumina does not provide installation or technical support for networking in the dedicated
workstation. Customers must use a one gigabit connection between the iScan System
computer and their data management system. This connection can be made either directly
or through a network switch.
If multiple microarray scanning instruments all copy to the same server, the server drive
may not be fast enough to handle all the traffic. Customers should consider having the
instruments copy to different servers.
If multiple microarray scanning instruments share a connection to copy to their target
servers, the connection may not be fast enough to handle all the traffic. Customers should
consider having the instruments use different routes.

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 Inventory the System Components
Inventory the System Components
} Use the Systems Components checklist below to identify the system components are
present and undamaged.
} Record a description and part number for damaged or missing components in the
Notes section on the iScan System IQOQ, document # 15021804.

System Components
Table 8 Blue box contents
√ Blue Box Contents Part Number

□ iScan System 11279781

□ Isolation platform 222009S

□ Uninterruptible power supply (UPS) Varies. See Table 9 on page 13

□ Hybridization Oven (115v) 11277582

□ Hybridization Oven (230v) 11277591

□ Hybex Heat Block, 115v 11191471

□ Hybex Heat Block, 220v 11191480

□ Shaker (USA model) 190318

□ Shaker (International model) 11140324

□ Heat Sealer (110v) 11142944

□ Heat Sealer (230v) 11143103

□ Accessories Box Contents

□ Computer 11287975

□ Monitor and stand 15004087

Table 9 UPS Part Numbers by Region

Region Part Number

AMR 15034121

Japan 15034122

UK 15034123

Europe 15034125

China 15034126

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14 iScan System Installation Guide
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   Chapter 3  iScan System Setup

iScan System Setup

Chapter 3
Unpack and Install the Uninterruptible Power Supply (UPS) 16
Install the Computer and Monitor 17
Software Installation 18
Windows OS and iScan System Software Compatibility 19
Install ATS 20
API Key Installation 21
Install iScan Control Software 22
Unpack and Place the Isolation Platform 23
Qualify the Isolation Platform 24
Unpack and Connect the iScan System 25
Remove the Covers 26
Unlock the Z-Stage 28
Unlock the Optical Bench 29
Remove Optical Bench Foam 30
Turn on and Initialize the System 31

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iScan System Setup
Unpack and Install the Uninterruptible Power Supply
(UPS)
1 Open the UPS shipping container and:
a Remove the packing material from around the unit.
b Lift the UPS out and onto the bench.
2 Record the UPS serial and model numbers on the iScan System IQ/OQ (Document #
15021804).
3 Remove warning labels from the unit.
4 Plug the 2-prong battery connection into the back of the UPS.
Figure 4 UPS back panel

5 Connect the UPS power cable to a wall outlet.

6 Power on with the I (Test) button and observe the correct LED power-up sequence:

Sequence Green LED Activity

Battery Charge Solid

On Line Flashing

On Battery Solid

On Battery Off

On Line Solid

7 Record the power on success on the iScan System IQ/OQ (Document # 15021804).
8 Power off by pressing the power button to O.

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 Install the Computer and Monitor
Install the Computer and Monitor
1 Place the computer and monitor on the bench.
NOTE
If the iScan System is being installed with an AutoLoader, follow the AutoLoader assembly
instructions to install the monitor on the stand.
2 Record the computer service tag and model information on the iScan System IQ/OQ
(Document # 15021804).
3 Connect the mouse, keyboard, and monitor to the computer.
NOTE
If the iScan System is being installed with an AutoLoader, attach the mouse and keyboard
that are installed in the baseplate drawer.
4 Connect the computer and monitor to the UPS.
5 Turn on the UPS with the I (Test) button.
6 Turn on the computer and monitor.
7 Log in as the Illumina account using the default password.
The OS automatically prompts you to change the password.
8 Create a new password 10-character for use during installation.
At the end of the installation, help the customer change the password for their use.

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iScan System Setup
Software Installation
NOTE
New instruments and spare PCs are shipped with the ATS and ICS software pre-installed.
Check to see if the latest version is installed before proceeding.
1 Create a folder called FSE at the root of the D:\ drive.
2 Download the latest versions of iscan-ats-software and iscan-control-software from ICE
to the D:\FSE folder and unzip them.

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 Windows OS and iScan System Software
Windows OS and iScan System Software Compatibility
Table 10 Windows OS and iScan System software compatibility matrix
Windows OS ATS iScan Control Software

Windows 7 v3.1.17 and v3.1.32 v3.4.8

Windows 10 v1.2.0.9 v.4.0.0.147

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iScan System Setup
Install ATS
1 Navigate to the D:\FSE\ATS folder.
2 Create a shortcut to ATS.EXE on the desktop.

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 API Key Installation
API Key Installation
1 Download the API key zip file from the instrument's Installed Product page in SFDC.
2 Unzip the file.
3 Confirm that the API key name is CloudApiKey.xml.
4 Open CloudApiKey.xml in a text editor and verify that the serial number matches the
serial number of the installed instrument.
5 Navigate to E:\Archimedes_Flash.
6 Copy CloudApiKey.xml to the E:\Archimedes_Flash folder.

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iScan System Setup
Install iScan Control Software
1 Navigate to the D:\FSE\iscan-control-software folder and double-click
InstallSoftware.bat.
2 Click Next at the Welcome screen.
3 Accept the license agreement, and then click Next.
4 In the Destination Folder screen, leave the default installation folder and click Next.
5 Click Install.
6 When the installation is complete, click Finish.
The installer creates a shortcut for iScan Control Software on the desktop.

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 Unpack and Place the Isolation Platform
Unpack and Place the Isolation Platform
Unpack and Install the Isolation Platform as follows:
1 Open the shipping container and:
a Remove the packing material from around the unit.
b Remove the plastic wrapping from the isolation platform.
c Lift the isolation platform onto the bench.
2 Remove the accessory bag (user guide, tubing, hex driver and tubing adapter) and set
aside for later use.
3 Open the air pressure regulator container and remove the packing material from
around the unit and place the regulator with the accessory bag.
4 Position the platform where the iScan System will be installed as the instrument sits on
top of the isolation platform. Record successful platform positioning on the  iScan
System IQ/OQ (Document # 15021804).
5 Retrieve the tubing from the accessory bag.
6 Cut an appropriate length of tubing and connect one end of it to the barbed adapter
coming from the isolation platform and the other end to the air pressure regulator.

7 With the remaining tubing, connect the air pressure regulator to the air supply
ensuring the regulator is oriented in the proper direction for the flow of air.

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iScan System Setup
Qualify the Isolation Platform
1 Place the Isolation Platform on the bench so that the adjustment valves on the front are
accessible.
2 Close the air supply to the air pressure regulator.
3 Using the hex nut driver provided in the accessory bag, fully close all three adjustment
valves.
Figure 5 Three Adjustment Valves

4 Slowly open the Both Rear center valve two complete turns.
5 Slowly open the Left Front and Right Front valves ¼ turn each.
6 Open the compressed air supply to the air pressure regulator.
7 Turn on the air supply and set the regulator to 25–35 PSI.
8 Record the regulator PSI value on the iScan System IQ/OQ (Document # 15021804).
9 Verify that all four corners of the isolation platform are floating and that none of the
corners sink after inflating.
10 If the air table oscillates after inflation, the valves are open too much. To correct, slowly
close Left Front and Right Front valves by turning in 1/16 increments until the
oscillation stops.
Figure 6 Floating corners

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 Unpack and Connect the iScan System
Unpack and Connect the iScan System
1 Cut and remove the black bands securing the shipping container and remove the two
boxes on top of the blue container.
2 Inspect the shipping indicators on the interior and exterior of the blue shipping
container. Record the status of the shipping indicators on the iScan System IQ/OQ
(Document # 15021804).
3 Remove the adapter tray and blue adapter plate taped to the top of the unit and put
them aside for later use.
4 Remove the tape and black plastic antistatic material covering the instrument.
5 With at least two people lifting, center the iScan System on the isolation platform.
6 Rebalance the isolation platform and verify that the platform floats correctly and record
on the iScan System IQ/OQ (Document # 15021804).
7 Connect the USB cable from the iScan System to a USB port on the back of the
computer.
8 Connect the Camera Link cable from the iScan System to the frame grabber card on the
back of the computer. Ensure both terminals are tight.
IMPORTANT
The Camera Link cable is fragile. Handle with care, and do not shape it into a tight loop.
9 Record the serial number of the iScan System on the iScan System IQ/OQ (Document #
15021804).

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iScan System Setup
Remove the Covers

1 Use an 8 mm Allen wrench to unscrew the top panel.

2 Slide the top panel toward the back of the scanner, and lift it off.
Figure 7 Loosen Top Panel

3 Unscrew the two thumb screws holding the side panels on and let them hang away
from the scanner.
Figure 8 Loosen Side Panels

4 Unscrew the front thumb screw and separate the top sheet metal frame from the front
panel.
Figure 9 Separate Top Sheet Metal Frame

5 Allow the front panel to lie down in front of the instrument with all of the cables to the
front panel still connected.

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 Remove the Covers
Figure 10 Front Panel Cables

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iScan System Setup
Unlock the Z-Stage
1 Insert a M2.5 hex Allen wrench into the hole on the lower–right side of the instrument
and engage the lock screw.
Figure 11 Engage the Lock Screw

2 Push the screw inward approximately 3mm. You will feel resistance when pushing the
screw inward.
3 Turn the screw counterclockwise until it stops, about 180 degrees. Make sure that the
spring and cord are loose, or you might encounter Z-movement errors during
qualification.
4 Record your successful unlocking of the Z-stage on the iScan System IQ/OQ (Document
# 15021804).

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 Unlock the Optical Bench
Unlock the Optical Bench
1 Insert a M2.5 hex Allen wrench into one of the holes on the lower left side of the
instrument and engage the lock-screw.
Figure 12 Unlocking the optical bench

2 Turn the screw approximately 12 turns counterclockwise until it stops turning.

3 Remove the M2.5 hex Allen wrench from the hole.
4 Repeat procedure on the second hole on the lower–left side of the instrument.
5 Record successful unlocking of the optical bench on the iScan System IQ/OQ
(Document # 15021804).

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Remove Optical Bench Foam
1 Partially open the side panels of the instrument.
2 Remove the foam located on each side of the optical bench.
3 Hand-tighten the objective.
4 Record successful packing foam removal on the iScan System IQ/OQ (Document #
15021804).

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 Turn on and Initialize the System
Turn on and Initialize the System
1 Turn on the instrument with the power switch above the power cord.
2 Wait for the flash drive to load. The Archimedes_Flash folder appears when loading is
complete.
Figure 13 Archimedes_Flash folder

3 Create a folder D:\Installation and copy the entire Archimedes_Flash folder into it.
4 Verify that the Y-stage solenoid brake is released when the iScan System powers up.
NOTE
If the Y-stage solenoid does not release automatically, it must be released manually
before the iScan System can be used.

Figure 14 Release Y-solenoid

5 Start ATS and log in with the password sandiego. The instrument initializes
automatically.
6 Click Home All to home all of the motors.
Figure 15 ATS Buttons

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7 Click the Main | About tabs and record the following information on the iScan System
IQ/OQ (Document # 15021804):
• ATS version (called Tool Version)
• iScan System serial number (Scanner ID)
• FPGA version
• Camera Firmware
• Camera Driver
• Camera Model
Figure 16 Record This Info on Checklist

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   Chapter 4  Qualify the iScan System

Qualify the iScan System

Chapter 4
Verify Stage and Tray Function 34
Verify Data CC 36
Measure the Laser Power at the Objective 38
Load the BeadChip and Carrier 42
Check the Barcode Reader 43
Align the BeadChip 44
Check the Laser Line Quality 46
Measure Adapter Tray Skew 51
Measure the Z-offset 55
Verify Color Offset, X-Offset, and Camera Rotation 58
Check Tip Tilt and Chromatism 63
Perform the Functional Test 67
Perform Functional Test at + 0.0015mm From Best Focus 70
Perform Functional Test at -0.0015mm From Best Focus 71
Interpreting Results 72
Manually Activate Windows 10 for Offline Instruments 73
Final Installation Tasks 75

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Verify Stage and Tray Function
1 Click Open Tray and visually verify that the tray:
• Is roughly centered in the door opening.
• Is not hitting or rubbing on one of the sides.
• The back lip does not hit the array height sensors or the cabling around the array
height sensors.
2 Click Close Tray while holding the door open by hand. Then check that:
• The tray retracts and hits the hard stop. You will hear the metal on metal contact.
• The stage retracts to a position where the openings for the tilt motors are centered
in X and Y over the tilt motors.
NOTE
If you cannot easily see the tilt motor locations, you can raise them in the Hardware|
Motors tabs by entering 5.5 in the All Tilts position box and pressing Enter.

Figure 17 Tilt Motor Raised

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 Verify Stage and Tray Function
Figure 18 Hardware | Motors Tabs

3 If there are problems, select from the following:

If the... Then, see...

Tray does not eject Remove the Front-Door Latch on page 88

X-stage is hitting the door hinges, is unable X-Soft Limit Adjustment on page 90
to home, or soft limits exceeded error
messages appear
Back lip hits the array height sensors or Adjust array height sensor to clear back lip, or
wiring rearrange cabling.

Tilt motors are not centered front to back Adjust tray retract limit switch position.

If the tilt motors are not centered left to Adjust Undocked Y position in override.cfg.
right when the stage is retracted

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Verify Data CC
1 Click the Main | Sample tabs and change the Output Repository to
D:\Installation\DataCC.
2 Click the Operations | Scan tabs and set up the manual scan as follows:
a Click to clear the Image Correction check box.
b Set the Length of Scan to 2048.
c Select Data CC Verification.
Figure 19 Manual Scan

3 Click Manual Scan.

The scan will generate four graphs, two for each channel, with values for raw and
corrected data. The following figure shows sample output.
4 Review the graphs to check if the Data CC values are within spec.
Table 11 Data CC Specs
Spec: If Out of Spec See:

Max ≤ 650 Create New DataCC Files on page 113

Min ≥ 350

Diff ≤ 100

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 Verify Data CC
Figure 20 Data CC Graphs

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Measure the Laser Power at the Objective
1 In ATS, click Open Tray.
2 Place the adapter tray into the instrument tray.
3 Place the color balancing tool on the adaptor.
4 Place the laser power meter wand into the slot on the color balancing tool.
Figure 21 Adaptor Tray, Color Balancing Tool, and Wand

A Color balancing tool

B Adapter tray
C Laser power meter wand

5 Click Close Tray. The tray door does not close completely due to the wand wire.
Figure 22 Wand wire

\
A Tray door
B Wand wire

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 Measure the Laser Power at the Objective
6 Click the Main | Sample tabs.
7 Select the beadtype: 206252 – 12x1 in slide 2 and slide 3 locations.
Figure 23 Setup the Sample

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8 Click the Location tab, then click on a point between the two BeadChips and midway
between the 1st and 2nd stripes from the top to position the power meter sensor under
the objective lens.
Figure 24 Selecting Sensor Position

A Stripes
B Selected sensor position

Measure the Green Laser Power

1 On the laser power meter, set the wavelength to 532 nm.
2 Put on laser safety goggles.
3 Click on the Hardware | Filters/Lasers tabs.
4 Under Optical Path One – Filters (green laser), set the Excitation Filter field to
OpenBandPass.
5 Note the laser power reading on the meter and record it on the iScan System IQ/OQ
(Document # 15021804).
6 Under Optical Path One – Filters (green laser), set the Excitation Filter field to Blocked.

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 Measure the Laser Power at the Objective
Figure 25 Setting Filters

Measure the Red Laser Power

1 On the laser power meter, set the wavelength to 662 nm.
2 Under Optical Path Two – Filters (red laser), set the Excitation Filter field to
OpenBandPass.
3 Note the laser power reading on the meter and record it on the iScan System IQ/OQ
(Document # 15021804) (spec = 70 mW ± 4 mW).
If the green or red laser power do not meet spec, adjust the corresponding settings in
the Override.cfg file and repeat the measurements until the spec is met.
See Laser Power Adjustments on page 92 for information.

NOTE
The green/red power ratio should be 0.5 ± 0.05 at the end of this process.
4 Under Optical Path Two – Filters (red laser), set the Excitation Filter field to Blocked.
5 Click Open Tray and remove the color balancing tool and laser wand from the
instrument.

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Load the BeadChip and Carrier
1 Install the BeadChip on the BeadChip carrier in position 2.
Figure 26 BeadChip on Carrier

2 Install the BeadChip carrier on the adapter tray.

Figure 27 BeadChip Carrier on Tray

3 Click Close Tray.

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 Check the Barcode Reader
Check the Barcode Reader
1 In ATS, click Hardware | Barcode Reader tabs.
Figure 28 Barcode Test

2 Click Scan to start the test and check the Scan Values.
Table 12 Scan Values
If... Then...

Positions 1, 3, and 4 do not show Adjust the barcode scanner starting positions. In
EMPTY the [Barcode_Reader] section of Override.cfg file,
change the X_Offset or Y_Offet if required.
Position 2 and the Carrier Barcode are
not populated

3 Record results on the iScan System IQ/OQ (Document # 15021804).

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Align the BeadChip
1 Click the Tools | Auto Align tabs.
2 Click the Image tab, then click the green camera icon.
3 Click Auto Tilt.
If there are auto-tilt errors, see Tilt Motor Adjustment on page 109.
Figure 29 Auto Tilt Tab

4 Click Auto Center.

The system will find three fiducials at the extremities of the stripes. Use the sliders to
the left of the image to adjust image quality.
5 Verify that each fiducial is centered in the image. If there are auto-center errors, refer to
Measure and Adjust XY Offsets on page 102.

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 Align the BeadChip
Figure 30 Fiducial is Centered

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Check the Laser Line Quality
This test is used to evaluate how close the laser lines are to the center of each CCD, as well
as to check for line rotation and clipping. This is done by moving a blank section of the
slide (where no cores exist) under the laser beam, and imaging the reflected line on the
camera.

Green Laser Line Quality

1 Click the Location tab in the right pane, and click on a region of the BeadChip outside
the stripes.
Figure 31 Region Outside the Stripes

2 Click the Hardware | Camera tabs and do the following:

a Click Set Default Camera Mode.
b Select Full Frame twice.
c Click Continuous.

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 Check the Laser Line Quality
Figure 32 Camera Tab

3 Click the Hardware | Filters/Lasers tabs.

4 In the Optical Path One (green) set the Excitation Filter to OD3 and the Emission Filter
to Open.
5 On the Image tab, select the green camera icon.
6 Adjust the contrast bars to the left of the Image tab to clearly see the laser line on the
camera.
7 Click the Hardware | Motors tabs and focus the line by jogging the Z-stage up or down
in progressively finer increments from 0.01 to 0.001 mm. (Enter increments in the Δ
field.)

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Figure 33 Motors Tab

8 Measure and record line centering. Zoom in and place the cursor on the middle of the
line and verify that the line is centered at Y = 64 ± 2. (Middle X coordinate = 1024
pixels).
If line is not centered, see Line Centering Adjustment on page 93.

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 Check the Laser Line Quality
Figure 34 Verify Line is Centered

9 Measure and record line rotation by placing the cursor at the extreme ends of the
focused line and noting differences between the Y positions.
If line is rotated more than 2 pixels, see Check and Correct Green Line Rotation on page
96.
Figure 35 Measure Line Rotation

10 Verify and record that the line extends all the way to the ends of the display. If not, it
might indicate clipping.

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IMPORTANT
If the line is clipped, contact Regional Product Support.
11 Set the green excitation and emission filters to BlockPosition.

Red Laser Line Quality

1 Repeat the steps in the Green Laser Line Quality on page 46 for the red laser, setting the
Excitation Filter to OD5 under Optical Path Two (red). Also, click the red camera icon.
HINT
Sometimes it helps to add a drop-in OD filter to reduce image saturation when testing the
red channel.
2 Set the red excitation and emission filters to BlockPosition.
3 Click Pause followed by Stop to stop the camera.

Review the Results

The following table provides an overview of the laser line results and what to do if out-of-
spec.
Table 13 Laser Line Results
If... Then...

The green line is not centered at Y = 64 ± 2 See Line Centering Adjustment on page 93.
(middle X coordinate = 1024 pixels)

The green line is rotated more than 2 pixels See Check and Correct Green Line Rotation on
page 96.

The green line does not extend all the way This might indicate clipping. Contact
to the ends of the display Regional Product Support.

The red line is rotated more than 2 pixels Rotate the red camera to match the line. See
Camera Rotation Adjustment on page 105 for
information.

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 Measure Adapter Tray Skew
Measure Adapter Tray Skew
This test measures beads along the long edge of a stripe to verify that the adapter tray is
aligned to the scan (Y) axis of the iScan System.
1 Click the Tools | Auto Align tabs, then click Entire Alignment.
When this routine is complete, the system leaves the top right fiducial of the first stripe
parked under the objective lens as shown in .
Figure 36 Objective Centered Over Top-right Fiducial

2 Perform a 4000 line manual scan at this location as follows:

a Click the Scan tab.
b Select the Grn channel and clear the Red channel.
c Click to clear the Image Correction check box.
d Click the Reflective Mode Only check box.
e Enter 4000 in the Length of Scan field.
f Click Manual Scan.

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Figure 37 Manual Scan Settings

3 View the green channel.

4 If the image appears out of focus, increment the Z-motor (Δ field) by 0.001 in either
direction and rescan.
5 Adjust X and Y motor positions (Hardware | Motors tabs) and repeat the scan until
the corner of the stripe is approximately in the middle of the image.
Figure 38 Right Corner of Well is Visible

Corner of stripe

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 Measure Adapter Tray Skew
NOTE
The scan image is rotated 270° from the actual position of the slide. The image of the top-
right corner of the stripe will appear as the top-left corner as shown in the previous figure.
6 Change the length of the scan to 32000 and click Manual Scan.
7 Check that the scan image contains the top-left and the bottom-left wells.
Figure 39 Corners of Wells

8 If needed, adjust the X and Y motors so the next scan will contain both corners of the
wells.
9 Repeat steps 6–8 until both corners are visible.
10 Zoom in on the top-left corner of the image (Figure 40). Hold the cursor over this corner
and record the X position at this point. (This corresponds to the top-right well on the
stripe.)
Figure 40 X Position on Top-Left Corner

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11 Scroll to the bottom-left corner of the image. Hold the cursor over this well and record
the X position at this point. (This corresponds to the top left well on the stripe.)

If... Then...

The difference between the two X positions Deskew the adapter plate. See Adapter Plate
is > 15 pixels De-Skew on page 97.

Figure 41 X Position at Bottom-Left Corner

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 Measure the Z-offset
Measure the Z-offset
1 Click the Main | Sample tabs and change the Output Repository to
D:\Installation\ZOffset2.
2 Select five beaded stripes.
Figure 42 Select Five Beaded Stripes

3 Click Operations | Z-offset 2, then click Start Test.

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If... Then...

The test fails to run. The Z-offset value might be out-of-range.

1. Set the approximate Z-offset.
2. Rerun the Z-offset 2 test.
See Z-Offsets Verification on page 106 for more
information.
3.Try a fresh BeadChip.

4 When the test completes, note the Recommended Z-offset value in the Results area.
Figure 43 Z-offset 2 Tab

5 Click Edit | Calibration Parameters and enter the value in the Z-Offset Value text box.

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 Measure the Z-offset
Figure 44 Calibration Parameters Screen

6 Record the Z–Offset value on the iScan System IQ/OQ (Document # 15021804).
7 In the Override.cfg file, navigate to the [calibration/Analytical Adapter Plate
#3/Analytical 4-Slide Holder #3] section, and update the zFocusOffsetForEmmissive
parameter with the new value.
Figure 45 Override.cfg File

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Verify Color Offset, X-Offset, and Camera Rotation
A physical offset is introduced between the red and green lasers in the Y direction at the
sample to avoid crosstalk. This test measures the color (Y-) offset and X-offset between the
two beams, as well as camera rotation.
1 Click the Main | Sample tabs and change the Output Repository to
D:\Installation\XYOffset.
2 Click the Tools | Auto Align tabs, then click Auto Tilt.
3 Click the Location tab, park the objective on a corner of a beaded stripe.
Figure 46 Location

4 Click the Operations | Scan tabs and set up the scan.

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 Verify Color Offset, X-Offset, and Camera
5 Click Manual Scan.
6 View the green image, and put the mouse on the left-most column of beads. Record the
X value at this position.
7 Similarly, put the mouse on the top-most row of beads, and record the Y value at this
position.
8 View the red image, and record the X and Y positions of the left-most column and top-
most row of the red beads.
9 Calculate and record the values of the:
a X- offset: the difference between the X positions of the left-most column of the green
and red beads.
b Color (Y-) offset: the difference between the Y positions of the top-most column of
the green and red beads.
Note X and Y positions in the Green Image

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Top row of green beads: Note Y value

Left column of green beads: Note X value

note

When viewing the green and red images together, the green beads should be above

the red beads, else the color offset direction is wrong.

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 Verify Color Offset, X-Offset, and Camera
Figure 47 Green Beads Above Red Beads

A Green beads should be above red beads

Camera Rotation
1 View the green image, and measure the Y value of beads at the top left and top right.
The difference between these values is the green camera rotation.

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Figure 48 Measure Y Value

A Measure Y value at top left

B Measure Y value at top right

2 Similarly, view the red image and measure the red camera rotation.
3 Record the values of X-Offset, Color Offset, and green and red camera rotations on the
iScan System IQ/OQ (Document # 15021804).

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 Check Tip Tilt and Chromatism
Check Tip Tilt and Chromatism
1 Click the Main | Sample tabs, then select one stripe to scan.
Figure 49 Select One Stripe

2 Set the Output Repository to D:\Installation\TipTilt.

3 Click the Operations | Tip Tilt Test tabs, and the set up the test as shown.
4 Set the Z-offset to the value recommended by the Z-Offset 2 test.

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Figure 50 Tip Tilt Test Tab

5 Click Start Test.

6 Once the system finishes scanning, open summary_data.csv file and review the results.
This file is located at D:\Installation\TipTilt\Img2. shows an example of the results
file. The specs are listed in the iScan System IQ/OQ (Document # 15021804).

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 Check Tip Tilt and Chromatism
Table 14 Tip Tilt and Chromatism Specs
Check: If Out of Spec:

Green residual tip tilt See Adjust Optical Bench Tilt on page 98.

Red residual tip tilt See Adjust Optical Bench Tilt on page 98

Chromatism See Chromatism Adjustment on page 100.

7 Record the following values in the iScan System iScan System IQ/OQ (Document #
15021804):
• Residual Tip Tilt for the green channel
• Residual Tip Tilt for the red channel
• Residual Chromatism (Grn& Red)

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Figure 51 Summary_Data.csv File Sample Results

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 Perform the Functional Test
Perform the Functional Test
This test measures data for four different stripes at the calibrated focus (Z) position, and
provides information on uniformity of the laser line as well as focus metrics.
1 Click the Main | Sample tabs and change the Output Repository to
D:\Installation\FunctionalTest.
2 Select four beaded stripes between 2 and 6.
3 Click Functional Test and complete the following:
a Enter a name in the Operator Name text box.
b (Optional) Enter notes and comments in the Experiment Notes text box.
c Copy the file path from the Output Repository and paste it into the data file path
text box.
d Add .xml at the end of the path you pasted in step c. above.
e Leave other parameters at default.
Figure 52 Functional Testing Window

A Operator name
B Data file path

4 Click Next.
5 Leave the next screen at default values and click Start Test to begin the functional test.
Once the functional test has completed, ATS Reporter launches and loads the
completed xml test file.
6 Generate a Functional Test in ATS Reporter:
a In the left pane, click the + next to the instrument serial number (N381 in this
example) to expand it, then click the + next to FunctionTest.xml.
b Right-click on the slide name.

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c Click Generate Reports.
d Click Stability Summary.
Figure 53 Generate report

7 The ATS Functional Test Summary Report is generated.

Figure 54 Test Summary

A Average Cy3 (green) Section Uniformity score (as a percentage)

B Average Cy5 (red) Section Uniformity score (as a percentage)
C Average Green Focus Score
D Average Red Focus Score

8 Record the uniformity and focus scores on the iScan System IQ/OQ (Document #
15021804).
9 Examine the uniformity plots for both channels and take the following actions:

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 Perform the Functional Test
a If the green plot has a large slope making the uniformity < 60% at the low end,
translate the Powell lens in the X direction.
b If the red plot has a large slope making the uniformity < 60% at the low end, re-
point the red final excitation mirror at the Powell lens.
c If either plot has a parabolic profile dropping the uniformity to < 60% in the middle
or at the ends, adjust the corresponding beam expander magnification (input) lens
as follows:
If the profile curves upwards at the ends (happy face) reduce the beam size by
turning the magnification lens to a higher value. Increment by single units.
If the profile dips down at both ends (unhappy face), increase beam size by turning
the magnification lens to a lower number
Table 15 Uniformity and Focus
Check: If Out of Spec:

Cy3 (green) Section Uniformity Rerun functional test with a different section or
dyed dead BeadChip.
Cy5 (red) Section Uniformity

Average Green Focus

Average Red Focus Score

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Perform Functional Test at + 0.0015mm From Best
Focus
1 In ATS, click “Edit” then select “Calibration Parameters”.
2 Add 0.0015 to the ZFocusOffsetForEmissive”to obtain the abovefocus Z-offset value.
} Example:
} Original Z-offset = -0.0053
} abovefocus Z-offset = (-0.0053) + 0.0015 = -0.0038
3 On the next window, click “OK”.
4 Repeat the functional test.
5 Look in ATS reporter and generate a “Stability Summary” report by right clicking the
name of the slide.
6 Find the green (Cy3) and red (Cy5) Focus Stability and Uniformity. Record the readings
from the report in the IQOQ.

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 Perform Functional Test at -0.0015mm From
Perform Functional Test at -0.0015mm From Best
Focus
1 In ATS, click “Edit” then select “Calibration Parameters”.
2 Subtract 0.0015 to the best Z-offset value in step 1.5 to obtain the belowfocus Zoffset
value and replace into “ZFocusOffsetForEmissive” in “Calibration Parameters”.
} Example:
} Original Z-offset = -0.0053
} belowfocus Z-offset = (-0.0053) - 0.0015 = -0.0068
3 On the next window, click “OK”.
4 Repeat the functional test.
5 Look in ATS reporter and generate a “Stability Summary” report by right clicking the
name of the slide.
6 Find the green (Cy3) and red (Cy5) Focus Stability and Uniformity. Record the readings
from the report in the IQOQ.

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Interpreting Results
1 If above or below focus score is greater than atfocus then retry with an atfocus Z-offset
equal to that from the greatest (above or below) focus score.
2 If above or below focus score is approximately equal to atfocus then retry with an
average Z-offset for these two values.
3 Use another beadchip if suspect (swath dropout, poor uniformity, burn marks) making
sure to generate the Z-offset from the Z-Offset 2 test.
4 Once the best Z for functional test is established, repeat the Tip-Tilt test.

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 Manually Activate Windows 10 for Offline
Manually Activate Windows 10 for Offline Instruments
The Windows 10 license is a volume license and should self-validate. When the instrument
is not connected to the internet, Windows self-activation might fail. Windows OS will show
an error as shown in the following figure. However, this error does not impact sequencer
operation.
Figure 55 Windows Failed Activation Error

To clear the error and activate Windows, do the following:

1 Open a command prompt (enter CMD in the Windows search field).

2 Type slui 4 and press Enter.
A dialog box appears prompting you to select the country or region.
3 Select the appropriate country or region from the drop-down list and then select Next.
A dialog box appears with the activation phone number and the installation ID.
Figure 56 Activation Phone Number and Installation ID

4 To receive a confirmation ID, call the phone number on the screen and provide the
Installation ID.

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5 Select Enter confirmation ID and enter the confirmation ID provided.
Figure 57 Enter ID

6 Select Activate Windows.

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 Final Installation Tasks
Final Installation Tasks
1 Clean up the computer by doing the following:
a Delete all non-customer files from the desktop.
b Move ATS to the D:\ drive or delete it all together.
c Verify that the C:\ drive has at least 30GB of free space.
d Record the results on the iScan System IQ/OQ (Document # 15021804).
2 Complete the iScan System IQ/OQ (Document # 15021804) and attach it to the Work
Order in SFDC.
3 Complete the Installation Certification and give it the customer.
4 Update the asset details in the Installed Products page for the instrument in SFDC.
5 Update the "OS Version" attribute in Technical Attributes of the Installed Products page
for the instrument in SFDC.
• In the "OS Version" attribute, select the correct Windows OS version.
• If the "OS Version" attribute is unavailable, record the Windows OS version in the
"PC " attribute.
6 Upload the latest copy of "override.cfg", "dataCC.txt", and "CloudApiKey.xml" (for ICS
v4.0.0.147) from the Archimedes_flash folder to the Installed Products page for the
instrument in SFDC.
7 Before turning the instrument over to the customer, help the customer change the
password for their use.
a Press ctrl+alt+del, then select Change Password.
b Enter the current password.
c Have the customer enter their password and confirm it, then press Enter.

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 Appendix A  Install Accessory Equipment

Install Accessory Equipment

Appendix A
Unpack and Install the Hybridization Oven 78
Unpack and Install the Heat Block 81
Unpack and Install the Shaker 84
Unpack, Install, and Qualify the Heat Sealer 86

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Unpack and Install the Hybridization Oven
Figure 58 Hybridization Oven

1 Open the shipping container and remove the packing material from around the unit.
2 Lift the unit to the lab bench.
3 Remove from the shipping packing material:
a Drip tray
b Rocker platform
c Rubber insert
4 Secure the rocker platform set screw to the flat portion of the drive shaft.

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 Unpack and Install the Hybridization Oven
Figure 59 Secure Rocker Platform Set Screw

5 Secure the positioning of the rocker tray on the drive shaft by sliding the shaft collar as
far left as possible.
6 Place the rubber insert mat on the rocker platform.
7 Manually move the rocker platform to ensure it moves without restrictions.
8 Connect the power cable to the back of the unit and then to the wall outlet.

Qualify the Hybridization Oven

IMPORTANT
The temperature must be tested twice, once at 40.0°C and then again at 60.0°C (see step 5).
1 Power on the oven (switch at the back of the instrument).
2 Record the oven serial number on the BeadLab Ancillary Equipment IQOQ (Document
# 1000000067830).
3 Press F once to change the display to TSET. The display alternates between TSET and
the set temperature value.
4 Press S to enter the set temperature mode.
5 Set the increment dial to 40.0°C.
6 Press S to accept and store the new temperature.
7 Tape a thermocouple probe to the interior of the oven with the probe tip in the air at
the center of the oven.
8 Select the appropriate digital meter type for the thermocouple being used.
9 Wait for the temperature to stabilize. If the temperature is within specification, test
again at 60.0° C.

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10 If the temperature is out of specification:
a Access the Offsets.
b Calibrate the temperature using the appropriate offset as shown in the following
table:
Table 16 Offsets

Offset How to Access When to Use

T1 Press F once When adjusting an offset for operating temperatures between

30.0 and 49.9°C

T2 Press F twice When adjusting an offset for operating temperatures between

50.0 and 74.9°C

T3 Press F three Use when adjusting an offset for operating temperatures

times between 75.0 and 99.9°C

c Press and hold F and S simultaneously and then release to enter calibration mode.
d Press F once, twice, or three times to access offsets (see previous table). Then press
S to set.
e Use the increment dial to calibrate to the temperature shown on the digital meter.

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Unpack and Install the Heat Block
Figure 60 Heat Block

Unpack and install the heat block (Hybex Microsample Incubator).

1 Open the shipping container and remove all packing material from around the heat
block.
2 Remove the heat block from the shipping box and place it on a level surface.

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IMPORTANT
Be sure the heat block has enough clearance to open the lid on top.
3 Connect the power cable to the heat block at rear and then to the wall outlet.

Qualify the Heat Block

IMPORTANT
The temperature must be tested twice, once at 95.0°C and then again at 37.0°C (see step 3).
1 Power on the heat block using the power switch.
2 Record the heat block serial number on the BeadLab Ancillary Equipment IQOQ
(Document # 1000000067830).
3 Set the temperature controller to 95.0°C, depending on customer needs, and allow the
heat block to come to temperature.
4 Plug one end of the T-type thermocouple extension cable into the Fluke digital meter
and the other end into the blue receptacle found on the back panel of the heat block.
IMPORTANT
The digital meter must be set to T-type measurements for the following reading in step
5.
5 Power on the digital meter to display the heat block temperature.
6 If the temperature is within specification, record the results on the BeadLab Ancillary
Equipment IQOQ (Document # 1000000067830) and then skip to the end of this section.
7 For the older-style heat block, do the follwoing. For the Walton SD31 temperature
controller, continue to step 8.
a Press the down arrow four times until Cal appears.
Figure 61 Secure Rocker Platform Set Screw

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 Unpack and Install the Heat Block
b Press and hold the SET key. The existing offset value between the controller and
digital meter displays.
c Calculate the difference in the temperature shown on the controller and the digital
meter (that is, subtract the lower from the higher number).
d Press and hold the SET key and use the up and down arrows to enter the offset
value calculated in step #8. Example: if the controller displays a temperature that is
1.0° C higher than the digital meter, adjust the offset to -1.0.
e Press the infinity key (∞) to exit calibration. The block temperature is now
calibrated for the set temperature.
8 For Walton SD 31 temperature controller, do the following:

9 Record results on the iScan System IQ/OQ (Document # 15021804).

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Unpack and Install the Shaker
Figure 62 Shaker

1 Open the shipping container and remove all packing material from around the shaker.
2 Record the shaker serial number on the iScan System IQ/OQ (Document # 15021804).
3 Place the shaker on a level surface.
4 Press down on the shaker to secure it in place with the 12 rubber suction cup feet.
5 Level the cover plate with the four adjustable height guides at each corner. Secure the
cover plate by folding the four hooks down and engaging the rubber washers.
6 Connect the power cable to the back of the unit and then to the wall outlet.

Qualify the Shaker

1 Power on the shaker with the rocker switch on the front of the unit.

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 Unpack and Install the Shaker
2 Set the stroboscope to the desired revolutions-per-minute (RPM) and position it above a
target on the top the shaker. Example: on one of the corner metal posts or on one of the
four hooks.
3 Use the up/down speed arrows to set the shaker RPMs to match the stroboscope RPMs.
4 Press Run.
5 After the shaker comes to speed, power on the stroboscope above your target.
NOTE
Up/down speed increments are 25 RPM.
6 Adjust the speed of the shaker with the up/down speed arrows until your target is
completely (or nearly) stopped under the stroboscope.
7 Record the shaker setting that correlates with the desired stroboscope setting on the
BeadLab Ancillary Equipment IQOQ (Document # 1000000067830).
8 Repeat this section for the remaining stroboscope settings.
9 Record remaining stroboscope results on the BeadLab Ancillary Equipment IQOQ
(Document # 1000000067830).

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Unpack, Install, and Qualify the Heat Sealer
Figure 63 Heat Sealer

1 Open the shipping container and remove all packing material from around the heat
sealer.
2 Record the heat sealer serial number on the BeadLab Ancillary Equipment IQOQ
(Document # 1000000067830).
3 Place the unit on a level surface.
4 Plug one end of the power cable into the heat sealer and the other end into the wall
outlet.
5 Power on the heat sealer.
6 Record power on success on the BeadLab Ancillary Equipment IQOQ (Document #
1000000067830).
7 Record successful heat up on the BeadLab Ancillary Equipment IQOQ (Document #
1000000067830).

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 Appendix B  Manual Adjustments and Corrections

Manual Adjustments and Corrections

Appendix B
Remove the Front-Door Latch 88
X-Soft Limit Adjustment 90
Laser Power Adjustments 92
Line Centering Adjustment 93
Check and Correct Green Line Rotation 96
Adapter Plate De-Skew 97
Adjust Optical Bench Tilt 98
Chromatism Adjustment 100
Color Offset Adjustment 101
Measure and Adjust XY Offsets 102
X-offset Adjustment 104
Camera Rotation Adjustment 105
Z-Offsets Verification 106
Tilt Motor Adjustment 109
Create New DataCC Files 113

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Remove the Front-Door Latch
If the adapter tray is unable to eject, the front-door latch might be bent. Thus, the tray is not
able to push the door open when it is ejected. Remove the latch to resolve this problem as
follows:
1 Remove the front panel.
Figure 64 Front Panel Removed

2 Unscrew the SHCS that fastens the door latch to the door-latch mount.
Figure 65 Door-latch Mount

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3 Remove the door-latch assembly.
Figure 66 Door-latch Assembly

4 Re-install the front panel.

5 Repeat Verify Stage and Tray Function on page 34 to make sure the tray can eject.

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X-Soft Limit Adjustment
Adjust the X-Soft Limits so that the X-stage is able to home properly, has sufficient
clearance with the door hinges on the front panel, and does not generate error messages
during movements due to trying to exceed the soft limits.
1 Close ATS.
2 Navigate to H:\Archimedes_Flash,
3 Open the Override.cfg file, go the [XMotor_MDrive] section, and change the softlimits
in small increments of 1 or 2 mm at a time. Do one of the following:

If the X-stage... Then change the...

Is hitting the door hinges pos_limit_mm to a smaller positive number

Is unable to home, or error says it is trying neg_limit_mm to a larger negative number

to exceed the negative X limit

Trying to exceed positive soft limit pos_limit_mm to a larger positive number

Trying to exceed both limit pos_limit_mm to a larger positive number and

neg_limit_mm to a larger negative number

Figure 67 Softlimits in Override.cfg

4 If the neg_limit_mm value is changed, then change XCorrection value by the same
amount.
This parameter is in the [calibration/Analytical Adapter Plate #2/Analytical 4-Slide
Holder #2] section.
Figure 68 XCorrection Value in Override.cfg File

5 Save and close the file. Then, verify the X-soft limits as described in the next section.

Verify the X-Soft Limits

1 Start ATS, click Home All, then click Open Tray and load an empty BeadChip.
2 Click Close Tray while holding the door open.

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3 With the door held open, click Home All and observe the position of the X-stage to
verify that it is not hitting the door hinges.
4 If the X-stage is hitting the door hinges then repeat steps 1–3.
5 Close the door.
6 Click the Main | Sample tabs and enter the sample information.
7 Click the Tools | Auto Align tabs, then click Entire Alignment.
8 Verify that the entire alignment completes successfully and that the system is able to
find all three fiducials.
If the system is unable to locate all three fiducials or if the fiducials are not roughly
centered, then perform the XY correction procedure.
9 Click Open Tray, remove the empty BeadChip, click Close Tray, and then close ATS.
10 Launch GenomeScan and load a chip with a good quality barcode.
11 Verify that the system is able to successfully scan the barcode.
If the system is unable to scan a barcode of good quality, then perform the barcode
reader XY adjustment procedure.

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Laser Power Adjustments
1 Close ATS.
2 Navigate to H:\Archimedes_Flash.
3 Open the Override.cfg file.
4 The laser power settings are located in:
• For green: [AnalyticalLaser1] section
• For red: [AnalyticalLaser2] section
5 Set the LaserPower parameter to the desired value.
NOTE
The laser power settings go from 0–255. Do not set the LaserPower value outside of this
range.

Figure 69 Laser Power Section in Override.cfg File

6 Restart ATS and verify the laser power is at desired power.

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Line Centering Adjustment
1 In ATS, click the Auto Align tab and then the Image tab.
2 From the Set Default Camera Mode drop-down menu, click Full Frame twice.
3 Click Continuous.
4 On the Image tab, select the color channel to be adjusted by clicking the color icon
(located below the Load Image to Optical Path 2 button).
Figure 70 Settings for Camera Setup

A OD1
B OD3

5 Click the Filters | Lasers tabs.

6 For the color channel in either Optical Path One (or Two) - Filters area:
a Select OD 5 in the Excitation Filter drop-down menu.
b Select Open in the Emission Filter drop-down menu.

Center Camera Line

1 Rotate the final turning mirror knob to center the line on pixel 64.

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Figure 71 Final Turning Mirror Knob

NOTE
To determine the location of the pixel line, hover the mouse over the center of the line
after zooming in (until the pixels are roughly the same size as the mouse cursor hand).
The coordinates that the cursor hand hovers over are displayed in the far right side of
the Image tab in ATS.

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 Line Centering Adjustment
Figure 72 X and Y Coordinates and Intensity Values

2 Click Pause, followed by Stop in the lower right corner to stop camera acquisition.
3 Close the excitation and emission filters.

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Check and Correct Green Line Rotation
1 If the difference in the Y value from end to end is greater than 3 pixels, rotate the
Powell lens while monitoring the line on the green camera.
2 Depending on the severity of the rotation, you may have to re-center the line at pixel 64
if it disappears off the mask and then continue the rotation correction.
Figure 73 Old Style Powell Lens

A Locking screws
B Rotation adjustment screw

Figure 74 New-style Powell Lens

A Rotation adjustment screw

B Rotation locking screw
C X-axis locking screw
D X-axis adjustment screw (uniformity)
E Locking screw for raising and lowering the lens

3 Once you adjust the line to match the green camera, measure the line rotation on the
red camera as well. If it now shows rotation, you will need to adjust the red camera
rotation to match the line. For information, see Camera Rotation Adjustment on page 105.

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 Adapter Plate De-Skew
Adapter Plate De-Skew
1 Eject the tray and remove the BeadChip carrier and adapter tray.
2 Loosen the set screw (B) that locks the adjustment screw (C) and the two lockdown
screws (A) that secure the adjustable alignment ball.
Figure 75 Set Screw and Lockdown Screws Locations

A Lockdown screws
B Set screw
C Adjustment Screw

3 Turn the adjustment screw (½ a turn is roughly 30 pixels) as needed to compensate for
the difference in X positions.
For example, if the left side is at pixel 800, and the right side is at pixel 700, then the
right side is higher than the left. In this case, turn the screw clockwise roughly 1½
turns.
4 Re-measure the skew and repeat until the skew is less than 15 pixels.
5 Tighten the lockdown and adjustment screws.

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Adjust Optical Bench Tilt
1 Open the Tilt Test results file. See Run Tilt Test on page 1.
2 In this Excel file, locate the tilt adjustment values in red and green (see columns A and
B of this spreadsheet).
3 Measure the gap between the optical bench and the top of the front left post (use
calipers) while facing the iScan System front door.
4 Add the number of mm of tilt adjustment from Step 2 to the gap measured.
5 Set and lock the calipers to this new combined value.
Figure 76 Gap Measurement Area

6 Loosen/remove these items:

} Loosen all four screws holding the optical bench to the four posts.
} Remove the front right SHCS completely.
} Back off the adjustment screw to create a gap between bottom side of optical bench and
the top of the front right post.

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 Adjust Optical Bench Tilt
Figure 77 Optical Bench Mounting Screws and Gap

7 Perform the following manual adjustments:

} Set the height of the optical bench using the locked caliper and the front left adjustment
screw.
} Lower the front right adjustment screw so it is just touching the post, and reinsert the
SHCS.
} Go clockwise around the bench and slowly tighten each screw until all are tight.
8 Repeat steps 3 -7 until the residual tilt on green is equal to or less than 0.75 µm and
the residual tilt on red is equal to or less than 1.5 µm.

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Manual Adjustments and Corrections
Chromatism Adjustment
1 Open the summary_data.csv file located at D:\Installation\TipTilt\Img2.
2 Locate the chromatism adjustment value. See Check Tip Tilt and Chromatism on page 63.
3 Measure the gap in the red projection lens with calipers.
Figure 78 Gap in Red Projection Lens

4 Add the chromatism adjustment value to the measured value, set and lock the calipers
to this new combined value.
5 Loosen the two red projection lens barrel lock down screws.
Figure 79 Red Projection Lens Barrel Lockdown Screws

6 Slide the barrel in or out, using the locked down caliper as a gauge, to set the gap to
this new combined value.
7 Lock down the barrel, and repeat the tip tilt test (see Check Tip Tilt and Chromatism on
page 63).

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Color Offset Adjustment
1 Set up the system to look at a reflected red line from an unpopulated area of the
BeadChip.
2 Turn the X-axis adjustment knob on the final red emission mirror to move the line by
the number of pixels required to set the green/red separation to 36 ± 4 pixels.
For example, if the separation was 26 pixels, move the red line down by 10 pixels.
Zoom-in on the line to accurately measure its position.
Figure 80 X-axis Adjustment Knob

3 Return the line to pixel 64 with the Y-axis adjustment knob on the final red excitation
mirror.
Figure 81 Y-axis Adjustment Knob Insertion Location

4 Repeat steps 1–3 until the color separation is 36 ± 4 pixels.

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Measure and Adjust XY Offsets
1 Load a slide.
2 Select the Sample tab then fill in the information.
3 Select the Auto Align tab, and click Auto Tilt.
4 Click Auto Center.
5 Select the Motors tab and record the X and Y motor values as the system values.
6 Perform a 4000 line manual scan in reflective mode.
7 If necessary, move X and/or Y to center the fiducial in the manual scan image. Repeat
manual scan after each adjustment.
8 After manual centering, record the X and Y motor values as my values.
Figure 82 Manual Scan Parameter Settings

9 Read the current X and Y Correction values from the Override.cfg file. These are the cfg
values.
10 Calculate the new X and Y Correction Values using these formulas:
} X = (my value - sys value) + cfg value
} Y = my value -sys value) + cfg value
11 Record the new X and Y Correction Values in the Override.cfg file and in Edit |
Calibration Parameters.
12 Select the Auto Align tab, and click Auto Tilt. Then click Auto Center to verify the
settings. If the settings are correct, the fiducials should be centered during Auto Center
process.

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 Measure and Adjust XY Offsets
Figure 83 Fidicials Centered on CCD Display

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X-offset Adjustment
If the measured X-offset is > 8 pixels, adjust the X-offset as follows:
1 Turn the Y-axis adjustment knob on the final red emission mirror. Turn the screw in
1/16th turn increments and remeasure the X-offset after each adjustment.
NOTE
Turn the Y-axis adjustment knob clockwise to move red toward the right on the display.

Figure 84 Y-axis Adjustment Knob

2 Repeat step 1 until the red and green cores are superimposed within 8 pixels.

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Camera Rotation Adjustment
1 Determine the direction to rotate the image by noting the higher Y-coordinate number.
The side with the higher Y-coordinate is lower than the other side.
For example, if the left core is at a Y-coordinate of 500 and the right core is at a Y-
coordinate of 400, then the left side is lower than the right side. The camera needs to be
rotated counterclockwise.
2 Loosen and rotate the camera barrels by loosening the two barrel mounting screws and
turn the adjustment screw to compensate for the difference in Y-coordinates (found in
Verify Color Offset, X-Offset, and Camera Rotation on page 58).
NOTE
One full turn of the camera adjustment screw is roughly equal to moving 17 pixels.

Figure 85 Camera Barrel Mounting and Adjustment Screw Locations

A Adjustment screws
B Two screws per camera barrel mount

3 Retighten the two screws and run another manual scan.

4 Repeat Verify Color Offset, X-Offset, and Camera Rotation on page 58 and steps 13 of this
procedure, until the difference in the Y-coordinates for both red and green is ≤ 4 pixels.
5 Unrotate the green line on the image using the Powell lens mount.
6 Check that the red line is unrotated on the image.
7 If the red line is rotated more than 2 pixels on the image, fix it with the red camera
rotation.

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Manual Adjustments and Corrections
Z-Offsets Verification
1 Click Open Tray, load a dyed bead standard, then click Close Tray.
2 Click the Main | Sample tabs, then enter the appropriate sample settings.
3 Select a single stripe to be scanned.
Figure 86 Sample Tab

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 Z-Offsets Verification
4 Click the Operations | Tip Tilt Test tabs, set up a single stripe test.
5 Click Edit | Calibration Parameters, note the ZFocusOffsetForEmissive value, and
enter it in the Z-offset field. This is the current Z-offset value.
Figure 87 Calibration Parameters

6 Make sure the Camera Correction check box is cleared, then click Start Test.
When the test finishes, a window opens and displays the tip tilt plots for channel 1
(green) and channel 2 (red).
NOTE
If the graph window does not appear, check that you only have one stripe selected on
the Sample tab. If this is the case, then the graphs should be available in the specified
save folder.

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Figure 88 Tip Tilt Plots

7 Inspect the tip tilt plots for both channels. The peaks should be visible in both plots
and roughly centered. If not, change the Z-offset (step 5) and repeat the Tip Tilt test.

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 Tilt Motor Adjustment
Tilt Motor Adjustment
If the auto tilt fails, refer to this procedure for information about fixing the problem.
NOTE
Before attempting to recalibrate the tilt-motor positions, verify that the BeadChip is seated
perfectly flat in the carrier.
1 Click the Hardware | Motors tabs.
2 Enter 5.5 in the All Tilts absolute field (not the Δ field), and then press Enter.
This brings all three tilt motors up to 5.5 mm.
Figure 89 Enter 8.0 in All Tilts field

3 Click the Hardware | Camera tabs.

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Figure 90 Hardware | Camera tabs

4 Click Set Default Camera Mode and select Full Frame twice.
5 Click Continuous.

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 Tilt Motor Adjustment
a In the Location tab, click on a non-beaded area of the sample.
b In the Image tab, select the green camera icon.
6 Click the Hardware | Filters/ Lasers tabs.
7 In Optical Path One - Filters (green laser) area, from the Excitation Filter list, select
OD3.0.
8 From the Emission Filter list, select Open.
9 Click the Hardware | Motors tabs.
10 Enter -0.12 in the Z Motor absolute field (not the Δ field), and then press Enter.
11 Enter 0.01 in the All Tilts Δ field.
NOTE
The lowest value that you can set for increments is 0.002.
CAUTION
Be careful not to crash the slide holder tray into the objective when jogging the tilt
motors.
12 Click the All Tilts up or down arrows until the reflected laser line is visible.
Figure 91 Laser Line is Visible

13 Change to smaller increments in the All Tilts Δ field and continue moving All Tilts up
or down until the line is in sharp focus.
14 Once the green laser beam image is in focus in sensor 2, subtract 8.0 from the current
tilt motor positions (Tilt 1, Tilt 2, and Tilt 3 motors) in the Motors tab. For example:
• Tilt Motor 1 = 8.94 - 8.0 = .94

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These correction values are reported below the Δ field for each motor.
15 Enter the new values in the Calibration Parameters file for all three tilt motors.
a Click Edit, and then click Calibration Parameters.
b In the Tilt Settings area, enter the value in the NominalTilt#Correction field (where
# is the number of the tilt motor).
c Click OK.
16 Click Stop to stop the camera acquisition.
17 Fine-tune the tilt values as follows:
a Click the Tools | Auto Align tab, and then click Auto Tilt.
b After the iScan System auto-tilts the sample, select the Motors tab.
c Record the new tilt motor correction values. These are reported below the Δ box for
each tilt motor.
d Click Edit, and then select Calibration Parameters.
e In the Tilt Settings area, enter the new correction value in the
NominalTilt#Correction field (where # is the number of the tilt motor).
18 Repeat auto tilt and verify that the image is centered.
19 Update the tilt values in Override.cfg by updating the Analytical 4-Slide
Holder #3 section.
20 Restart ATS.

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 Create New DataCC Files
Create New DataCC Files
1 Baseline your current DataCC by running the Data CC Verification. See Verify Data CC
on page 36.
2 Capture images for DataCC as follows:
a Load a fluorescent coated slide in the BeadChip carrier.
Figure 92 Load Slide

b Perform Auto Tilt on the fluorescent coated slide.

c Click the Sample tab. Enter D:\dataCC in the Output Repository field.
d On the Location tab, place the cursor on an area of the BeadChip where the
fluorescence is not visibly degraded.

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Figure 93 Location Tab

e Place an OD 1.0 filter in the green laser path.

If you do not do this, you will get saturated pixels in the bright images.
f Install the optical bench cover.
g On the Camera tab, set the camera Gain and Offset to zero.

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 Create New DataCC Files
Figure 94 Set Camera Gain and Offset to 0

h Click the Operations | Scan tab. Then, select Data CC Scan and change the length
of scan to 2048. Verify the settings are as shown in the following figure.

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Manual Adjustments and Corrections
Figure 95 Select Data CC Scan and Set Length of Scan to 2048

i Click Manual Scan.

j Open your bright images in image viewer (ATS | Tools | Image Viewer) and
verify the images are not overly saturated (100+ saturated pixels).
3 Generate camera correction files as follows:
a Download the file iscan-cameradatacc.zip from ICE.
b Extract the contents of the zip file to a temporary location on the D:\ drive (eg.,
D:\FSE).
c Navigate into the extracted file structure and move the V6.5 folder to the top level
of the D:\ drive.
d Move the bin folder and cameradatacc.bat to the folder containing the images.

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 Create New DataCC Files
Figure 96

e Double-click cameraDataCC.bat.
Two files are created in the DataCC folder.
f Move the generated channel1cc.txt and the channel2cc.txt files to the Archimedes_
Flash folder. First rename the old files (add 'old' or the date to the name).
g Remove any filters.
h Repeat Verify Data CC on page 36 and confirm that it passes spec.

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Index

Index
A
adjusting
optical tilt bench 98
alignment
BeadChip 109 Heat sealer
flow cell 109 installing 86
Archimedes Test Software see, qualifying 86
Software 67 unpacking 86
ATS help, technical 121
generating Functional Test report Hybridization oven
in 67 installing 78
qualifying 79
B unpacking 78
BeadChip I
alignment 109
camera rotation, correcting 96 Installation
tilt motor, adjusting 109 electrical requirements 10
tools required 5
C workflow 3
Installation Guide
camera intended audience 3
rotation, correcting 96 reference documents 3
centering Installing
laser line on ’pixel 64’ computer 17
using X-axis knob on final heat sealer 86
turning mirror 93 isolation platform 23
Computer monitor 17
installing 17 shaker 84
unpacking 17 iScan
Connecting dimensions of 9
iScan 25 electrical requirements for 10
UPS 16
customer support 121 L
D Laboratory
bench guidelines 10
documentation 121 electrical requirements 10
Documents inspection of 8
reference 3 requirements for 8
E M
Electrical Monitor
power consumption 10 installing 17
requirements 10
Environmental conditions N
humidity requirements 12
temperature requirements 12 Network 12

F O
flow cell OD filter
alignment 109 green CCD 93
tilt motor, adjusting 109 red CCD 93
Functional Test Optical bench
creating report for 67 unlocking 29
performing 67 optical bench tilt, adjusting 98

H P
Heat block Packing material
installing 81 removal 30
unpacking 81 Power line regulator
when needed 10

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Index

Q
qualification
camera rotation 96
Qualifying
heat sealer 86
hybridization oven 79
isolation platform 24
monitor 17
shaker 84
R
red projection lens
barrel lockdown screws 100
Reference documents 3
S
Shaker
qualifying 84
upacking 84
System
logins 4
passwords 4
T
technical assistance 121
Tip Tilt Test
’Tilt Adjustment’ values 98
measuring gap between the
optical bench and the top
front left post 98
U
Uninterruptible Power Supply, see
UPS 16
Unlocking
optical bench 29
Z-stage 28
Unpacking
computer 17
heat block 81
hybridization over 78
iScan 25
isolation platform 16
monitor 28
shaker 84
UPS
connecting 16
systems specifications for 10
W
Workflow
installation procedure 3
Y
Y-axis adjustment knob
location to insert in final red
excitation mirror (Image) 101
Z
Z-stage
unlocking 28

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 Technical Assistance
Technical Assistance

For technical assistance, contact Illumina Technical Support.

Website: www.illumina.com
Email: [email protected]

Illumina Customer Support Telephone Numbers

Region Toll Free Regional

North America +1.800.809.4566

Australia +1.800.775.688

Austria +43 800006249 +43 19286540

Belgium +32 80077160 +32 34002973

China 400.066.5835

Denmark +45 80820183 +45 89871156

Finland +358 800918363 +358 974790110

France +33 805102193 +33 170770446

Germany +49 8001014940 +49 8938035677

Hong Kong, China 800960230

Ireland +353 1800936608 +353 016950506

Italy +39 800985513 +39 236003759

Japan 0800.111.5011

Netherlands +31 8000222493 +31 207132960

New Zealand 0800.451.650

Norway +47 800 16836 +47 21939693

Singapore +1.800.579.2745

South Korea +82 80 234 5300

Spain +34 911899417 +34 800300143

Sweden +46 850619671 +46 200883979

Switzerland +41 565800000 +41 800200442

Taiwan, China 00806651752

United Kingdom +44 8000126019 +44 2073057197

Other countries +44.1799.534000

Safety data sheets (SDSs)—Available on the Illumina website at

support.illumina.com/sds.html.

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Technical Assistance
Product documentation—Available for download in PDF from the Illumina website. Go
to support.illumina.com, select a product, then select Documentation & Literature.

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March 2020 Internal Use Only
FOR RESEARCH USE ONLY