Azure Biosystems Sapphire User manual

Sapphire™ Biomolecular Imager User Manual Page 1
Sapphire™
Biomolecular Imager
User Manual
Rev 20190405

Sapphire™ Biomolecular Imager User Manual Page 1
Safety and Regulatory Compliance
Radiation
Radiation hazard prevention
The Sapphire Molecular Imager is not equipped with any radioisotope or radiation generating unit, and is
therefore not regulated by radiation hazard prevention laws. However, the Sapphire is capable of scanning
storage phosphor screens, which may be polluted by radioisotopes.
CAUTION: If radioisotope (RI) pollution occurs, stop use of the instrument immediately and follow the
instructions of your radiation administrator.
Laser Safety
WARNING: Making adjustments or carrying out procedures not specied in this manual, can result in
harmful exposure to laser radiation.
The Sapphire Biomolecular Imager is a Class I laser instrument that houses four Class IIIB lasers inside the
instrument.
Under the specied operating procedures, the instrument does not allow operator exposure to laser light. The
lasers, with power of 5–25mW, are accessible in the interior of the instrument.
General Information
The Azure Biosystems Sapphire imaging systems include a laser illumination system that provides up to
four narrow band excitation wavelengths for uorescent applications. The imaging systems are certied to
comply with CE, cTUVus and CB Scheme compliance standards and consists of two fully enclosed electronic
modules located inside of the imager. This laser system is by its appropriate classication and denition
a non-removable laser system as it is not operable when the laser modules themselves are removed from
within the system.
Safety Features
Azure Biosystems Sapphire Biomolecular Imaging Systems are designed to prevent direct and collateral
human exposure to radiation by means of a safety switch on the front side of the imager. The switch reacts to
“lid open” and “lid closed” states and defeats all power to internal light sources when the lid is in the “open”
position. Lasers and other internal system light sources will not power on unless the lid is fully closed. If the
access lid is opened during imaging, all light sources will immediately power off to prevent human exposure
to internal illumination sources. In addition, the entire laser system is fully enclosed within the system
enclosure and there are no viewing ports, windows, or openings to facilitate viewing of, or exposure to,
radiation elds from direct impact, reection, or leakage.
Maintenance
The Azure Biosystems Sapphire laser systems do not require regular, periodic, or preventative maintenance
in the form of adjustments, calibrations, or other standard maintenance procedures to maintain optimal
performance, thereby removing the need for users or their service technicians to initiate any actions where
exposure to laser radiation would occur.

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Serviceability
Replacement of faulty laser modules is a manufacturer-only repair action and not a customer-service
action. Laser repair or replacement may be performed in the eld by Azure Biosystems authorized service
technicians, or by return of the entire system to Azure Biosystems, or its authorized service location(s) for
laser repair or replacement. Lasers are deemed to be faulty or defective if users discover images that show
evidence of output signal level loss, a signicant difference between the output signal levels between laser
modules, or complete loss of output signal level in a laser module. Users or their service technicians should
make no attempt to determine the cause of faulty laser operation, and should promptly contact Azure
Biosystems at [e-mail] or their nearest Azure Biosystems authorized service location.
Caution
The safety switch in the Sapphire is designed to prevent you from being exposed to the laser radiation. If
you open the sample lid while the scanner is in operation, the laser safety switch cuts power to the lasers.
Exposure to laser radiation can be harmful, and viewing laser light directly, can cause blindness.
Azure Biosystems Sapphire systems contain a defeatable safety switch system. It is not recommended or
advised by Azure Biosystems, under any circumstances, for users to defeat the safety system and perform
laser imaging, or imaging with any light source with the access lid open. The access lid must be fully closed.
Electrical Safety Precautions
Be sure to take proper precautions when handling any electrical equipment. NEVER work on any live circuit,
xture, receptacle, or switch. Safety rules you should follow whenever working with any electrical appliance
include:
•Always shut off power at the main disconnect before changing a fuse.
• Always shut off power to the circuit before repairing or replacing a switch, receptacle, or xture.
• Always tape over the main switch, empty fuse socket, or circuit breaker you are working on.
• Always check that the circuit is dead before beginning work on it. Using a circuit tester or voltmeter can
help you determine this.
•Always unplug any appliance before repairing it.
Protective earth terminal
The ground terminal, intended for connection to an external protective conductor for protection
against electric shock in case of a fault, is located on the inside back panel.
For Research Use Only
This instrument is suitable for research use only. It must be used, therefore, only by personnel who know the
health risks associated with the reagents that are normally used with this instrument.

Sapphire™ Biomolecular Imager User Manual Page 3
Warranty
The Azure Sapphire products are warrantied against defects in materials and workmanship for one year
unless otherwise outlined on your sales order or www.azurebiosystems.com/warranty. If any defect occurs in
the instrument during this warranty period, Azure Biosystems, Inc. will repair or replace the defective parts at
its discretion without charge. The following defects, however, are specically excluded:
•Defects caused by improper operation.
• Repair or modication done by anyone other than Azure Biosystems or the company’s authorized agent.
•Use of spare parts supplied by anyone other than Azure Biosystems.
•Damage caused by accident or misuse.
•Damage caused by disaster.
•Corrosion caused by improper solvents or samples.
Voltage Setting Information
The Azure Sapphire Biomolecular Imaging System has a power supply that automatically chooses the correct
voltage for your country or region.
Certicates of Conformity
CE Conformity
The following Azure™ Sapphire Biomolecular Imager, models: RGB, NIR, RGBNIR, are in conformity with the
provisions of the following CE Directives, including all amendments, and national legislation implementing
these directives:
•Low Voltage Directive 2006/95/EC
•EMC Directive 2014/30/EU
And that the following harmonized standards have been applied:
• EN61010-1: 2001
• EN61326-1: 1997+A1:1998+A2:2001+A3:2003 Class A
• EN61000-4-2, EN61000-4-3, EN61000-4-4, EN61000-4-5, EN61000-4-6, EN61000-4-11
Protection category: IP20 according IEC 60529
Contact
6747 Sierra Court, Suite A-B •Dublin, CA 94568 •USA
Phone: [phone] (9am-4pm Pacic time) •To dial from outside of the US: [phone]
Fax: [phone] •Email: [e-mail]
Legal
Sapphire is protected by one or more U.S. and/or foreign patents listed at
www.azurebiosystems.com/patents.

Sapphire™ Biomolecular Imager User Manual Page 4
Table of Contents
1. Introduction 5
1.1 Key Components and Applications 5
1.2 Optional Modules 5
1.3 Optional Modications 5
1.4 Table of Specications 6
2. Installation and Setup 7
2.1 System Placement 7
2.2 Connecting to Power 7
2.3 Power On/Off the System 7
2.4 Software Installation 7
2.5 Connecting Other USB Devices to the System 8
3. Proper Usage – Read Before Use 9
4. Sapphire Capture Software Overview 10
4.1 Launch the Sapphire Capture Software 10
4.2 Fluorescence Imaging 10
4.2.1 Scanning a Fluorescent Membrane 13
4.2.2 Scanning a Fluorescent Gel 14
4.2.3 Scanning a Fluorescent Slide 15
4.2.4 Scanning a Fluorescent, Plate-Based Assay 16
4.3 Chemiluminescence Imaging 18
4.3.1 Taking a Chemi Image 20
4.4 Phosphor Imaging 21
4.4.1 Scanning a Storage Phosphor Screen 22
4.5 Visible Imaging 23
4.6 The Image Gallery 24
5. Settings 28
5.1 General Settings 28
5.2 Advanced Settings, Create Darkmasters, Create Flats 28

Sapphire™ Biomolecular Imager User Manual Page 5
1. Introduction
The Azure Sapphire Biomolecular Imager is a next generation laser scanning system that provides you
with exceptional data quality through extremely sensitive detection, ultra-high resolution and broad linear
dynamic range.
The Sapphire family of instruments includes the following products:
• Sapphire NIR
•Sapphire RGB
• Sapphire RGBNIR
•Sapphire PI
All models are compatible with optional chemiluminescence and phosphor imaging modules.
1.1 Key Components and Applications
Model Key Components Applications
Sapphire RGB 488nm LD, 520nm LD, 658nm LD RGB visible uorescence imaging
Sapphire NIR 685nm LD, 784nm LD NIR uorescence imaging
Sapphire RGBNIR 488nm LD, 520nm LD, 658nm LD,
784nm LD
RGB and NIR uorescence imaging
Sapphire PI 658LD Phosphor-imaging
1.2 Optional Modules
•Phosphor – Imaging phosphor screens exposed to radioactive samples
•Chemi – Imaging chemiluminescent samples with sensitivity of lm
•Q-Module – Add dye exibility and increase quantitative capability by adding 520 laser channel to
Sapphire Biomolecular Imager – NIR
•488 Laser Module – Add dye exibility by adding 488 laser channel to Sapphire Biomolecular Imager – NIR
1.3 Optional Modications
•Cy5 Modication – Modify the red channel of any Sapphire Biomolecular Imager to a 638nm laser
and detector
•Cy5.5 Modication – Modify the 685 channel of a Sapphire Biomolecular Imager - NIR to a 658nm laser
and detector
•NIR700 Modication – Modify the red channel of any Sapphire Biomolecular Imager to a 685nm laser
and detector

Sapphire™ Biomolecular Imager User Manual Page 6
1.4 Table of Specications
Sapphire NIR Sapphire RGB Sapphire RGBNIR Sapphire PI
Part number IS1024 IS1025 IS1026 IS1027
Laser excitation
wavelengths
685, 784 488, 520, 658 488, 520, 658, 784 658
Bit depth 16 bit 16 bit 16 bit 16 bit
Scanning area 25 cm X 25 cm 25 cm X 25 cm 25 cm X 25 cm 25 cm X 25 cm
Scanning modes Simultaneous, Sequential Simultaneous, Sequential Simultaneous, Sequential Phosphor-imaging
Pixel size 10 micron – 1000 micron 10 micron – 1000 micron 10 micron – 1000 micron 10 micron – 1000 micron
Detectors Avalanche Photodiode Photomultiplier Tube,
Avalanche Photodiode
Photomultiplier Tube,
Avalanche Photodiode
Photomultiplier Tube
Scanning speed 50 cm/s 50 cm/s 50 cm/s 50 cm/s
Filters Red 725BP40,
IR 832BP37
Blue 518BP22,
Green 565BP24,
Red 710BP40
Blue 518BP22,
Green 565BP24,
Red 710BP40,
IR 832BP37
Blue 390BP40
Dimensions
(W X H X D)
75 cm X 45 cm X 70 cm 75 cm X 45 cm X 70 cm 75 cm X 45 cm X 70 cm 75 cm X 45 cm X 70 cm
Weight 140 lbs 140 lbs 140 lbs 140 lbs
Power
requirements
100 – 240 VAC ± 10%,
50/60 Hz
100 – 240 VAC ± 10%,
50/60 Hz
100 – 240 VAC ± 10%,
50/60 Hz
100 – 240 VAC ± 10%,
50/60 Hz
Computer Options Windows 10 laptop
OR Windows 10 Pro
desktop with HD monitor
Windows 10 laptop
OR Windows 10 Pro
desktop with HD monitor
Windows 10 laptop
OR Windows 10 Pro
desktop with HD monitor
Windows 10 laptop
OR Windows 10 Pro
desktop with HD monitor
Chemiluminescent
Upgrade
Optional Optional Optional Optional
Imaging area,
chemiluminescent
16 cm X 13 cm 16 cm X 13 cm 16 cm X 13 cm 16 cm X 13 cm
Bit depth 16 bit 16 bit 16 bit 16 bit
Resolution 2688 X 2200 2688 X 2200 2688 X 2200 2688 X 2200
Imaging time 0-60 minutes 0-60 minutes 0-60 minutes 0-60 minutes
Visible imaging Yes Yes Yes Yes
Phosphor Imaging
Module
Optional Optional Optional N/A
Sample types Storage phosphor screen
(imaging plate)
Storage phosphor screen
(imaging plate)
Storage phosphor screen
(imaging plate)
Storage phosphor screen
(imaging plate)

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2.1 System Placement
WARNING! Excessive Weight Hazard – Please use two or more people to lift the system. Failure to do so
can result in system damage and personal injury.
As with all electrical instruments, the Azure Sapphire Biomolecular Imager should be located away from
water, solvents, or corrosive materials, on a at and stable surface with adequate clearance on all sides. The
system must remain stationary during operation. Further, the system should be placed away from interfering
electrical signals and magnetic elds. If possible, a dedicated electrical outlet should be used to eliminate
electrical interference from other instrumentation in your laboratory. The Azure Sapphire Biomolecular Imager
should be installed at no more than 3000 meters above sea level.
2.2 Connecting to Power
The power entry module is located in the lower right on the back panel of the system. Connect the power cord
to a secure power outlet.
It is important to connect the system to a well-grounded power source.
2.3 Power On/Off the System
To turn on the system
1. Switch on the system master power by ipping the power switch on the back right panel
of the instrument to the on ( | ) position.
2. Once the power is on to the system, wait for the light panels to stop changing color, and
then the system is ready to turn on.
3. Press and hold the power button on the front left of the instrument for 5 seconds. The
system is now ready to use.
To turn off the system
1. Push the power button on the front of the system for 5 seconds to put the system in standby mode
2. Turn off master power to the system using the power switch on the back of the instrument.
Azure Biosystems recommends leaving the system master power turned on via the switch on the back panel,
as this switch may not be easily accessible.
2.4 Software Installation
The Azure Sapphire Software is pre-installed. To launch the software, double click on the
desktop icon. The system will take a few seconds to initialize.
Once the system is done initializing, the software displays the Imaging tab, and is ready
to use.
2. Installation and Setup

Sapphire™ Biomolecular Imager User Manual Page 8
2.5 Connecting Other USB Devices to the System
The external computer is connected to the Sapphire system via a USB 3 connection.
You may attach regulatory approved, Windows OS supported USB keyboard, USB mouse or other USB input
devices to any of the unused USB ports that remain on the external PC.

Sapphire™ Biomolecular Imager User Manual Page 9
3. Proper Usage – Please Read Before Use
DO DO NOT
Wipe the imaging surface with ultrapure water,
70% ethanol or isopropyl alcohol if available, and a
lint free wipe.
Wipe the surface with anything else. Many
detergents and cleaning chemicals have uorescent
properties which will interfere with the scanning of
uorescent blots.
Leave the system master power on at the back. Attempt to access the back switch unless it is
readily accessible.
Keep the system computer connected, on a table
near by.
Put the system computer on top of the scanning
apparatus. The heat generated by the PC may
damage the unit.
Keep the top of the Sapphire Biomolecular
Imager clear.
Put anything on top of the imager. The Sapphire
was not designed to withstand forces acting down
on top of the imager.
Remove your samples from the imager
when nished.
Leave your samples in the imager. Many samples
can contain hazardous chemicals, such as ethidium
bromide or radiolabeled proteins, that can cause
damage or distress to the next samples or users.
Leave your system where it is installed. Move your Sapphire. The Sapphire Imager weighs
135lbs (61kg) and is not designed to be moved.
Moving the Sapphire Imager, without the express
permission of Azure Biosystems, may void warranty
or service contracts covering the imager.
Close the imaging lid whilst imaging. Leave the imaging lid open while imaging. A
safety mechanism disarms the lasers and prevents
them from turning on when the imaging lid is not
properly shut.
Call Azure Biosystems, or email
support@azurebiosystems, in the event of an
issue with the instrument.
Attempt to x the instrument yourself as some of
the components may be hazardous.