Molecular Devices SpectraMax iD3 User manual

5054747 H
January 2022
SpectraMax iD3
Multi-Mode Microplate Reader
User Guide

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
2 5054747 H
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©2022 Molecular Devices, LLC.
All rights reserved.

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Contents
Safety Information 5
Warnings, Cautions, Notes, and Tips 5
Chapter 1: Introduction 11
Computer Integration 11
Applications 15
Environmental Control 15
Optics 15
Plate Controls 16
Injectors 16
Chapter 2: Setting Up the Instrument 17
Package Contents 17
Unpacking the Instrument 19
Removing the Transport Locks 21
Connecting Instrument Cables 24
Assembling and Maintaining Injectors 25
Chapter 3: Getting Started 29
Welcome 30
Defining Date, Time, and Global Read Settings 31
Getting the Instrument on Your Network 32
Maintaining Users 33
Chapter 4: Home Page 35
Changing PIN/Logout 36
Quick Start and Favorites 37
Protocol Libraries 38
External Shake Settings 40
Temperature Settings 41
Maintaining Injectors 42
Maintenance Page 52
Loading and Unloading Plates 53
Chapter 5: Protocols 55
Viewing Protocol Settings 55
Defining Protocol Settings 57

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
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Read 70
Result Library 71
Chapter 6: Read Modes and Read Types 77
Absorbance Read Mode 79
Fluorescence Intensity Read Mode 83
Luminescence Read Mode 87
Chapter 7: Maintenance and Troubleshooting 91
Preventive Maintenance 91
Cleaning the Instrument 91
Cleaning Injectors and Accessories 92
Troubleshooting 93
Before You Move the Instrument 95
Obtaining Support 100
Appendix A: Instrument Specifications 101
Measurement Specifications 101
Physical Specifications 104
Injector Specifications 106
Appendix B: Accessories 109
Injector Accessories 109

Safety Information
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Safety Information
Information about the safe use of the instrument from Molecular Devices® includes an
understanding of the user-attention statements in this guide, the safety labels on the
instrument, precautions to follow before you operate the instrument, and precautions to follow
while you operate the instrument.
Make sure that everyone involved with the operation of the instrument has:
Received instruction in general safety practices for laboratories.
Received instruction in specific safety practices for the instrument.
Read and understood all Safety Data Sheets (SDS) for all materials being used.
Read and observe all warnings, cautions, and instructions. The most important key to safety is
to operate the instrument with care.
WARNING! If the instrument is used in a manner not specified by Molecular Devices,
the protection provided by the equipment might be impaired.
Warnings, Cautions, Notes, and Tips
All warning symbols are framed within a yellow triangle. An exclamation mark is used for most
warnings. Follow the related safety information. Other symbols can warn of other types of
hazards such as biohazard or electrical warnings as are described in the text of the warning.
The following user attention statements can display in the Molecular Devices user
documentation. Each statement implies the amount of observation or a recommended
procedure.
WARNING! A warning indicates a situation or operation that could cause personal
injury if precautions are not followed.
CAUTION! A caution indicates a situation or operation that could cause damage to the
instrument or loss of data if correct procedures are not followed.
Note: A note calls attention to significant information.
Tip: A tip provides useful information or a shortcut, but is not essential to the completion
of a procedure.

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Symbols on the Instrument
Each safety label on the instrument contains an alert symbol that indicates the type of potential
safety hazard.
Symbol Indication
Consult the product documentation.
Potential lifting hazard. To prevent injury, use a minimum of two people to lift the
instrument.
Potential pinch hazard.
Potential biohazard.
Potential heat hazard.
Electrostatic sensitive device (ESD). Observe precautions to handle electrostatic
sensitive devices.
Potential laser hazard. The instrument is rated a Class 1 Laser Product because it can use
an optional read module that contains a laser. The laser light cannot be accessed.
Near-field Communication
This equipment has been tested and found to comply with the limits for a Class A digital device,
pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable
protection against harmful interference when the equipment is operated in a commercial
environment. This equipment generates, uses, and can radiate radio frequency energy and, if
not installed and used in accordance with the instruction manual, may cause harmful
interference to radio communications. Operation of this equipment in a residential area is likely
to cause harmful interference in which case the user will be required to correct the interference
at their own expense. Changes or modifications made to this equipment not expressly
approved by the party responsible for compliance may void the FCC authorization to operate
this equipment.

Safety Information
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A sticker on the back of the instrument displays the following symbols:
Symbol Indication
The instrument serial number.
The instrument manufacture date.
You should consult the instructions for use.
CSA certification.
European technology conformity.
United Kingdom and/or Korean technology conformity.
The instrument complies with Australian radio communication requirements.
This symbol is required in accordance with the Waste Electrical and Electronic
Equipment (WEEE) Directive of the European Union. It indicates that you must not
discard this electrical or electronic product or its components in domestic
household waste or in the municipal waste collection system.
For products under the requirement of the WEEE directive, contact your dealer or
local Molecular Devices office for the procedures to facilitate the proper collection,
treatment, recovery, recycling, and safe disposal of the device.
Indicates the environmental friendly use period.
There is an authorized representative in the European community.
The instrument manufacturer.
The manufacturer catalog number.
- California proposition 65 requires businesses to provide warnings to
Californians about significant exposures to chemicals that cause cancer, birth defects, or other
reproductive harm.

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Laser Safety
WARNING! LASER LIGHT. This symbol indicates that a potential hazard to personal
safety exists from a laser source. When this symbol displays in this guide, be careful to
follow the specific safety information related to the symbol.
The SpectraMax iD5 is rated a Class 1 Laser Product because you can install an optional read
mode module that contains a laser. The laser light cannot be accessed.
The instrument is equipped with a redundant laser safety system. A hardware interlock prevents
the laser in the module from turning on, unless the plate chamber door and the instrument left
hood are closed. The user or the service engineer is not exposed to radiation from any laser
module during operation, maintenance, or service. The closed plate chamber provides the
protective housing.
WARNING! LASER LIGHT. Operate the instrument only when the plate chamber door
and the instrument left hood are closed.
Some modules can have a laser or laser diode up to Laser Class 4 that is inside the module. The
lasers are non-operational until after the module is properly installed in the instrument.
Note: At the time this user guide was authored, no SpectraMax iD5 modules contain a
laser but future modules are being considered.
Electrical Safety
To prevent electrical injuries and property damage, inspect all electrical equipment before use
and report all electrical deficiencies. Contact Molecular Devices technical support for
equipment service that requires the removal of covers or panels.
WARNING! HIGH VOLTAGE. Within the instrument is the potential of an electrical
shock hazard existing from a high voltage source. Read and understand all safety
instructions before you install, maintain, and service the instrument.
To prevent electrical shock, use the supplied power cord and connect to a properly grounded
wall outlet.
To ensure sufficient ventilation and provide access to disconnect power from the instrument,
maintain a 20cm to 30cm (7.9in. to 11.8in.) gap between the rear of the instrument and the
wall.
Power off the instrument when not in use.

Safety Information
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Moving Parts Safety
The instrument contains moving parts that can cause injury. Under normal conditions, the
instrument is designed to protect you from these moving parts.
WARNING! If the instrument is used in a manner not specified by Molecular Devices,
the protection provided by the equipment might be impaired.
To prevent injury:
Never try to exchange labware, reagents, or tools while the instrument is operating.
Never try to physically restrict the moving components of the instrument.
Keep the instrument work area clear to prevent obstruction of the movement. Provide
clearance in front of the instrument of 18 cm (7.1 in.) for the plate drawer.
The instrument has adjustable optics to define the read height, or z-height. In a top read,
the read height is the gap between the lens and the top of the plate, or the top of the lid if
the plate is lidded.
A transport lock is placed on the plate drawer to protect the instrument from damage during
shipping. You must remove the transport lock before you power on the instrument. See Plate
Controls, see page 16.
WARNING! Do not attempt to access the interior of the instrument unless specifically
instructed to do so. The moving parts inside the instrument can cause injury. Do not
operate the instrument with any covers or panels removed.
Chemical and Biological Safety
Normal operation of the instrument can involve the use of materials that are toxic, flammable, or
otherwise biologically harmful. When you use such materials, observe the following
precautions:
Handle infectious samples based on good laboratory procedures and methods to prevent
the spread of disease.
Observe all cautionary information printed on the original containers of solutions before
their use.
Dispose of all waste solutions based on the waste disposal procedures of your facility.
Operate the instrument in accordance with the instructions outlined in this guide, and take
all the required precautions when using pathological, toxic, or radioactive materials.
Splashing of liquids can occur. Take applicable safety precautions, such as using safety
glasses and wearing protective clothing, when working with potentially hazardous liquids.
Observe the applicable cautionary procedures as defined by your safety officer when using
hazardous materials, flammable solvents, toxic, pathological, or radioactive materials in or
near a powered-up instrument.
WARNING! Never use the instrument in an environment where potentially damaging
liquids or gases are present.
CAUTION! When you use aggressive or corrosive reagents, you should have the plate
automatically move out of the instrument after a read.

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
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Chapter 1: Introduction
The SpectraMax® iD3 Multi-Mode Microplate Reader from Molecular Devices is a
monochromator-based, multi-mode plate reader. The touchscreen interface provides
integrated instrument control, data display, and the ability to export results over your network
for statistical data analysis.
There are several instrument configurations.
Base
SpectraMax®Injector System with SmartInject™ (factory installed or by a Molecular Devices
field representative)
The instrument supports the following read modes:
Absorbance Read Mode, see page 79
Fluorescence Intensity Read Mode, see page 83
Luminescence Read Mode, see page 87
The instrument supports four read types. See Read Modes and Read Types on page 77:
Endpoint
Kinetic
Well Scan
Spectrum
You can integrate the instrument with the StakMax® Microplate Handling System.
Computer Integration
The instrument touchscreen uses the embedded SoftMax Touch Software to run basic non-
injector reads. You must use a computer running the SoftMax® Pro Data Acquisition and
Analysis Software to operate the instrument for advanced acquisition settings and for protocols
that use the SpectraMax Injector System.
Optional integration of the instrument with a computer allows you to export data over your
intranet or to a USB drive in an Excel format for further analysis.
You can use the SoftMax Pro Software - Standard edition or the SoftMax Pro Software - GxP
edition to have the instrument collect data from one or more plates and store the data in a
single file, using the same or different instrument settings for different plates. Assays that
require a read in two or more read modes or read types can be combined in a single
experiment and run with a single command in the SoftMax Pro Software, by defining separate
plate reads and enabling Auto Read. See the SoftMax Pro Data Acquisition and Analysis
Software User Guide .
Note: When you use a computer running the SoftMax Pro Software to operate the
instrument, the instrument touchscreen is locked.
For users that use the SoftMax Pro Software - GxP edition to operate the instrument, the user
must have the following permission to lock and unlock the instrument touchscreen:
SoftMax Pro Software - GxP edition version 7.0.3 users require the Sign Signature
permission.
SoftMax Pro Software - GxP edition version 7.1.x users require the Lock/Unlock Instrument
permission.
1

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In the Ribbon, on the GxP tab, users with appropriate permission can use the following icons to
lock and unlock the instrument touchscreen:
Click GxP Mode On to lock the instrument touchscreen and operate the instrument
from the computer running the SoftMax Pro Software in GxP mode. This locks the
instrument touchscreen for all users and you must operate the instrument from a computer
running the SoftMax Pro Software - GxP edition.
Click GxP Mode Off to release the lock from the instrument touchscreen and allow
users to use the instrument touchscreen to run experiments.
Note: The instrument remains locked until the user with the appropriate permission
clicks GxPMode Off to stop the GxP mode. You cannot use the Instrument
Connection dialog to disconnect from an instrument that is locked in GxP mode.
Installing SoftMax Touch Software Updates
The instrument's SoftMax Touch Software version number displays on the Maintenance page -
System Information tab: > System Information.
SoftMax Touch Software version 1.1 is compatible with SoftMax Pro SoftwareSoftMax® Pro
Data Acquisition and Analysis Software version 7.0.2.
SoftMax Touch Software version 1.2 is compatible with SoftMax Pro Software version 7.0.3
and later.
The SoftMax Touch Software update uses a USB drive. When you insert the USB drive into one
of the USB ports below the touchscreen, the update automatically starts and runs with no other
user interaction required. You cannot uninstall an update.

Chapter 1: Introduction
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Update File Explanation
The update file has the following naming convention: iDx_update_n_n_nnnnnn.mdup
iDx_update: Use the SoftMax Touch Software update files to update the software in both
the SpectraMax iD3 AND the SpectraMax iD5 instruments. The update is intelligent and
knows which instrument software to update.
<n>_<n>: Major software version and minor software version, for example: 1.2 displays as 1_
2.
<nnnnnn>: Build number. This is the most relevant number that you should compare to what
displays on the instrument Maintenance page.
.mdup: File extension.
Requirements:
1 empty USB drive with at least 500 MB free space
To update the SoftMax Touch Software:
1. From any web-enabled computer, go to www.moleculardevices.com/touchscreenupdate to
display the latest available
iDx_update_n_n_nnnnnn.mdup file.
2. On the instrument touchscreen, tap > System Information and confirm that the
instrument software number/build number combination is lower than the
iDx_update_n_n_nnnnnn.mdup file numbers. If yes, continue to update.
3. Download the iDx_update_n_n_nnnnnn.mdup file to the USB drive.
4. Right-click the iDx_update_n_n_nnnnnn.mdup file and select Properties.
5. If the file is blocked (usually for downloads) select the Unblock check box and click OK.
6. Power on the instrument and wait for the initialization to complete. Confirm that the
instrument is not performing any operations.
7. If the instrument is being operated by a computer running the SoftMax Pro Software or is
locked by the SoftMax Pro GxP Software, turn off GxP mode and/or disconnect the
instrument from the SoftMax Pro Software.

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8. Insert the USB drive into one of the USB ports below the instrument touchscreen. The
update starts automatically.
9. When the update message displays, tap OK to start the update process. An update can
take up to 5 minutes.
10. When the update completes the instrument does a system restart. After the system restart
finishes, remove the USB drive.
11. On the touchscreen, tap > System Information and confirm that the software
number/build number is same as the name of the update file.
Installing the QuickSync Tool
The QuickSync Tool allows a computer to receive the raw data that the instrument exports,
within the security and firewall restrictions of your network. The computer on which you install
the QuickSync Tool must be able to communicate with the instrument over your intranet or you
can directly connect the computer to the instrument. This is usually the computer that runs the
SoftMax Pro Software. After you synchronize the computer with the instrument, the instrument
exports result data to the computer for further analysis. See Using The QuickSync Tool on page
76.
Tip: You can synchronize multiple computers to an instrument and multiple instruments
to a computer.
To install the QuickSync Tool:
1. Insert the SoftMax Pro Software USB drive, DVD, or use alternative media. Locate and
double-click QuickSyncInstaller n.n .exe file to start the install.
2. When the " Do You Want to Allow This App... " message displays, click Yes. The installation
starts.
3. On the Completing the Setup page, click Finish. The QuickSync Tool icon appears on
your desktop.
4. Double-click to display the message QuickSync Ready and a smaller version of the
appears in the computer tray near the clock at the bottom of the computer screen. Wait for
the computer to find the instrument.
5. Right-click in the tray near the clock to display a menu and select Available Services to
display the list of SpectraMax iD3 and SpectraMax iD5 instruments on your intranet and/or
the instrument to which you connect the computer through an Ethernet cable.
6. Click the name of instruments to which to synchronize the computer. A check mark appears
next to each instrument name to which the computer is synchronized.

Chapter 1: Introduction
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Add Service by IPAddress
If the name of the instrument does not appear in the list of available services, do the following:
1. Right-click in the tray near the clock and select Add Service by IP to display the
following.
2. Enter the IPaddress of the instrument to which to connect. See Getting the Instrument on
Your Network on page 32.
3. Click Add Connect.
Tip: If the computer still cannot find the instrument, contact your IT help desk to make
sure that your company network setup and company intranet security allow the
communication between the computer and the instrument.
Applications
The high sensitivity and flexibility of the instrument make it useful for applications in the fields of
biochemistry, cell biology, immunology, molecular biology, and microbiology.
Typical applications include ELISA, nucleic acid, protein, enzymatic type homogeneous and
heterogeneous assays, microbial growth, endotoxin testing, and pipettor calibration.
Application notes with specific application protocol suggestions are in the Information Center
and Knowledge Base on the Molecular Devices web site at www.moleculardevices.com.
Environmental Control
The instrument can maintain the temperature inside the plate chamber at 5°C (9°F) above
ambient to 66°C (150°F). The temperature sensors detect the temperature of the air inside the
chamber, not the temperature of the samples in the plate. If you use the instrument to warm the
samples, use a seal or lid on the plate to prevent evaporation of the sample. See Temperature
Settings on page 41.
Optics
The 2x2 monochromators permit individual optimization of wavelengths for both excitation and
emission in fluorescence readings. Mirrored optics shape the light, and a height-adjustable
objective lens focuses the beam into the sample volume. PMT Gain can be set to automatic,
high, medium, or low.
Dynamic Range
The dynamic range of detection is approximately from 10-6 to 10-12 molar fluorescein. Variations
in measured fluorescence values are virtually eliminated by internal compensation for detector
sensitivity, photomultiplier tube voltage and sensitivity, and excitation intensity. The
photometric range is 0.000 to 4.000ODs with a resolution of 0.001OD.
CAUTION! Never touch the optic mirrors, lenses, filters, or cables. The optics are
extremely delicate, and critical to the function of the instrument.

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
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CAUTION! Use of organic solvents can cause harm to the optics in the instrument.
Extreme caution is recommended when you use organic solvents. Always use a plate lid
and do not place a plate that contains these materials in the plate chamber for prolonged
periods of time. Damage caused by the use of incompatible or aggressive solvents is
NOT covered by the instrument warranty.
Plate Controls
You can place plates up to a height of 22mm in the instrument plate drawer. A camera detects
the height of a plate and confirms that the height is consistent with the plate type you select and
that you position the plate properly on the plate drawer.
Depending on the application, the instrument can read 6, 12, 24, 48, 96, and 384-well plates.
For micro-volume measurements, the instrument supports SpectraDrop 24-well Low Volume
Microplate and SpectraDrop 64-well Low Volume Microplate. See Plate Format and Plate Type
Settings on page 59.
To read cuvettes, the instrument supports the use of the SpectraCuvette™ adapter that has the
22 mm plate height sticker.
CAUTION! SpectraCuvette Adapters without a sticker have a plate height of 24 mm and
cannot be used in the SpectraMax iD3 or SpectraMax iD5. To prevent damage to the
instrument, the height of the plate must not exceed 22mm, including the lid if the plate is
lidded.
Shake
You can operate a shake feature independently from a protocol to mix the contents of the wells
in a plate outside of the plate chamber for visual inspection. This makes it possible to do kinetic
analysis of solid-phase, enzyme-mediated reactions. See External Shake Settings on page 40.
You also define shake settings as part of each protocol. The protocol shake setting depends on
the read mode you select. See Shake Settings on page 68.
Injectors
Instruments configurations that include the SpectraMax Injector System can deliver a reagent to
the wells of a plate. You can use injectors for all read modes.
When your instrument configuration includes injectors, the instrument right hood has a handle,
and the icon is enabled on the left side of the Home page.
Note: You must use a computer running the SoftMax Pro Software to operate the
instrument for advanced acquisition or injector protocols.
The SoftMax Pro Software can set up the instrument to inject and read well by well to reduce
signal loss. To define the settings for a read with injection, you must use the Acquisition View on
the Settings dialog. See the SoftMax Pro Software application help for details.
Use the Injector Maintenance page to wash, prime, and calibrate the injectors. See Maintaining
Injectors on page 42.
WARNING! BIOHAZARD. Depending on your usage, the injectors can have
biohazardous material in and on them. Always use the personal protective equipment
(PPE) prescribed by your laboratory.

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Chapter 2: Setting Up the Instrument
Before you unpack and setup the SpectraMax iD3, prepare a flat work area that has sufficient
space for the instrument and required cables. See Instrument Specifications on page 101.
All software required to run basic non-injector reads is installed in the instrument and is
accessible from the touchscreen.
You can export data to a computer over your intranet, through a direct Ethernet cable, or to a
USB drive in an Excel format for further analysis.
You must use a computer running the SoftMax Pro Software to operate the instrument for
advanced acquisition settings and for protocols that use the SpectraMax Injector System. If you
use the SoftMax Pro Software to operate the instrument, you must install the QuickSync Tool
software on the computer running the SoftMax Pro Software. See the SoftMax Pro Data
Acquisition and Analysis Software User Guide and Installing the QuickSync Tool on page 14.
Note: When you use a computer running the SoftMax Pro Software to operate the
instrument, the instrument touchscreen is locked.
Package Contents
The package contains the instrument plus a box that contains the tools and accessories.
Illustration Part Number Description
SoftMax Pro Software Latest Version SoftMax Pro Software with Product Key and QuickSync
tool
5054744 Installation guide
YW 000 006 Hex key, 2.0mm
YW 000 012 Holex HEXAGONballhead bolt driver 3 mm
5052189 CAT6 Ethernet cable, 2meter (6.56foot)
4400-0002 or
4400-0036
Power cord, 115 V
or Power cord, 230 V
5061514 Near Field Communication (NFC)magnets.
5056339 Near Field Communication (NFC)key fob (NTAG 213,
180 byte).
2

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When your instrument has the SpectraMax Injector System the package also contains the
following.
Illustration Part Number Description
5055247 Injector Nozzle
5044164 Tubing
5055251 Bottle Holder
5044165 Bottle Adapters
5044163 Waste Plate
Cannot order from Molecular Devices
Wide-neck bottle, HDPE
50mL capacity
36mm square by 68mm high
24mm diameter inside neck
Recommended supplier: VWR (215-0440)
Bottles
Cannot order from Molecular Devices
Strip wells, polystyrene
1x8, clear, flat-bottomed
Recommended supplier: Greiner Bio-One (762001)
Strip well
Package Contents for Injectors
For a complete list of the contents of the package, see the enclosed packing list.

Chapter 2: Setting Up the Instrument
5054747 H 19
Unpacking the Instrument
The packaging is designed to protect the instrument during transportation.
Transport locks are placed on the transport slide and the plate drawer to protect the instrument
from damage during shipment. You must remove the transport locks before you power on the
instrument.
WARNING! LIFTING HAZARD. To prevent injury, use a minimum of two people to lift
the instrument.
Note: Retain the shipping box and all packaging materials for future transport needs. Do
not use tools that can damage the packaging or the instrument.
CAUTION! When transporting the instrument, warranty claims are void if improper
packing results in damage to the instrument.
To unpack the instrument:
1. Check the box for damage that occurred during transportation. Inform the supplier
immediately and keep the damaged packaging.
CAUTION! Keep the box upright. Do not tip or tilt the box or place it on its side.
2. With the box facing up as indicated, cut open the tape on the side of the box labeled Open
Here.

SpectraMax iD3 Multi-Mode Microplate Reader User Guide
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3. Grasp the handle on the cardboard and slide the instrument out of the box.
4. Remove the accessories tool box.
CAUTION! Keep the instrument upright and level when lifting. Do not tip or shake
the instrument to prevent damage to the instrument.
5. Remove the foam packaging from both ends and then remove the plastic bag from the
instrument.
6. With one person on each end, lift the instrument to a dry, flat area. You will need to access
the back of the instrument to remove the transport lock and to connect the instrument
cables.