LI-COR Odyssey CLx User manual

Odyssey® CLx
Operator’s Manual

CE Marking:
This product (model number 9140) is a CE-marked product. For conformity information, contact
LI-COR Support at http://www.licor.com/biotechsupport. Outside of the U.S., contact your local sales
office or distributor.
Doc. #53-15960-A
June 20, 2016
page 1 of 1
Odyssey CLx Imager
Part Name Toxic and Hazardous Substances or Elements
(Pb) (Hg) (Cd) (Cr(VI)) (PBB) (PBDE)
PCBs)
X O O O O O
Electro-
mechanical Parts)
X O O O O O
Optics)
X O X O O O
Cables and Wires)
X O O O O X
(Metal Parts)
X O O O O O
(Plastic Parts)
O O O O O O
(Batteries)
O O O O O O
SJ/T 11364
O = GB/T 26572
(indicates that the content of the toxic and hazardous substance in all the Homogeneous
Materials of the part is below the concentration limit requirement as described in GB/T 26572).
X = GB/T 26572
(indicates that the content of the toxic and hazardous substance in at least one Homogeneous
Material of the part exceeds the concentration limit requirement as described in GB/T 26572).
德CLX
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Notes on Safety
LI-COR products have been designed to be safe when operated in the manner described in this manual. The safety
of this product cannot be guaranteed if the product is used in any other way than is specified in this manual. The
Odyssey® CLx Imager is intended to be used by qualified personnel. Read this entire manual before using the
Odyssey CLx Imager.
Equipment Markings:
The product is marked with this symbol when it is necessary for you to refer to the
manual or accompanying documents in order to protect against damage to the product.
The product is marked with this symbol when a hazardous voltage may be present.
Manual Markings:
WARNING Warnings must be followed carefully to avoid bodily injury.
CAUTION Cautions must be observed to avoid damaging your equipment.
NOTE Notes contain additional information and useful tips.
IMPORTANT Information of importance to prevent procedural mistakes in the operation of the
equipment or related software. Failure to comply may result in a poor experimental
outcome but will not cause bodily injury or equipment damage.
Federal Communications Commission Radio Frequency Interference Statement
WARNING: This equipment generates, uses, and can radiate radio frequency energy and if not installed in
accordance with the instruction manual, may cause interference to radio communications. It has been tested and
found to comply with the limits for a Class A computing device pursuant to Subpart J of Part 15 of FCC rules,
which are designed to provide a reasonable protection against such interference when operated in a commercial
environment. Operation of this equipment in a residential area is likely to cause interference in which case the
user, at his own expense, will be required to take whatever measures may be required to correct the interference.
Page 4

Notice
The information contained in this document is subject to change without notice. LI-COR MAKES NO
WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING, BUT NOT LIMITED TO
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
LI-COR shall not be liable for errors contained herein or for incidental or consequential damages in connection with
the furnishing, performance, or use of this material.
This document contains proprietary information that is protected by copyright. All rights are reserved. No part of
this document may be photocopied, reproduced, or translated to another language without prior written consent of
LI-COR, Inc.
Printing History
Publication Number 977-19527
Printed April 7, 2019
Revised: January 2021
Global Headquarters
4647 Superior Street • Lincoln, NE 68504
Toll free: 800-645-4267 • Fax: [phone] • [e-mail] •licor.com/bio
Regional Offices
LI-COR Biosciences GmbH
Siemensstraße 25A • 61352 Bad Homburg • Germany
Phone: [phone] • Fax: [phone] • [e-mail]
LI-COR Biosciences UK Ltd.
St. John’s Innovation Centre • Cowley Road
Cambridge • CB4 0WS
United Kingdom • Phone: [phone] • Fax: [phone] • [e-mail]
LI-COR Biotechnology Distributor Network: www.licor.com/bio/distributors
LI-COR is an ISO 9001:2015 registered company. © 2021 LI-COR Inc. All rights reserved. Specifications subject to
change. LI-COR, Odyssey, MPX, IRDye, Image Studio, and In-Cell Western are trademarks or registered trademarks
of LI-COR Inc. The Odyssey CLx Imager is covered by U.S. patents, foreign equivalents, and patents pending.
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Chapter 1: Installation and Safety Information
Safety Considerations 9
Laser Safety 9
Safety Interlocks 11
Placement in the Laboratory 11
Ambient Laboratory Conditions 11
Instrument Ventilation 11
Space Requirements 12
Level the Imager 12
Moving the Imager 12
Chemical Safety 12
Electrical Considerations 12
Power Cords 12
Power Switch 13
Fuse Information 13
Computer Connections and Networking 13
Routine Maintenance 13
Networking Cables 14
Chapter 2: System Overview
External Panels and Controls 15
Front Panel and Scanning Surface 15
Rear Panel 16
Scanning Surface 17
General Description of Scanning 17
Continuous Operation 17
Disconnecting the Power 17
Optical System Description 17
Software Overview 18
Use Empiria Studio® Software for Quantitative Western blot analysis 18
Use ImageStudio Software for other types of analysis 18
Chapter 3: Operation
Before You Begin... 19
Odyssey® CLx
Imager
Table of Contents
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Cleaning the Scanning Surface 19
Scanning 19
Using Membranes 19
Using Gels 21
Using Multiwell Plates 23
Scanning Slides 25
Obtaining Technical Support 26
Exporting ImageStudio Software Log Files 26
Finding Empiria Studio Software Log Files 27
Chapter 4: Appendix
Specifications 29
Imaging System 29
Operating Specifications 29
Embedded Firmware Source Code 29
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Chapter 1: Installation and Safety Information
Safety Considerations
Laser Safety
The Center for Devices and Radiological Health (CDRH) was established in October 1982, by the
U.S. Food and Drug Administration (FDA) to protect the public health in the fields of medical
devices and radiological health
Manufacturers of products subject to performance standards under the Radiation Control for Health
and Safety Act of 1968 are required to furnish various reports to the CDRH.
The Odyssey CLx is certified as a Class I laser product. This means that hazardous laser radiation is
not emitted outside the instrument. Radiation emitted inside the Odyssey CLx is confined within
protective housings and external covers. A series of safety interlocks ensures that the laser beam
cannot escape during any phase of user operation.
The CDRH implemented regulations for laser products on August 1, 1976 (CDRH radiation
performance standard 21, Code of Federal Regulations Chapter 1, Subchapter J). Compliance for
products marketed in the United States is mandatory. The label that must be attached to laser
products marketed in the United States is illustrated in Figure 3-2 and is located on the rear panel of
the Odyssey® CLx, indicating compliance with CDRH regulations.
WARNING: Use of controls or adjustments or performance of procedures other than those
specified herein may result in hazardous radiation exposure.
AVERTISSEMENT: L'utilisation des commandes ou le réglage ou la performance des procédures
autrement qu'il a été indiqué dams le présent texte peut résulter en de dangereuses expositions aux
radiations.
The manufacturer label is illustrated in Figure 3-1 and is also on the rear panel of the instrument.
The Odyssey CLx Infrared Imaging System contains two lasers; one emitting at 785 nm, and one at
685 nm. The 685 nm laser emits visible laser radiation - direct exposure to either beam may cause
eye damage. Laser radiation is emitted through apertures at the top of the Odyssey CLx microscope
assembly. Because the microscope assembly moves in both planes relative to the glass scanning
surface, laser radiation could be focused at any position on this surface. Safety interlocks (described
below) automatically turn the lasers off when the Odyssey CLx lid is opened.
The label shown in Figure 3-3 is affixed to the inside of the Odyssey CLx case at two locations; one
near the laser/microscope assembly scanning bed, and the second on the cover that is used to seal
the above mentioned assembly.
Odyssey® CLx
Imager
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Chapter 1: Installation and Safety Information
INPUT
50/60Hz
100-240V 4A
DISCONNECT POWER BEFORE SERVICING
THIS DEVICE COMPLIES WITH PART 15 OF
THE FCC RULES. OPERATION IS SUBJECT
TO THE FOLLOWING TWO CONDITIONS:
(1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE
MUST ACCEPT ANY INTERFERENCE
RECEIVED, INCLUDING INTERFERENCE
THAT MAY CAUSE UNDESIRED OPERATION.
CONFORMS TO UL STD 61010-1
CERTIFIED TO CAN/CSA
STD C22.2 NO. 61010-1
Class 1 Laser Product
Complies with
IEC 60825-1:2014
3rd Edition
DÉBRANCHER LE POUVOIR
AVANT D’ENTRETENIR
THIS PRODUCT COMPLIES WITH CDRH
RADIATION PERFORMANCE STANDARD 21
CFR CHAPTER 1 SUB-CHAPTER J.
CE PRODUIT EST CONFORME À LA
PERFORMANCE DE RAYONNEMENT CDRH
CHAPITRE CFR NORME 1 SOUS-CHAPITRE J.
Figure 3-1. Manufacturer label.
VISIBLE AND INVISIBLE LASER RADIATION WHEN OPEN
AVOID DIRECT EXPOSURE TO BEAM
AVGER SYNLIG OCH OSYNLIG LASERSTRÅLNING NÄR DEN ÄR ÖPPEN
UNDVIK DIREKT STRÅLEXPONERING
SYNLIG OG USYNLING LASERSTRÅLING NÅR ÅBEN
UNDGÅ DIREKTE EKSPONERING AF STÅLE
RAYONNEMENT VISIBLE ET INVISIBLE LASER EN CAS D'OUVERTURE
EXPOSITION DANGEREUSE AU FAISCEAU
DANGER/VARNING/FARE
Figure 3-2. CDRH regulation compliance label. Figure 3-3. Laser radiation danger label.
See "Rear Panel" on page16 for the location of the labels in Figure 3-1 and Figure 3-2. The label in
Figure 3-3 is affixed to the inside of the Odyssey® CLx Imager case at two locations; one near the
laser/microscope assembly scanning bed, and the second on the cover that is used to seal the above
mentioned assembly.
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Odyssey® CLx Imager
Safety Interlocks
Interlocks
Figure 3-4. Location of interlocks on the Odyssey® CLx
instrument bezel.
The Odyssey CLx has two safety interlocks that
prevent access to the laser when the instrument
lid is opened during operation. Do not attempt
to defeat these interlocks. The interlocks are
located on the front of the instrument bezel
(Figure 3-4). Audible tones sound when the lid
is opened and closed (Figure 3-4).
Placement in the Laboratory
The Odyssey CLx CLx Near-Infrared Imaging System weighs approximately 33kg (72lbs). The
instrument should be placed on a laboratory bench that is sufficiently sturdy to bear its weight. The
bench should also be able to bear the weight of the computer if the computer will be installed
beside the Odyssey CLx Imager.
Ambient Laboratory Conditions
Place the Odyssey CLx Imager away from external heat sources (furnaces, windows, etc.). Additional
heating can cause high temperatures within the enclosure. Place the instrument away from sinks or
other sources of water that pose a shock hazard. Recommended operating conditions are 15-35°C
and a dew point not greater than 20°C to prevent condensation on the laser/microscope assembly
during operation. Allow the instrument to adjust to the temperature and humidity of the room
before powering it on to avoid damaging the instrument. It may be necessary to allow up to a day in
the new location in cases of extreme temperature and/or humidity change.
Instrument Ventilation
The instrument enclosure and circuit boards are cooled with multiple internal fans. The fan on the
rear of the instrument serves as an exhaust port, so the fan shrouds are not filtered and the cover
serves only as an exhaust outlet. There are no restrictions regarding placement of the instrument as
spacers on the rear of the instrument ensure sufficient airflow for the exhaust port. However, it is
important to not allow any objects (e.g., paper or a cover) to block airflow from the exhaust port
while the instrument is on.
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Chapter 1: Installation and Safety Information
Space Requirements
The Odyssey CLx Imager requires an area approximately 37H x 53W x 62Dcm (15 H x 21 W x
24.5 D inches). With the hood fully open, the Odyssey CLx requires 74cm (29”) of vertical
clearance.
Level the Imager
The instrument can be leveled by turning the threaded metal inserts located in each of the 4 plastic
feet (Figure 3-5).
Figure 3-5. Turn feet to adjust height.
Moving the Imager
LI-COR recommends that you do not move your imager. Instead, please contact LI-COR Technical
Support for options.
LI-COR cannot be held responsible for any damage incurred while moving, transporting, or
shipping the Odyssey CLx Imager, even if an existing warranty and/or service contract
applies. LI-COR cannot be held responsible for any injury incurred while moving,
transporting, or shipping the Odyssey CLx Imager.
Chemical Safety
LI-COR Biosciences recommends that all biochemicals be handled carefully, and that safe laboratory
procedures be followed at all times. Be aware of the hazards associated with any chemical before you
begin work.
The LI-COR Odyssey CLx should not be used with any radioactive materials.
Electrical Considerations
Power Cords
The Odyssey CLx is equipped with a 3-wire grounding-type plug. This plug will only fit into a
grounding-type outlet. This is a necessary safety feature. If you are unable to insert the plug into the
outlet, you will need to replace the outlet. Do not defeat the purpose of the grounding-type plug.
Do not locate the Odyssey CLx where the power cord will be walked on or exposed to water or
chemical spills.
The Odyssey CLx draws at most 4 amperes at 120V. If an extension cord is used, make sure the total
of the ampere ratings on the instruments plugged into the extension cord does not exceed the
extension cord ampere rating. Also make sure the total amperage of instruments plugged into the
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Odyssey® CLx Imager
wall outlet does not exceed the amperage capacity for the outlet (usually 15 or 20 amperes in the
United States).
To disconnect power before servicing, first disconnect the instrument from the software, briefly
press the power button to power down the instrument, and then remove the power cord from the
power receptacle on the Odyssey CLx back panel (Figure 3-6). See Disconnecting the Power on
page17 for more information.
Power Switch
To power on the imager, ensure the power switch on the back of the imager is enabled, then press
the power button on the front. Do not use the power switch on the back of the imager to power the
imager on and off. Use the power button on the front instead.
To enable power to the imager, press the side of the power switch with the line icon on the
power switch. Press the side of the switch with the circle symbol to cut power to the imager.
O
Power Switch
Power Receptacle
Figure 3-6. Location of the power switch and power receptacle on the Odyssey® CLx back panel. Note: The
appearance of your instrument's back panel may vary slightly from the one shown.
Fuse Information
There are no user-serviceable fuses.
Computer Connections and Networking
Note: Use only the supplied Cat. 5e network cable to connect the Odyssey CLx and computer.
When ImageStudio™ Software starts, it searches for and discovers any Odyssey CLx Imagers
automatically. If only one instrument is found, ImageStudio Software establishes communication.
If more than one instrument is found, the user is presented with a list of instruments and asked
which to use.
Routine Maintenance
The Odyssey CLx requires only minimal maintenance. However, as with any equipment utilizing
electrical voltages, there is a danger of fire or electrical shock if the equipment is not properly
maintained.
LI-COR Biosciences recommends that you routinely inspect the system and the scanning surface.
The following are some general maintenance guidelines:
lWipe all chemical spills from the case and/or scanning surface to prevent damage to the surface
coating.
lInspect all cables and power cords for evidence of fraying, exposed wire, or loose connections.
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Chapter 1: Installation and Safety Information
lKeep the scanning surface free of organic solvents and other combustibles.
lClean the exterior case parts with warm water and a damp cloth. The exterior case parts are
painted with a durable urethane coating that is resistant to chemical spills. Do not use scouring
compounds or solvents (e.g., acetone, benzene, carbon tetrachlorides, lacquer thinner, or alco-
hol) to clean the case.
Networking Cables
LAN
Figure 3-7. Networking
port label.
A Cat. 5e network cable is provided with the Odyssey® CLx Imager. Do not
use networking cables other than the one provided. The use of other
networking cables may result in improper electrical performance. The
networking port is on the back panel of the instrument and is marked with
the label illustrated in Figure 3-7.
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Chapter 2: System Overview
External Panels and Controls
Front Panel and Scanning Surface
Figure 4-1. Front panel features and power button on the Odyssey CLx.
Power On/Off Button: Briefly pressing this button turns the instrument on and off, when the
instrument is not connected to the ImageStudio™ Software. If the instrument is connected,
pressing the button results in the red error light blinking along with a warning sound to alert the
user that the instrument is connected to the software. Continuing to hold the power button for 5
seconds will turn the instrument off and the software connection will end.
Green Image Acquisition Indicator: This indicator light blinks during image acquisition and is
continuously on at other times, as long as communication with ImageStudio is maintained. The
indicator light is off before the instrument is connected to the software and if the Image Studio
Software is closed or communication is otherwise lost.
Odyssey® CLx
Imager
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Chapter 2: System Overview
Figure 4-2. Location of the green image acquisition light and red error light.
Red Error Indicator: The error indicator light illuminates when a particular process could not be
completed.
Rear Panel
Power
switch
Power
receptacle
CDRH
regulation
compliance label
LAN
networking
port
Manufacturer
label
Figure 4-3. Closeup of the Odyssey® CLx Imager rear panel showing the power receptacle and LAN port (use only the
supplied networking cable). Also shown are the CDRH regulation compliance label, the manufacturer label and the
power switch. The power switch should be left in the ‘on’ position. Note: The appearance of your instrument's back
panel may vary slightly from the one shown.
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Odyssey® CLx Imager
Scanning Surface
Width
25
Height
Origin (X,Y)
X-Axis (cm)
Y-Axis (cm)
0
025
Sample
Figure 4-4. Scans progress across the X-axis and
then incrementally move along the Y-axis after each
X-axis pass.
The scanning surface is a 25 cm x 25 cm glass
plate (Figure 4-4), upon which the samples to
be scanned are placed. The scanning surface is
sealed from the instrument interior so no
moisture can penetrate to the detection optics
and electronics below.
General Description of Scanning
Scans are initiated using the ImageStudio Software Acquire ribbon. On the Acquire ribbon the user
chooses the settings for the scan as well as the area to scan. Scanning progresses first across the X-
axis, and then moves incrementally along the Y-axis of the scanning surface after each X-axis pass.
Continuous Operation
The Odyssey CLx is designed to operate continuously. During idle times, the Odyssey CLx can
remain powered on or be powered off at your discretion. When idle, the Odyssey CLx typically
draws approximately 0.5 Amp of current when powered with 120V (see Specifications on page29).
If the Odyssey CLx needs to be disconnected (when moving it, for example), see below.
Disconnecting the Power
First, exit the ImageStudio Software by selecting Instrument > Disconnect on the Application
menu or by closing the application window. Next, briefly press the power button on the front panel
to power off the Odyssey CLx. Then remove the power cord from the power receptacle as described
in Electrical Considerations on page12.
Note: Do not unplug the power cable or push ‘O’ on the rear power switch while the system is
running, except for an emergency situation.
Optical System Description
Solid state diode lasers simultaneously provide light excitation at 685 and 785 nm. Collimating
lenses, optical bandpass filters, and a focusing lens focus and tune the laser beams to produce an
excitation spot on the scanning surface. The microscope electronics then modulate the laser beams
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Chapter 2: System Overview
to discriminate the infrared dye signal fluorescence from background fluorescence. The scanner
detection optics focus on the excitation spot and collect light from the fluorescing infrared dyes.
The light is passed to a dichroic mirror after collection by the microscope objective. The mirror
splits the light and essentially sorts the fluorescent signals by transmitting the light above 810 nm
and reflecting light below 750 nm. Transmitted and reflected light travels two independent paths
through optics designed to remove scattered and stray light. The light is ultimately focused onto one
of two avalanche photodiodes that converts the light to an electrical signal for processing by the
microscope detection electronics.
In the microscope electronics the signal is amplified, filtered, and finally converted to a digital value
by an analog-to-digital converter. The digital signal is demodulated, filtered again, and coordinated
with the microscope position by a Digital Signal Processor (DSP) to produce the image file.
The entire compact laser/microscope assembly travels on a platform that moves beneath the
scanning surface along both the X- and Y-axes. It is adjustable in the Z-dimension to allow for
focusing at the scan bed up to 4 mm above the scan bed to accommodate membranes, gels, and
microplates.
The Odyssey® CLx Imager has two modes for dynamic range, Automatic and Manual. In Automatic
mode the Odyssey CLx acquires images with virtually no saturated pixels on the first attempt with
no user adjustments. More than six logs (22 bits) of dynamic range are available for each image. In
Manual mode the intensity of each channel can be manually adjusted across a 12 bit dynamic
range.
Software Overview
Choose the right software for the type of analysis you are doing.
Use Empiria Studio® Software for Quantitative Western blot analysis
Empiria Studio software is designed for reliable analysis of near-infrared Western blots using
publisher guidelines. Empiria Studio uses workflows to minimize user-to-user variation, provides
more extensive analysis options, and can compute vital statistical values.
To get started using Empiria Studio, please see the Empiria Studio Quick Start Guide or visit
licor.com/empiria-support.
Use ImageStudio Software for other types of analysis
Use ImageStudio Software for quick signal quantification and for analyzing images from other
assays. Further information about image analysis in ImageStudio Software can be found here
licor.com/bio/image-studio/resources.
Page 18

Chapter 3: Operation
Before You Begin...
Cleaning the scan surface before and after every scan is recommended.
Cleaning the Scanning Surface
The scanning surface is plate glass. It is very important that the scanning surface glass and silicone
mat be free of smudges, dust, and dye before scanning any samples on the Odyssey CLx.
Contaminated surfaces in contact with the membrane surface may cause blotches and streaks that
cannot be removed with further washing.
1) Thoroughly clean the glass scanning surface with ultrapure water and a lint-free wipe.
2) Repeat the wash with 70% ethanol and a lint-free wipe or 70% isopropanol and a lint-free wipe.
If additional cleaning is necessary, 100% methanol may be used.
3) If the silicone mat is used, rinse it under warm water. Gentle lab soap may be used, but the soap
must be completely rinsed away before use. The silicone mat may also be rinsed with iso-
propanol or ethanol if needed. Dry the silicone mat with a lint-free tissue.
Scanning
Samples should be placed on the scan surface in the lower-left corner next to the arrow (Figure 5-1).
Grid
25
0
0
25
Sample
Not drawn to scale
Figure 5-1
Using Membranes
For Western blotting methods, nitrocellulose or PVDF membranes may be used (see
licor.com/membranes for the latest membranes and kits).
Odyssey® CLx
Imager
Page 19

Chapter 3: Operation
The following are general tips for handling membranes and imaging membranes with the
Odyssey® CLx.
Handling Near-Infrared Western Blot Membranes
lImportant: Do not touch the membrane – handle only with clean forceps. Lift the membrane
only by the corners. Fingerprints, even from a glove, will show clearly when imaged.
lUse clean containers to avoid cross-contamination and reduce background.
lProtect near-infrared (NIR) Western blot membranes from light prior to imaging.
lKeep the membrane wet if it is to be stripped and re-used.
lStore in PBS or TBS at 4 °C or store dry at room temperature. The fluorescent signal on a dried
membrane will remain stable for several months or longer if protected from light and air.
Scanning Membranes
Blots can be imaged wet or dry.
Scanning Dry Membrane
Place the membrane on the scan surface sample-side down with the silicone mat on top of the
membrane.
Scanning Wet Membrane
1. Place the membrane on the scan surface sample-side down.
Grid
25
0
0
25
Membrane
(Sample-side Down)
Top
Not drawn to scale
2. Remove any air bubbles using the 4" soft roller.
3. Place 1 - 2 mL of PBS or TBS on top of the membrane. If you are imaging multiple membranes,
place the silicone mat on top of the membranes.
If the signal on the membrane is too strong, saturated pixels will be shown in bright contrast to the
rest of the image. Re-scan at a lower intensity setting or use Auto Mode.
Page 20