logos biosystems CELENA X User manual

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USER MANUAL
LBSM-MD-ML-CLX-001
Rev. 5
www.logosbio.com

PUBLISHING DETAILS
CELENA®X High Content Imaging System, User manual
Document No.: LBSM-MD-ML-CLX-002
Rev. 5
Revision date: 2020. 11. 18.
COPYRIGHT
This document is protected by copyright. All rights reserved. Notably, no portion of this publication may be reproduced or made available to third parties,
in any form, online or offline, without the written consent of Aligned Genetics, Inc. Further, no portion of this publication may be translated into a language
or code that can be utilized for machines, in particular, data processing systems, or the internet. This document may exclusively be used to properly use
the products described herein in accordance with the contractual terms for such product.
Copyright © 2020 Aligned Genetics, Inc.
DISCLAIMER
The contents of this document are subject to change without notice.
The CELENA®X High Content Imaging System is for scientific research use only.
Do not disassemble the device on any occasion as this will invalidate your warranty.
TRADEMARKS
The trademarks used in this document are the property of Aligned Genetics, Inc. unless otherwise specified.
LED Filter Cubes are LTC Licensed Products provided under an intellectual property license from Life Technologies Corporation.
© 2020 Aligned Genetics, Inc. All rights reserved.
Logos Biosystems is the brand name of the life science business of Aligned Genetics, Inc.

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Table of Contents
1. GENERAL...................................................................................................................................................................4
1.1 ABOUT THIS USER MANUAL 4
1.2 EXPLANATION OF SYMBOLS 4
2. SAFETY INFORMATION........................................................................................................................................5
2.1 DEVICE SYMBOLS 5
2.2 DEVICE SAFETY 6
PERSONAL SAFETY 7
SAFETY STANDARDS 7
3. GETTING STARTED ...............................................................................................................................................8
3.1 PRODUCT CONTENTS 8
CELENA® X 11
CELENA® XMAIN UNIT 11
CELENA® XCONTROLLER 12
SOFTWARE 13
CELENA® XLABELS 13
3.3 SETTING UP 14
UNPACKING 15
CONNECTIONS 15
SHIPPING GUARD/RESTRAINTS 15
TURN ON THE CELENA® X 16
INSTALL FILTER CUBES AND OBJECTIVES 17
SHUT DOWN THE CELENA® X 17
4. CELENA® X EXPLORER ..................................................................................................................................... 18
4.1 USER INTERFACE 18
CHANNELS 19
VESSEL 23
Z-STACK 24
TIME LAPSE 25
PROJECT 26
TOOLBAR 27
MESSAGES 27
SETTINGS 28
4.2 WORKFLOW 30
CREATE A PROJECT PROTOCOL 30
SAVE A PROJECT PROTOCOL 36
LOAD A PROJECT PROTOCOL 37
RUN A PROJECT PROTOCOL 37
PAUSE/STOP A PROJECT PROTOCOL 37
VIEW PROJECT RESULTS 37
5. MAINTENANCE..................................................................................................................................................... 38
5.1 GENERAL CARE 38
5.2 CHANGE FILTER CUBES 38

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5.3 CHANGE OBJECTIVES 40
6.4 ADJUST OBJECTIVE CORRECTION COLLARS 43
6.5 VERSION UPGRADE 46
APPENDIX A: TROUBLESHOOTING.......................................................................................................................... 48
IMAGE QUALITY 48
EXPLORER 48
MECHANICAL 49
APPENDIX B: SPECIFICATIONS ................................................................................................................................. 50
CELENA® XHIGH CONTENT IMAGING SYSTEM 50
APPENDIX C: ORDERING INFORMATION............................................................................................................... 51
INSTRUMENTS 51
OBJECTIVES 51
LED FILTER CUBES 51
ACCESSORIES 52
APPENDIX D: PURCHASER NOTIFICATION........................................................................................................... 53
LIMITED USE LABEL LICENSE 53
LTC LICENSED PRODUCTS 53
DEVICE WARRANTY 53

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1. General
1.1 About this user manual
This user manual provides the information necessary to operate the CELENA® X High
Content Imaging System. PLEASE READ THIS USER MANUAL BEFORE OPERATING THE
SYSTEM. If any part of this user manual is not clear, please contact Customer Support for
assistance.
1.2 Explanation of symbols
Safety notes
Safety notes in this user manual are introduced with a symbol and a signal word to describe
the severity of the hazard.
Follow these safety notes and proceed with caution to avoid accidents, personal injury,
damages to property.
This symbol and the word “WARNING” indicate a possible hazardous situation that, if not
avoided, could cause death or serious injury.
This symbol and the word “CAUTION” indicate a possible hazardous situation that, if not
avoided, could result in minor or moderate injury.
This symbol and the word “NOTICE” indicate a possible hazardous situation that, if not
avoided, could result in damage to property or the environment.
Hints, recommendations
This symbol emphasizes useful tips and recommendations as well as information for the
efficient and trouble-fee use of the product.

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2. Safety information
2.1 Device symbols
Electrical symbols
Symbol
Description
Power symbol
Safety symbol
Symbol
Description
Risk group 3. UV emitted from this device may be hazardous. Avoid
eye exposure.
Invisible laser radiation. Avoid exposure to beam. Class 3b laser
product.
Follow instructions for use
Environmental symbol
Symbol
Description
Waste Electrical and Electronic Equipment (WEEE). Do not dispose of
this product as unsorted municipal waste. Follow local waste
ordinances for proper disposal provisions to reduce the
environmental impact of WEEE.
Package symbol
Symbol
Description
Fragile
Keep dry
Temperature limit
Atmospheric pressure limitation
Humidity limitation

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2.2 Device safety
General safety
Do not touch the device or its components with wet hands.
Use only the provided power cord. If the proper components are not used, electrical safety of
the device cannot be guaranteed.
Connect the grounding terminal of the device and electrical outlet properly. If the device is
not grounded, electrical safety of the product cannot be guaranteed.
Do not use a damaged electrical cord or an aged electrical outlet socket.
Do not use multiple sockets or extension cables. If the device is connected using them,
electrical safety of the product cannot be guaranteed.
Do not expose the device to intense ultraviolet light.
This device uses a Class 3B near infrared laser that is in accordance with IEC/EN 60825-1.
Direct exposure to and diffuse reflections of the laser can be hazardous to the eye.
Avoid eye or skin exposure to direct or scattered radiation.
Make the CELENA® X main unit door is closed when imaging to protect your eyes.
The device uses ultraviolet LEDs. The light emitted from this device may result in eye injury.
Avoid looking directly at the light.
Make the CELENA® X main unit door is closed when imaging to protect your eyes.
Always turn off the light before changing LED filter cubes or objectives.
Do not modify the device without authorization of the manufacturer. Modification can result
in electrical hazards or performance degradation.
The device is not suitable for use in the presence of a flammable anesthetics mixture with
air, or with oxygen, or nitrous oxide.
Operate the device in the conditions described in the Operating Conditions.
Ensure that the input voltage is compatible with the power supply voltage of the product.
Turn on the device only after connecting the power cord and AC adapter to both of the
power source and the instrument. Turn off the device before disconnecting the power cord
and/or moving the instrument.
Disconnect the power cord in the case of abnormalities.
Protect the computer from being infected with viruses and malware.
Do not locate the device to make it difficult to operate the device.
Install the device on a level and sturdy surface. Avoid vibrations from other devices. The
device can withstand light shock and vibration. However, excessive shock and/or vibration
may damage the instrument. Leave sufficient space around the device for air circulation and
cooling. Take care that the device does not overheat during long and continuous operation.
Use components provided or authorized by Logos Biosystems. If the proper combination of
components is not used, product safety cannot be guaranteed.
Electrical connection
CELENA® Controller
Rated voltage
100 –240 VAC
Rated supply frequency
50/60 Hz
Power consumption
3.0 –6.0 A
Environmental conditions
Operation
Installation Site
Indoor use only

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Operating Temperature
+10 °C –+35 °C
Relative Humidity
20 % –80 % at non-condensation
Atmospheric pressure
70 kPa –106 kPa
Altitude
≤ 2,000 m
Pollution Degree
2
Storage
Storage Temperature
-20 °C –+ 70 °C
Relative Humidity
10 % –90 % at non-condensation
Atmospheric pressure
70 kPa –106 kPa
Device disassembly
Do not disassemble the instruments or wipe the supplied computer in any event as this will
invalidate your warranty. If the device is damaged or malfunctioning, contact your local sales
representative.
Personal safety
Safety guidelines
Wear appropriate personal protective equipment (PPE) when handling reagents and samples
to avoid exposure.
When using toxic agents, radioactive materials, or pathogenic microorganisms belonging to
WHO Risk Groups 2-4, follow national laws and regulations for biosafety level requirements.
Read all user manuals thoroughly before using the instrument.
Keep all user manuals in a safe and accessible place for future reference.
Safety standards
European standards
Symbol
Description
The CE mark indicates that this device conforms to all applicable European
Community provisions for which this marking is required. Users must be aware
of and follow the conditions described in this manual for operating the
instrument. The protection provided by the device may be impaired if the
device is used in a manner not specified by Logos Biosystems.
Korean standards
Symbol
Description
The KC certification mark indicates that this device conforms with Korea’s
product safety requirements for electrical and electronic equipment and
components for which this marking is required.
United States standards
Type
Description
FCC Part 18
This device complies with Part 18 of the FCC Rules.

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3. Getting Started
3.1 Product contents
Your CELENA® X High Content Imaging System is shipped with the following components:
CELENA® X main unit
Camera module (installed as ordered)
Condenser (installed as ordered)
Filter cubes (installed as ordered)
Objectives (installed as ordered)
(Optional) Laser autofocus module (installed as ordered)
CELENA® X Controller
Software
CELENA® X Explorer
CELENA® X Cell Analyzer
PC
Desktop
Keyboard
Mouse
(Optional) Monitor
Accessories
Universal Vessel Holder
Microplate Holder
Single Slide Holder
Power Cord
Cable PS-1
Cable PS-2
Cable SIG
Cable USB 2.0
Cable USB 3.0
(Optional) Cable Laser AF (included with the Laser autofocus module)
Flathead Screwdriver
CELENA® X Cell Analyzer Verification Key
USB drive, 64 GB (includes the user manual and installation guide)
Inspect the product package upon delivery to ensure that all components have been
included. If anything is missing, contact your local sales representative. Damage that may
occur during shipping and handling is not covered by warranty and must be filed with the
carrier.

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CELENA® X Main unit
CELENA® X Controller
Accessories
Single Slide Holder
Microplate Holder
Universal Vessel Holder
Cable PS-1

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Cable PS-2
Cable SIG
Cable USB 2.0
Cable USB 3.0
(Optional) Cable Laser AF
Power cord

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Flathead Screwdriver
3.2 Product description
CELENA® X
CELENA® X is an integrated imaging system designed for rapid, high content image
acquisition. Customizable imaging protocols, image-based and laser autofocusing modules,
and motorized XYZ stage simplify slide scanning and well plate imaging.
CELENA® X main unit
CELENA® X main unit
①Door: Open the door to locate a vessel holder on the X/Y stage and close it before
operating CELENA® X Explorer.
②Condenser: The illuminating module for brightfield imaging and/or phase-
contrast imaging.
③Motorized X/Y stage: Scan a sample in X and Y direction.
④Power button: Turn on the power by pressing the power button. Turn off the
power by pressing the power button for 3-5 seconds.
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2
3
4

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Back of the CELENA® X main unit
①Laser AF: Deliver the output signal from the laser autofocus module.
②SIG: Transmit the communication signals between the main unit and the
controller.
③PS-1: Deliver DC power from the controller to the main unit.
④PS-2: Deliver power from the controller to LED light sources.
⑤USB 3.0: Deliver power to cameras and transmits the communication signals
between the cameras and the computer.
⑥USB 2.0: Transmit the communication signals between the main unit and the
computer.
This device uses Class 3B near infrared laser and ultraviolet LEDs. Make the CELENA® X
main unit door is closed when imaging to protect your eyes. Direct exposure to and diffuse
reflections of the laser can be hazardous to the eye.
CELENA® X Controller
The CELENA® X Controller controls the power supply to and mechanical stages of the
CELENA® X.
Front of the CELENA® X Controller
①Power switch: power on/off
CELENA® X cable connections
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1
2
3
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5
6

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Back of the CELENA® X Controller
①SIG: Transmit the communication signals between the main unit and the
controller.
②Laser AF: Deliver the output signal from the laser autofocus module.
③PS-1: Deliver DC power from the controller to the main unit.
④PS-2: Deliver power from the controller to LED light sources.
Software
CELENA® X Explorer
The CELENA® X is controlled by the integrated CELENA® X Explorer software. CELENA® X
Explorer is pre-installed to the computer supplied with the device.
CELENA X Explorer
CELENA® X Cell Analyzer
CELENA® X Cell Analyzer is used to process and analyze images to quantify numerous
cellular phenotypes simultaneously. CELENA® X Cell Analyzer also provides tools to edit
and annotate images as well as create videos.
CELENA X Cell Analyzer
CELENA® X Labels
CELENA® X cable connections
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2
3
4

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CELENA® X Labels
Top of the CELENA® X Main unit
Back of the CELENA® X main unit
Back of the CELENA® X Controller
3.3 Setting up
CELENA® X Controller label
CELENA® X main unit label
Laser safety label
UV light safety label

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Unpacking
Move the unpacked boxes to the site of operation.
CELENA® X main unit
Open the CELENA® X box and remove the Styrofoam top and sides. Lift the CELENA® X out
of its box by grasping its base firmly.
Place the CELENA® X on a flat, level surface that is free of vibration. Anti-vibration tables are
recommended for optimal use. Leave sufficient space around the device for proper
ventilation and to prevent overheating.
When moving the CELENA® X, do not attempt to lift or move the device without assistance.
It is recommended that two or more people lift the device together while taking the proper
safety measures to avoid injury
Do not subject the CELENA® X to sudden impact or excessive vibration. Handle the device
with care to prevent damage.
Do not expose the device to intense ultraviolet light.
Changing the configuration of the computer supplied with the CELENA® X (i.e., erasing the
hard drive to remove programs, etc.) voids the product warranty.
CELENA® X Controller
Place the Controller near the CELENA® X main unit. A separate surface is recommended for
optimal use but is not necessary.
Connections
Unpack the cables from the accessories box and attach as specified below:
CELENA® main unit & Controller
CELENA® X main unit & PC
Cable PS-1 (I10331)
USB 2.0 (I10335)**
Cable PS-2 (I10332)
USB 3.0 (I10336)**
Cable SIG (I10333)
Cable AF (I10334)*
*Included if the laser AF module was purchased and installed
**Make sure to plug into the blue USB 3.0 ports at the back of the PC, not the front
Back of the CELENA® X main unit
The CELENA® X is compatible with 4K Ultra HD (UHD) monitors only and not in accordance
with size of monitors.
Shipping guard/restraints
Your CELENA® X main unit is shipped with two shipping restraints installed (X/Y stage, LED
filter cube stage) to prevent damage to the device from shock and vibration during transport.
Controller
PC

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Remove shipping restraints
1. Unscrew screw A and pull it up to remove it from the LED filter cube stage cover.
2. Unscrew screw B and pull it up to remove it from the X/Y stage.
The shipping restraints must be removed before the CELENA® X is turned on.
Store the screws in the accessories box for future use. Make sure they are accessible in case
you need to pack up for maintenance and servicing purposes.
Turn on the CELENA® X
Turn on in this order:
Turn on CELENA® X Controller by pressing the power switch.
Turn on CELENA® X main unit by pressing the power button.
Run CELENA® X Explorer on the PC
A
B
A
B

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Using other programs as well as CELENA® X Explorer at the same time can affect both
imaging and analysis time. Using only CELENA® X Explorer is recommended when imaging
and acquisition.
Install filter cubes and objectives
CELENA® X Explorer must be on to install filter cubes and objectives.
For detailed instructions on how to install filter cubes, go to 5.2 Change filter cubes.
For detailed instructions on how to install objectives, go to 5.3 Change objectives.
Make sure the installed filter cubes and objectives match what is set in the CHANNELS panel.
Shut down the CELENA® X
Explorer must be shut down before the device to allow the stages to dock for safety.
Turn off in this order:
Close CELENA® X Explorer by clicking ⅹbutton on the top right corner of
Explorer.
Turn off CELENA® X main unit by pressing the power button for 3-5 seconds.
Turn off CELENA® X controller by pressing the power button.

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4. CELENA® X Explorer
4.1 User interface
The CELENA® X Explorer is the graphical user interface for the CELENA® X High Content
Imaging System.
CELENA® X Explorer
①CHANNELS: Gives control over light, camera, and focus settings.
②VESSEL: Allows you to select the appropriate vessel, wells, and fields to capture.
③Z-STACK: Allows you to capture multiple planes along the Z-axis.
④TIME LAPSE: Allows you to set up time lapse sequences.
⑤PROJECT: Allows you to run, load, save, and edit automated imaging projects.
⑥Toolbar: Has tools for capturing and visualizing the current field of view.
⑦Viewing area: Shows the current field of view.
⑧System messages: Displays system messages.
⑨Settings: Allows you to set system options and perform calibration procedures.
1
3
2
4
7
6
5
8
9

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Channels
This panel is used to set light, camera, and focus parameters for a project.
①Add: Adds the CHANNELS settings to the project protocol.
②Objectives: Allows you to select from the currently installed objectives.
③Channels: Allows you to select from the currently installed filter cubes and adjust
light and camera settings.
④Focus: Allows you to find focus and set up autofocusing.
⑤Offset: If this button is turned on the image-based autofocus will be automatically
executed to calculate user-defined focus offset when adding channels.
Objectives
This panel is used to select from the currently installed objectives.
The magnification and label on each objective reflects its profile, which can be modified in
Settings > Objectives.
Click the desired objective to select the corresponding magnification. You can select only one
objective at a time. The selected objective is highlighted in blue.
Channels
This panel is used to set the light and camera settings.
①ON/OFF: Use to turn the light source on and off. When the light is on, the viewing
area shows the sample illuminated with the selected light source.
②Condenser: Is installed at the time of purchase (BF: brightfield, PH: phase-contrast
condenser).
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3
5
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3
2
5
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