Invitrogen EVOS M5000 User manual

For Research Use Only. Not for use in diagnostic procedures.
EVOS™M5000 Imaging System
USER GUIDE
For Fluorescence and Transmitted Light Applications
Catalog Number AMF5000 and AMF5000SV
Publication Number MAN0017563
Revision F.0

Life Technologies Corporation | 22025 20th Ave SE Ste. 100 | Bothell, Washington 98021 USA
For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.
Revision history: MAN0017563 F.0 (English)
Revision Date Description
F.0 16 November
2023 Add Stage View tool and update screens and content.
E.0 14 December
2022 Update Connect account sign in, add information about Align Channels tool, update relevant screens.
D.0 1 April 2021 Add information about Transfection Eciency calculation and Batch Analysis, update Appendix B - Review tab,
update the screens throughout the document.
C.0 14 January 2020 Add information about adjustable scale bar, Clear All button for images in the memory buer, Hot Pixel Correction,
Z-Stack infographics, additional objective data, additional metadata for PNG and TIFF images, Time/Date setup,
automatic reconnect to WiFi networks and mapped network drives, new authentication code requirement for
first-time Connect account connection for added login security, and update the screens throughout the document.
B.0 8 January 2019 Add Connect account sign in and save, Confluence tool, Time Lapse video save, review, and playback, EVOS™
Onstage Incubator, and EVOS™Image Analysis sections, update GUI section and the screens throughout the
document.
A.0 7 August 2018 New user guide for the EVOS™M5000 Imaging System.
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE
LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR
ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these
products, you accept the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2018-2023 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER1About thisguide ...................................................... 9
Audience ....................................................................... 9
User attention words ............................................................ 9
Safety alert words ............................................................... 9
■CHAPTER2Productinformation ................................................ 10
Productdescription ............................................................ 10
EVOS™M5000 Imaging System ............................................. 10
EVOS™M5000 Software .................................................... 10
Productuse ............................................................... 11
Standard itemsincluded ........................................................ 11
EVOS™M5000 Imaging System ............................................. 11
EVOS™M5000 AccessoriesKit .............................................. 11
EVOS™M5000 Imaging System userdocumentation ........................... 12
Instrument exterior components and mechanical controls ........................... 13
Frontview ................................................................ 13
Rearview ................................................................. 14
Graphical user interface(GUI) .................................................... 15
GUIlayout ................................................................ 15
■CHAPTER3Installation ........................................................... 16
Operating environment and site requirements ...................................... 16
Cell culture hoodsetup ..................................................... 16
Prepare forinstallation .......................................................... 17
Receive and inspect theshipment ........................................... 17
Move the instrument to the installation site .................................... 17
Install theinstrument ........................................................... 17
Unpack theinstrument ..................................................... 17
Remove shipping restraints ................................................. 18
Install the UV lightshield .................................................... 20
Connect theinstrument ..................................................... 22
EVOS™M5000 Imaging System User Guide 3

Turn on the EVOS™M5000 Imaging System ....................................... 22
Connect the instrument to the internet ........................................ 22
Set date andtime .......................................................... 22
Connect to the Thermo Fisher™ConnectPlatform .................................. 23
About the Thermo Fisher™ConnectPlatform .................................. 23
Create a Connectaccount .................................................. 23
Create a PINnumber ....................................................... 23
Link instrument to your Connectaccount ..................................... 24
Add instrument to your Connect account with QR code (MobileDevice) .......... 25
Add instrument to Thermo Fisher™Connect Platform with linking code(PC) ....... 25
Sign in to your Connect account from the EVOS™M5000instrument ............. 25
Set up a new administrator .................................................. 26
■CHAPTER4Captureimages ..................................................... 27
Overview ...................................................................... 27
Workflow ................................................................. 27
Capturetab ............................................................... 28
Capture images in a singlechannel ............................................... 28
Select objective and light source ............................................ 28
Adjustbrightness .......................................................... 29
Focus on thesample ....................................................... 30
Optional: Adjust displaysettings ............................................. 31
Find a region of interest .................................................... 31
Capture images for eachchannel ............................................ 32
Capture images in multiplechannels ............................................. 34
Capture multiple channels automatically ...................................... 34
■CHAPTER5Measure, annotate, and analyze capturedimages .............. 36
Display settings and analysis tools ............................................... 36
Adjust image displaysettings .................................................... 37
Displaygrid ................................................................... 38
Display scalebar ............................................................... 39
Alignchannels ................................................................. 40
Alignchannels ............................................................. 40
View pixel intensity histogram ................................................... 41
Display histogram .......................................................... 41
Add measurements andannotations ............................................. 42
Analyze cell culture ............................................................. 44
Analysis tools ............................................................. 44
Count cells – autocount ........................................................ 45
Perform autocount ........................................................ 45
Contents
4EVOS™M5000 Imaging System User Guide

Count cells – manualcount ...................................................... 51
Perform manualcount ...................................................... 51
Measureconfluence ............................................................ 54
Confluence tool ........................................................... 54
Calculate transfectioneciency ............................................. 58
■CHAPTER6Save capturedimages .............................................. 62
Save ......................................................................... 62
Save imagesmanually ...................................................... 62
Quick Saveimages ............................................................. 63
(Optional) Enable QuickSave ................................................ 63
■CHAPTER7Capture time lapseimages ........................................ 65
Time lapse tool ................................................................ 65
Run a time lapse routine ........................................................ 65
Run a new time lapse routine ................................................ 65
Run a saved time lapse routine .............................................. 70
Review images and video captured in a time lapse routine ...................... 71
■CHAPTER8Capture Z-Stack .................................................... 74
Z-Stack tool ................................................................... 74
Capture Z-stackimages ........................................................ 74
■CHAPTER9Stage View .......................................................... 76
Overview ...................................................................... 76
Workflow ................................................................. 77
Set StageOrigin ............................................................... 78
Mark pinlocations ............................................................. 81
Find pins using the Find Target screen ............................................ 81
Load PinMap ................................................................. 84
Update the target pinlocation ................................................... 84
■CHAPTER10Review and analyze savedimages .............................. 85
Reviewimages ................................................................ 86
Reviewimages ............................................................ 86
Configure displaysettings ....................................................... 88
Adjust display settings for savedimages ...................................... 88
Displaygrid ............................................................... 89
Display scalebar .......................................................... 89
View pixel intensity histogram ................................................... 89
Display histogram .......................................................... 89
Contents
EVOS™M5000 Imaging System User Guide 5

Add measurements and annotations to savedimages .............................. 90
Analyze cell culture using savedimages .......................................... 90
Save analysis results ........................................................... 92
Save ..................................................................... 92
Batchanalysis ................................................................. 94
Batch Analysisfunction ..................................................... 94
Save current analysissettings ............................................... 94
Run batchanalysis ......................................................... 94
■CHAPTER11Configure instrumentsettings .................................... 96
Overview ...................................................................... 96
Settingstab ............................................................... 96
Adjust objectivesettings ........................................................ 98
Assignobjectives .......................................................... 98
Calibrate objectivemagnification ............................................ 99
Deleteobjectives .......................................................... 99
Calibrate whitebalance ........................................................ 100
Calibrate whitebalance .................................................... 100
Set saturated pixeloptions ..................................................... 101
Highlight saturated pixels .................................................. 101
Generalsettings .............................................................. 101
General settingsoptions ................................................... 101
Define Capture All checkboxbehavior ....................................... 101
Define Display Settings toolbarbehavior ..................................... 102
Show Align Channels tool .................................................. 102
Configure networksettings ..................................................... 102
Connect to a Wi-Finetwork ................................................ 103
Map networkdrive ........................................................ 103
Service ...................................................................... 105
Copy errorlogs ........................................................... 105
Set date andtime ......................................................... 105
Update fromcloud ........................................................ 106
Update fromUSB ......................................................... 106
■CHAPTER12Instrument care and maintenance .............................. 107
General care ................................................................. 107
Objective lens care ............................................................ 108
Stage care ................................................................... 108
Decontamination procedures ................................................... 108
Change EVOS™LED lightcubes ................................................ 109
Change LED lightcube .................................................... 109
Contents
6EVOS™M5000 Imaging System User Guide

Change theobjectives ......................................................... 110
Procedure for objectivechange ............................................ 110
Calibrate theobjectives ........................................................ 112
Calibrate objectivemagnification ........................................... 112
■APPENDIXATroubleshooting .................................................. 114
Image qualityissues ........................................................... 114
Stage viewissues ............................................................. 115
Software interfaceissues ...................................................... 115
Mechanicalissues ............................................................ 116
■APPENDIXBGraphical user interface(GUI) ................................... 117
Capturetab .................................................................. 117
Reviewtab ................................................................... 126
Auto count controls ........................................................... 128
Manual count controls ......................................................... 129
Cell culture – confluence controls ............................................... 130
Cell culture – transfection eciency controls ..................................... 131
Settings ..................................................................... 132
■APPENDIXCSystem overview ................................................. 135
Technicalspecifications ........................................................ 135
Physical characteristics ................................................... 135
Hardware ................................................................ 135
Operation principles and technical overview ...................................... 136
LEDillumination .......................................................... 136
LED lightcubes .......................................................... 136
■APPENDIXDEVOS™imageanalysis ........................................... 138
EVOS™imageanalysis ......................................................... 138
Gallery ...................................................................... 139
Editimage ................................................................... 139
Adjusttab ............................................................... 140
Analyzetab .............................................................. 141
■APPENDIXEGlossary ........................................................... 142
Software controls andfunctions ................................................ 142
Imagefiles ................................................................... 143
Microscope controls andoptics ................................................. 145
Stage View feature ............................................................ 146
Contents
EVOS™M5000 Imaging System User Guide 7

■APPENDIXFSafety .............................................................. 147
Symbols on thisinstrument .................................................... 147
Standard safetysymbols .................................................. 147
Location oflabels ......................................................... 149
Control and connectionsymbols ........................................... 149
Conformitysymbols ...................................................... 149
Safety information for instruments not manufactured by Thermo FisherScientific ..... 150
Instrumentsafety ............................................................. 150
General ................................................................. 150
Physical injury ............................................................ 151
Electricalsafety .......................................................... 152
Cleaning anddecontamination ............................................. 153
Instrument component and accessorydisposal .............................. 153
Safety and electromagnetic compatibility (EMC) standards ......................... 153
Safety standards ......................................................... 154
EMC standards ........................................................... 154
Environmental design standards ............................................ 155
Chemicalsafety .............................................................. 156
Biological hazardsafety ....................................................... 157
■APPENDIXGDocumentation and support .................................... 158
Customer and technical support ................................................ 158
Limited product warranty ...................................................... 158
Contents
8EVOS™M5000 Imaging System User Guide

About this guide
Audience
This user guide is for laboratory sta operating, maintaining, and analyzing data using the Invitrogen™
EVOS™M5000 Imaging System.
User attention words
Two user attention words appear in this document. Each word implies a specific level of observation or
action as described below.
Note: Provides information that may be of interest or help but is not critical to the use of the product.
IMPORTANT! Provides information that is necessary for proper instrument operation, accurate
installation, or safe use of a chemical.
Safety alert words
Three safety alert words appear in this document at points where you need to be aware of relevant
hazards. Each alert word—CAUTION, WARNING, DANGER—implies a particular level of observation
or action, as defined below:
CAUTION! Indicates a potentially hazardous situation that, if not avoided, may result in minor or
moderate injury. It may also be used to alert against unsafe practices.
WARNING! Indicates a potentially hazardous situation that, if not avoided, could result in death or
serious injury.
DANGER! Indicates an imminently hazardous situation that, if not avoided, will result in death or
serious injury. This signal word is to be limited to the most extreme situations.
1
EVOS™M5000 Imaging System User Guide 9

Product information
Product description
EVOS™M5000 Imaging System
The Invitrogen™EVOS™M5000 Imaging System (Cat. No. AMF5000SV) is a fully integrated, digital,
inverted cell imaging system for four-color fluorescence and transmitted-light applications.
It combines precision optics, a five-objective turret, an 18.5 inch high-resolution LCD display (1920 x
1080 pixel resolution), a highly sensitive monochrome CMOS camera (2048 x 1536 pixel resolution, 3.2
Megapixels) to acquire images seamlessly through an intuitive user interface using a mouse for easy
control, and a position-sensing stage that enables sample locations to be mapped and stored for fast
future acquisition.
EVOS™M5000 Software
The EVOS™M5000 Imaging System is controlled by the integrated Invitrogen™EVOS™M5000 Software
through a graphical user interface (GUI), which is accessed by the computer mouse and keyboard. The
software is pre-installed and starts automatically when the instrument is powered on.
Key features of the EVOS™M5000 Software include:
•Stage View: Integrates a precision manual stage with sensors for accurately mapping and marking
points of interest in various vessel types, including plates, slides, and petri dishes.
Note: Stage View requires an updated stage manufactured in early 2024 for all new EVOS™
M5000 systems. Prior EVOS™M5000 systems using a stage with separate X- and Y-axis control
knobs will not have access to the Stage View feature but can be updated to have all of the other
software features described in this quick reference guide.
•Capture: Enables control over every aspect of image capture through a simple user interface. All
images acquired can be saved in JPG, PNG, and TIFF formats, or compiled into a video sequence
in AVI or MP4 formats.
•Autofocus: Enables autofocus in fluorescence and brightfield modes.
•Z-stacking: Captures a series of images along the z-axis that can be saved individually or
combined into a Z-stack projection with a greater depth of field than any of the individual source
images.
•Time lapse: Enables creating a time-lapse movie using captured images.
•Review: Enables reviewing, measuring, and annotating captured images.
•Cell count: Enables automatic or manual counting of cells post-acquisition.
•Confluence: Enables calculating the percentage confluence of the culture based on selected
reference objects and background.
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10 EVOS™M5000 Imaging System User Guide