Thermo Scientific EVOS M5000 User manual

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

Information in this document is subject to change without notice.
Revision history MAN0017563
Revision
Date
Description
C.0 14 January 2020
Add information about adjustable scale bar, Clear All button for images in the
memory buffer, 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 08 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 07 August 2018 New user guide for the EVOS™M5000 Imaging System
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.
Manufacturer: Life Technologies Corporation | 22025 20TH Ave SE | Bothell, WA 98021.
Trademarks
All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
Cy is a registered trademark of GE Healthcare UK Limited. Windows is a registered trademark of Microsoft Corporation. Kimwipes is a
registered trademark of Kimberly-Clark Corporation. Hoechst is a registered trademark of Hoechst GmbH.
© 2020 Thermo Fisher Scientific Inc. All rights reserved.

EVOS™M5000 Imaging System User Guide 1
Contents
About this guide ...................................................................................................................... 4
1. Product information .......................................................................................................... 5
Product description......................................................................................................................................... 5
Standard items included................................................................................................................................. 6
Instrument exterior components and mechanical controls ....................................................................... 7
Graphical user interface (GUI)....................................................................................................................... 9
2. Installation .......................................................................................................................10
Operating environment and site requirements......................................................................................... 10
Prepare for installation ................................................................................................................................. 11
Install the instrument.................................................................................................................................... 11
Turn on the EVOS™M5000 Imaging System ............................................................................................. 15
3. Capture images................................................................................................................17
Overview ........................................................................................................................................................ 17
Capture images in a single channel ............................................................................................................ 18
Capture images in multiple channels ......................................................................................................... 24
4. Analyze and annotate captured images............................................................................25
Display settings and analysis tools ............................................................................................................. 25
Configure display settings ........................................................................................................................... 25
Add and show measurements and annotations........................................................................................ 28
Show cell count.............................................................................................................................................. 29
Measure confluence....................................................................................................................................... 36
Save analysis results...................................................................................................................................... 38
5. Save captured images ......................................................................................................39
Save ................................................................................................................................................................. 39
Quick Save images ........................................................................................................................................ 41
6. Capture time lapse images ..............................................................................................42
Time Lapse tool.............................................................................................................................................. 42
Run a time lapse routine............................................................................................................................... 42
7. Capture Z-Stack ...............................................................................................................54
Z-Stack tool..................................................................................................................................................... 54
Capture Z-stack images ................................................................................................................................ 54
8. Review saved images .......................................................................................................58
Review images ............................................................................................................................................... 58
Analyze saved images .................................................................................................................................. 60

2
EVOS™M5000 Imaging System User Guide
9. Adjust instrument settings...............................................................................................61
Overview ........................................................................................................................................................ 61
Adjust objective settings............................................................................................................................... 62
Calibrate white balance ................................................................................................................................ 64
Set saturated pixel options ........................................................................................................................... 65
General settings ............................................................................................................................................. 66
Configure network settings.......................................................................................................................... 67
Service ............................................................................................................................................................. 70
10. Instrument care and maintenance ...................................................................................72
General care.................................................................................................................................................... 72
Objective lens care......................................................................................................................................... 72
Stage care........................................................................................................................................................ 73
Decontamination procedures....................................................................................................................... 73
Change EVOS™LED light cubes ................................................................................................................. 74
Change the objectives ................................................................................................................................... 75
Calibrate the objectives................................................................................................................................. 76
Appendix A: Troubleshooting .................................................................................................78
Image quality issues...................................................................................................................................... 78
Software interface issues .............................................................................................................................. 79
Mechanical issues .......................................................................................................................................... 79
Appendix B: Graphical user interface (GUI)............................................................................80
Capture tab..................................................................................................................................................... 80
Review tab ...................................................................................................................................................... 86
Settings............................................................................................................................................................ 87
Appendix C: System overview ................................................................................................89
Technical specifications ................................................................................................................................ 89
Operation principles and technical overview............................................................................................ 90
Appendix D: EVOS™Onstage Incubator...................................................................................91
Technical specifications ................................................................................................................................ 92
EVOS™Onstage Incubator components..................................................................................................... 93
Set up the EVOS™Onstage Incubator......................................................................................................... 95
Use the EVOS™Onstage Incubator ........................................................................................................... 100
Appendix E: EVOS™Image Analysis ......................................................................................104

EVOS™M5000 Imaging System User Guide 3
Appendix F: Safety ...............................................................................................................106
Safety conventions used in this document............................................................................................... 106
Symbols on instruments ............................................................................................................................. 107
Safety labels on instruments ...................................................................................................................... 109
General instrument safety .......................................................................................................................... 110
Chemical safety............................................................................................................................................ 111
Chemical waste safety................................................................................................................................. 112
Electrical safety ............................................................................................................................................ 113
Physical hazard safety ................................................................................................................................ 114
Biological hazard safety.............................................................................................................................. 114
Safety and electromagnetic compatibility (EMC) standards................................................................. 115
Documentation and support.................................................................................................116

4
EVOS™M5000 Imaging System User Guide
About this guide
Audience
This user guide is for laboratory staff 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 particular
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.

EVOS™M5000 Imaging System User Guide 5
1. Product information
Product description
EVOS
™
M5000
Imaging System
The Invitrogen™EVOS™M5000 Imaging System (Cat. No. AMF5000) is a fully
integrated, digital, inverted 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 × 1080 pixel resolution), and a highly sensitive Sony IMX265
monochrome CMOS camera (2048 × 1536 pixel resolution, 3.2 Megapixels) to
acquire images seamlessly through the intuitive user interface using a mouse for
easy control.
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 to the
instrument and starts automatically when the instrument is powered on.
Key features of the EVOS™M5000 Software include:
•Capture:Allows control over every aspect of the system for image capture
through a simple user interface. All images acquired can be saved in BMP, JPG,
PNG, and TIFF formats, or compiled into a video sequence in AVI or WMV
formats.
•Autofocus: Allows 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: Allows you to create a time lapse movie using captured images.
•Review:Allows you to review, measure, and annotate captured images.
•Cell count: Allows you to automatically or manually count cells in
fluorescence mode post-acquisition.
•Conflunce: Allows you calculate the percentage confluence of your culture
based on selected reference objects and background.
•Network and Connect™connectivity: Allows Wi-Fi and Ethernet connectivity
to the network and to your Connect™account, Thermo Fisher’s cloud-based
platform, to store and access your data files.
Product use
For Research Use Only. Not for use in diagnostic procedures.

6
EVOS™M5000 Imaging System User Guide
Standard items included
EVOS
™
M5000
Imaging System
•
EVOS™M5000 Imaging System, includes the following components and pre-
installed accessories:
-18.5 in articulated LCD monitor (1920 ×1080 pixel resolution)
-Embedded PC (4 GB RAM)
-Light cube shipping restraint (remove before use)
-Stage lock pin (remove before use)
-EVOS™Condenser Light Shield, 110 mm
-Light cube tool (remove before use)
-Blank light cube (remove before use)
-LED light cubes, as ordered
-Objectives, as ordered
EVOS
™
M5000
Accessories Kit
•
EVOS™M5000 Accessories Kit (located in the instrument box), contains:
-Wireless mouse and keyboard
-USB receiver (for wireless mouse and keyboard connection)
-USB Wi-Fi adaptor (for wireless network connection to Connect™
applications and mapped network drives)
-USB 3.0 flash drive, 16 GB (for image storage, and preloaded with user
documentation)
-EVOS™Vessel Holder, Two 25 × 75 mm slides (Cat. No. AMEPVH001)
-EVOS™Vessel Holder, Universal (Cat. No. AMEPVH009)
-EVOS™Calibration Slide (Cat. No. AMEP4720)
-EVOS™Light Shield Box
-UV shield assembly
-Condenser Slider, Block (Cat. No. AMEP4688)
-Condenser Slider, 4X Pupil (Cat. No. AMEP4738)
-Condenser Slider, Diffusion for Brightfield Applications (Cat. No.
AMEPDFS1)
-Universal power supply (12 V, 5 A) and power cord (type B, North America)
-EVOS™Dust Cover
-Accessories box with adjustable compartments
-Hex driver, 2 mm
-Mouse pad
EVOS
™
M5000 user
documentation
•
EVOS™M5000 Quick Start Guide, printed (Pub. No. MAN0017765)
•EVOS™M5000 Imaging System Installation Guide, printed (Pub. No. MAN0017783)
•Pre-loaded to USB 3.0 flash drive (located in the accessories box):
-EVOS™M5000 User Guide (Pub. No. MAN0017763)
-EVOS™M5000 Quick Start Guide (Pub. No. MAN0017765)
-EVOS
™
M5000 Imaging System Installation Guide (Pub. No. MAN0017783)

EVOS™M5000 Imaging System User Guide 7
Instrument exterior components and mechanical controls
Front view
LCD monitor Focusing knobs
Condenser slider slot Objective selection wheel
Condenser head Vessel holder
Mechanical X-Y stage Objective
Stage X-axis positioning knob Phase annuli selector
Stage Y-axis positioning knob
Stage positioning
knobs and brakes
Mechanical X-Y stage
Stage X-axis positioning knob
Stage brake for X-axis
Stage Y-axis positioning knob
Stage brake for Y-axis

8
EVOS™M5000 Imaging System User Guide
Rear view
LCD monitor Network port
Mechanical X-Y stage USB-A 2.0 ports (4×)
Focusing knobs USB 3.0 port (1×)
Power switch Stage X-axis positioning knob
4-pin power input port (12 VDC, 5 A) Stage Y-axis positioning knob*
Display port (video output) * Not visible in this perspective.