Thermo Scientific EVOS M5000 User manual

For Research Use Only. Not for use in diagnostic procedures.
EVOS™M5000 Imaging System
Pub. No. MAN0017765 Doc. Part No. 710209 Rev. B.0
This document is intended as a benchtop reference for the users of the EVOS™M5000 Imaging System (Cat. No. AMF5000).
For detailed instructions and troubleshooting information, refer to the EVOS™M5000 Imaging System User Guide (Pub. No.
MAN0017563). For installation instructions, refer to the EVOS™M5000 Imaging System Installation Guide (Pub. No.
MAN0017783). These documents are provided on the USB flash drive and are also available for download at
thermofisher.com.
Note: For safety and biohazard guidelines, see the “Safety” appendix in the EVOS™M5000 Imaging System User Guide
(Pub. No. MAN0017563). Read the Safety Data Sheets (SDSs) and follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
Graphical user interface (GUI).......................................................................................... 1
Capture tab ...................................................................................................................... 2
Review tab ....................................................................................................................... 7
Settings ............................................................................................................................ 8
Instrument exterior components and mechanical controls.............................................. 10
Technical specifications.................................................................................................. 11
Related documentation and support .............................................................................. 12
Graphical user interface (GUI)
GUI layout
The GUI of the system consists of the Viewing area on the left and function tabs and buttons on the
right. Each tab and button opens the controls necessary to execute the selected function.
Sign In/User: Allows you to
sign in to the Thermo Fisher
Cloud for image storage and
analysis.
Viewing area: Displays the
sample.
Capture tab: Contains the
controls for image capture.
Review tab: Allows you to
review and annotate
captured images.
Keyboard button: Opens the
virtual keyboard.
Settings button: Opens the
Settings tab, which allows
you to select and adjust
basic and advanced system
settings.

2 EVOS™M5000 Imaging System Quick Reference Guide
Capture tab
Capture tab
Sign In/User:
Allows you to sign in to and sign out of your Thermo Fisher Cloud account. You can
choose to save your captured images in your Cloud account for image storage (in addition to local
storage) and subsequent analysis with the EVOS™Image Analysis application.
Viewing area: Displays the sample.
Zoom slider:Zooms in and out of the Viewing area. The zoom range is
100% to 1000%.
Active objective and phase ring: Displays
the active objective and phase ring
information.
Channel: Selects the light source from the
installed LED light cubes (fluorescent channels) or
from the condenser (transmitted light).
RGB Trans option outputs a color image from
interlaced RGB images in the Live mode.
•Select a channel to turn on the excitation light and enter the instrument in the Live
mode. In the Live mode, you can use the brightness and focus controls.
•Click the selected Channel button again to turn off the excitation light and exit the Live
mode. The current channel remains selected as indicated by the blue line underneath
the channel button.
Brightness mode: Toggles between Simple and Actual modes for brightness controls.
•Simple mode allows you to control light intensity as a single Light parameter.
•Actual mode allows you to adjust Brightness (i.e., LED intensity), Exposure, and Gain
parameters individually.

EVOS™M5000 Imaging System Quick Reference Guide 3
Brightness controls: Adjust the brightness for the selected channel.
Simple
Actual
Current Z (µm): Displays the current focus position in µm along the Z-axis.
To change the Z-axis focus position, enter the desired value.
Autofocus (Coarse and Fine): Runs the coarse and fine autofocus
algorithms in the selected channel.
Coarse and Fine focus sliders: Allow you to adjust the focus in the selected
channel when in the Live mode.
Using the Autofocus Maximum and Autofocus Minimum controls (blue
triangles on the Coarse focus slider), you can limit the autofocus algorithm
to the selected region along the Z-axis.
Saved Settings: Allows you to save and edit Z-axis focus positions
and brightness settings for future use.
Press the button to save the current settings.
Lock Z: Allows you to lock the Z-axis offsets, which specify the optimal focus position in
each channel relative to the focus position in other channels.
•When locked, movement of the Z-position in one channel changes the Z-position in all channels,
preserving their relative Z-positions.
•When unlocked, adjusting the Z-position only affects the currently selected channel.
Enable focus knob: Enables the manual focus knobs.
Capture: Captures an image using the current capture settings and stores it in the
image cache of the channel in which it was captured.
You can capture multiple channels by selecting the
corresponding channel checkboxes.
Thumbnails: Display the most recently captured
image stored in the memory buffer for the
channel.

4 EVOS™M5000 Imaging System Quick Reference Guide
Display settings and analysis tools: Allow you to
change image display settings for the Viewing area,
and analyze and annotate captured images.
To open a tool, click the corresponding button. Click the button again to close it.
Image Display Settings: Opens the Image Display Settings tool, which allows you to adjust
image display parameters (Brightness , Constrast , Gamma Correction ) for the
selected channels.
Grid/Grid Settings: Display Grid button switches the display of
the grid in the Viewing area on and off.
Grid Settings allows you to select the grid size.
Scale Bar/Scale Bar Settings: Display Scale Bar button switches the
display of the scale bar in the Viewing area on and off.
Scale Bar Settings allows you to select scale bar color and to display or
hide end bars.
Histogram: Opens the Intensity
Histogram window, which displays
the Pixel count vs. Intensity plot,
where Intensity is the number of
photons detected by the camera
sensor.
Measurements and Annotations:
Allows you to draw regions of interest
(rectangle, ellipse, polygon, line, or
free-form) on the captured image and
measure dimensions, area, or
perimeter of the drawn region.
Show Cell Count: Allows you to perform cell counts using the Auto Count or Manual Count
tools.
•Auto Count: Allows you define auto count parameters by selecting representative target
objects, then count the objects by intensity, area, and circularity.
•Manual Count: Allows you to manually mark items onscreen using up to six separate
labels and keep a running tally of the counts with percentages for each label.
•Confluence: Allows you to select up to 5 reference objects each for target (i.e., cells) and
background in your image to automatically calculate the percentage confluence of your
culture.

EVOS™M5000 Imaging System Quick Reference Guide 5
Auto Count Manual Count Confluence
Toggle pseudo color: Allows you to display images in pseudocolor or in grayscale in the
Viewing area. By default, color display is on.
Automate: Allows you to display the controls for the Time Lapse and Z-Stack
tools, and the EVOS™Onstage Incubator.
Time Lapse: Opens the Time Lapse tool, which allows you to
create and run time lapse routines to capture images at
given intervals over a time period based on your
specifications.

6 EVOS™M5000 Imaging System Quick Reference Guide
Z Stack: Opens the Z Stack tool, which allows you to capture
multiple images along the Z-axis based on your
specifications. You can use the images captured with the Z
Stack tool to generate a Z-Stack Projection.
Incubator: Opens the Incubator Controls, which allow you to
control the EVOS™Onstage Incubator and monitor its status
during your experiments.
Save: Opens the Save dialog, which allows you to select a
save location, set save options, and enable the Quick Save
option.

EVOS™M5000 Imaging System Quick Reference Guide 7
Review tab
Review tab
Viewing area: Displays the captured image currently selected from the list of image files.
Folder: Displays the location of the
current folder or image.
Up: Goes up one folder from the current folder.
Refresh: Refreshes the list or grid of images in the current folder.
Grid view and List view buttons: Display the folders or saved images in grid or list view.
Folder/Image display size:Increase and decrease the display size of the folders or
image files.
Browse: Allows you to navigate to the folder
containing your saved images and to select the
image to display in the viewing area. Currently
selected folder or image is indicated with a box
around it.
Image properties: Displays the metadata for the
selected image file.
Display settings and analysis tools: Allow you to
change image display settings in the Viewing area,
and analyze and annotate captured images.
Export: Allows you to export the currently selected folder or image to a storage
device.
Save: Saves the currently opened image.

8 EVOS™M5000 Imaging System Quick Reference Guide
Settings
Settings tab
Objectives: Allows you to assign and unassign
objectives on the objective turret, and to
calibrate objective magnification.
Visuals:Allows you to calibrate color channel
lighting (White Balance Calibration) and to
assign saturated pixel colors in the
Fluorescence, Transmitted, and RGB
Transmitted channels.
General:Allows you to define saving options for
TIFF files and Saved Settings, and to reverse
the focus wheel action.

EVOS™M5000 Imaging System Quick Reference Guide 9
Filter Cubes:Allows you to add or remove
EVOS™LED light cubes from the instrument
and to assign pseudocolors to specific
channels.
Network: Allows you to connect to a Wi-Fi
network and to map network drives.
Service:Displays the EVOS
™
M5000 hardware
and software information, allows you to update
the EVOS™M5000 firmware and software from
the Thermo Fisher Cloud or using a USB flash
drive, and to copy the error logs.
Done: Closes the Settings tabs and returns to the previously opened tab.

10 EVOS™M5000 Imaging System Quick Reference Guide
Instrument exterior components and mechanical controls
Front view
LCD monitor
Condenser slider slot
Condenser head
Mechanical X-Y stage
Stage X-axis positioning knob
Stage Y-axis positioning knob
Objective selection wheel
Focusing knob
Vessel holder
Objective
Phase annuli selector
Rear view
LCD monitor
Mechanical X-Y stage
Focusing knobs
Power switch
4-pin power input port (12 VDC, 5 A)
Display port (video output)
Network port
USB-A 2.0 ports (4×)
USB 3.0 port (1×)
Stage X-axis positioning knob
Stage Y-axis positioning knob*
* Not visible in this perspective.