CytoSMART Omni User manual

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CytoSMART® Omni
Instruction manual

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Table of Contents
Safety information ........................................................................................................................................3
1. Introduction ..............................................................................................................................................4
How easy the CytoSMART® Omni works ..................................................................................................4
Ideal circumstances for cell cultures.........................................................................................................4
System overview.......................................................................................................................................4
2. Getting started..........................................................................................................................................5
3. Setting up the CytoSMART®Omni.............................................................................................................6
Setup Procedure .......................................................................................................................................6
Registration of the Device.........................................................................................................................7
4. Performing an experiment........................................................................................................................9
Focusing on the Cells ..............................................................................................................................10
Starting an experiment ...........................................................................................................................11
During the Experiment............................................................................................................................12
Ending an experiment.............................................................................................................................14
5. Appending a scan to an experiment .......................................................................................................15
6. Connecting to the Cloud .........................................................................................................................16
Login to the cloud ...................................................................................................................................16
Project overview .....................................................................................................................................16
Experiment overview..............................................................................................................................17
Experiment results..................................................................................................................................17
Map view page....................................................................................................................................18
Graph pane .........................................................................................................................................21
Edit areas.............................................................................................................................................19
Scan overview pane ............................................................................................................................21
Area page............................................................................................................................................22
Group areas.........................................................................................................................................21
7. Cleaning and troubleshooting.................................................................................................................23
Cleaning and maintenance .....................................................................................................................23
Troubleshooting......................................................................................................................................23
8. Technical specification............................................................................................................................26
9. Warranty.................................................................................................................................................27

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Safety information
To avoid damage or malfunction of the CytoSMART®Omni:
•Be sure to set this device on a firm, stable and horizontal surface. The device may break or cause
injury if it falls.
•Shut down the device immediately if it produces smoke, a strange odor or unusual noise. Continued
use may lead to fire. Unplug the power cable and USB cable immediately.
•Do not connect cables in ways other than those mentioned in this manual, as this may cause damage
and lead to fire.
•If water or other liquid enters the device, discontinue use immediately. Continued use may lead to
fire. Unplug the power cable and USB cable immediately.
•Do not attempt to repair or remove the outer case of the device. If you open this instrument, you put
yourself at risk of bodily harm due to electrical shock in addition to damaging the device.
•Never attempt to repair, disassemble or modify this device yourself, tampering with this product may
result in injury or fire.
•Do not drop the device or allow objects to fall onto it.
•Do not allow the device to be submerged in liquid.
•Do not place heavy objects on top of this device and never stand or lean on this device. Failure to
follow this may cause the equipment fall or collapse, which results in possible breakage and/or injury.
•Do not autoclave the device.
•Do not perform the sterilization cycle of an incubator with the device inside.

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1. Introduction
Thank you for purchasing the CytoSMART® Omni. The CytoSMART® Omni is an in-incubator automated
live-cell imager that uses state of the art optics and image analysis software. Its innovative design allows
you to acquire a brightfield scan of any cell culture vessel within minutes and provides almost instant
cloud-based image analysis of your cell culture.
How easy the CytoSMART® Omni works
The CytoSMART® Omni can be installed within several minutes and requires minimal training.
Hardware and software work together like a charm. The system consists of the CytoSMART® Omni, an
automated live-cell imager, which operates inside a CO2-incubator. The device is linked to a Windows
laptop that is delivered together with the CytoSMART® Omni. Via the laptop, you can customize your
imaging settings and get started. The images are then transferred to the CytoSMART™ Cloud via an
internet connection. You can access the CytoSMART® Cloud via any web browser on any device with an
internet connection. In the cloud, it is possible to view both the unprocessed and analyzed data and
download the images, videos and Excel-files regarding the cell culture. All your data is right there when
you need it.
Ideal circumstances for cell cultures
With the CytoSMART® Omni, cells can remain in their ideal culture conditions inside the incubator by
monitoring them online. There is no need to disturb the best environment of your experiment.
The CytoSMART® Omni is ideal for performing viability experiments or migration assays in multi-well
plates. The system can also be used for cell culture quality control or experiments in microfluidic devices.
System overview
The hardware of the CytoSMART® Omni consists of:
1. Light arc –Contains the light source (LED) for imaging.
2. Cable ports –For connecting the device to power and to the laptop via USB.
3. Optical window –Can hold most transparent culture vessels.
4. Camera –Camera that takes the images.

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2. Getting started
The content of the CytoSMART® Omni package contains:
1. CytoSMART® Omni
2. USB cable
3. Power adapter
4. CytoSMART® Omni Instruction manual
5. CytoSMART® Omni quick starter guide
6. License key
Remember, if you ever have any questions regarding your purchase, please visit
https://www.cytosmart.com/support or contact our support staff via [e-mail] or the
live chat function in the software or in the cloud. We are happy to help you out.

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3. Setting up the CytoSMART®Omni
It is really easy to set up the CytoSMART® Omni. All you need are these items:
•An incubator
•The CytoSMART® Omni
•USB-cable
•Power-adapter for the Omni
•Omni adapter plate
•License key (delivered with the Omni)
•A Windows tablet, laptop or PC with internet access (preferably via a LAN-cable) and a USB 3.0 port.
The Windows device needs to be on AC power to make sure the device does not power off during
the experiment.
Be sure to remove any wrapping before placing the CytoSMART® Omni inside the incubator. Also clean
the device with a lint-free wipe and 70% ethanol or isopropanol.
Important: Do not use acetone to clean the device and do not autoclave the device.
Setup Procedure
Important: Place the CytoSMART® Omni in the incubator at least 1 hour before the start of your
experiment to make sure the device has equilibrated to incubator temperature.
1. Turn on the tablet, laptop or PC. Make sure the laptop or tablet is connected to the power plug.
2. Check if the incubator has a cable port in the back.
a. If so, guide the USB cable and the power cable through it.
b. If no port is present, place the cables between the door and frame of the incubator.
3. After the cables are properly guided, place the CytoSMART® Omni inside the incubator and plug in
the cables (fig. 1).
4. Plug the other end of the power cable in a power socket.
5. Plug the other end of the USB cable in a USB-3.0 port of the PC
or tablet. You can recognize a USB-3.0 port by the superspeed
logo (and a blue bar; fig. 2).
a. After plugging in the USB cable, the device will home to
its start position.
Important: make sure to first plug in the power cable before plugging in the USB
cable.
6. Clean the Omni adapter plate with a damp lint-free wipe with 70% ethanol or
isopropanol (IPA).
7. Place the adapter plate on the CytoSMART® Omni in such a way that the curved
edges of the adapter plate align with the curved edges of the glass plate (fig. 3A).
fig. 2. Examples
of a USB-3.0 port.
fig. 1. USB port (left) and power port
(right) of the CytoSMART® Omni.

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Registration of the Device
Before you can use the CytoSMART® Omni, you must register it. This only needs to be done the first
time you use the CytoSMART® Omni.
1. Start the preinstalled CytoSMART® Omni app by double clicking on the icon on the desktop (fig. 4).
2. In case you are asked if you want to allow this app to make changes to your device, answer with
“Yes”.
3. Once the app has started you will be asked to log in using you email and password (fig. 5). In case you
do not have an account yet, press “Register” to create a new account. You will be led to the
registration form (fig. 6). Please fill in all the details and click “Sign up”.
The next step is to register the device. The license key for this device is provided on a card that is delivered
together with the device. Enter the license key that is provided in the field “License” on the card and click
“Register” (fig. 7).
fig. 3. Top view images of A) Correct placement of the Omni adapter plate
on the CytoSMART®Omni, B) Correct placement of a well plate, and C)
correct placement of a T-flask.
fig. 5. Log in screen of the CytoSMART®Omni app. Sign in
with your email and password or create a new account.
fig. 6. Sign up registration form.
fig. 4. CytoSMART®Omni app icon.

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Congratulations, you have now successfully registered and activated your CytoSMART®Omni!
fig. 7. Register your device by entering the license key.

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4. Performing an experiment
Before you can start an experiment, you need to place your culture vessel on the CytoSMART® Omni. In
case you are using a well plate, place it with well A1 in the corner of the adapter plate (fig. 3B).
Subsequently you can select the well plate size in the CytoSMART® Omni app by clicking “Select Your
WellPlate” (fig. 8).
Choose the correct well plate from the dropdown list that appears (fig. 9). In case you are using another
cell culture vessel, select “Other Vessel”.
fig. 8. Experiment page. Select the well plate size by clicking “Select your WellPlate”.
fig. 9. Select the correct cell culture vessel from the drop-down menu.

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Once you have selected your well plate size, an image of the well plate appears on the right side of the
screen (fig. 10A). In case you have selected “Other”, a light blue rectangle will appear (fig. 10B). Click on a
certain spot on the blue well plate image/rectangle to move the camera to that position, a red cross will
appear indicating the current position of the camera. Use the arrow keys for fine movements.
Focusing on the Cells
1. Go to the middle of one of the wells, use the arrow keys for fine movement to go exactly to the
middle of a well.
2. To focus, move the slider bar (bar on the bottom left; fig. 10) by dragging it with your mouse. Click
the plus- or minus-sign for fine changes in focus. For proper analysis of your cells, you should see a
contrast. You can choose the type of contrast that you prefer:
•Set the focus such that the cells are dark with sharp edges (fig. 11A)
•Set the focus such that the cells are white with a sharp dark edge (fig. 11B)
3. Once you have set the focus, move to the middle of a couple of other wells spread throughout the
well plate to check whether the cells in the other wells are also in focus.
•In case the cells in the other wells are not in focus, set the focus such that the cells in most wells
are clearly visible (try to find an average focus level).
fig. 10. A) Use the image of the well plate on the right to navigate to one of the wells. B) Navigate though your cell culture
vessel using the mouse or arrow keys. A red cross indicates the current position of the camera. Use the slider bar on the
bottom left for focusing. Click and drag the arrows for coarse adjustment of the focus, click the plus- or minus for fine changes.
A
B
fig. 11. Examples of the correct focus. Left: cells are completely black with sharp edges. Right: cells are white
with a clear black edge.
A
B