GRUNDIUM OCUS 40 User manual

Jukka Mattila, Grundium Ltd.
USER GUIDE
MGU-00002

Ocus®40 MGU-00002 User Guide version 7.0
1
Saavutustenkatu 3, 33720 Tampere, Finland
©2022 Grundium. All rights reserved.
6-8G, 33720 Tampere, Finland
©2022 Grundium. All rights reserved.
CONTENT
1Sales package contents .............................................................................................................................................................. 3
2To use the Ocus®40 scanner, you also need .............................................................................................................................. 3
3Introduction to the Ocus®40 Whole Slide Image Scanner ......................................................................................................... 3
4Technical specifications.............................................................................................................................................................. 4
5Before you start ......................................................................................................................................................................... 5
6Scanner parts ............................................................................................................................................................................. 6
6.1 Scanner connectors ........................................................................................................................................................... 7
6.2 Power button lights........................................................................................................................................................... 8
7First use...................................................................................................................................................................................... 8
7.1 Setting up the network firewall configuration based on the MAC-address...................................................................... 9
7.2 Creating user account...................................................................................................................................................... 10
7.3 Registering a new Ocus Scanner ..................................................................................................................................... 11
7.4 Connecting the scanner using an ethernet connection .................................................................................................. 13
7.5 Connecting the scanner using A mobile hotspot............................................................................................................. 13
7.6 Configuring a WiFi- connection ....................................................................................................................................... 14
8Logging in to the scanner ......................................................................................................................................................... 14
8.1 Logging in to the scanner with Internet connection ....................................................................................................... 14
8.2 Logging in to the scanner USING THE Offline Mode (Access point mode)...................................................................... 15
9Scanning ................................................................................................................................................................................... 16
9.1 Scan mode ....................................................................................................................................................................... 19
9.2 Image adjustments.......................................................................................................................................................... 20
9.3 Annotations..................................................................................................................................................................... 21
10 Scan archive ............................................................................................................................................................................. 22
10.1 Deleting scans.................................................................................................................................................................. 22
11 Exporting an image................................................................................................................................................................... 23
12 Sharing ..................................................................................................................................................................................... 25
13 Controlling multiple scanners .................................................................................................................................................. 26
14 Switching off the scanner......................................................................................................................................................... 26
15 Scanner settings ....................................................................................................................................................................... 26
15.1 Network settings ............................................................................................................................................................. 27
15.1.1 Internet................................................................................................................................................................... 27
15.1.2 Ethernet.................................................................................................................................................................. 27
15.1.3 WLAN...................................................................................................................................................................... 28

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15.1.4 WLAN-AP ................................................................................................................................................................ 28
15.1.5 Proxy....................................................................................................................................................................... 28
15.2 Device tab........................................................................................................................................................................ 29
15.3 File name ......................................................................................................................................................................... 29
15.4 Plugin Management ........................................................................................................................................................ 29
15.5 Language ......................................................................................................................................................................... 29
16 Team management .................................................................................................................................................................. 30
16.1 Create new team ............................................................................................................................................................. 30
16.2 Adding new team members ............................................................................................................................................ 32
17 Keeping the software up to date.............................................................................................................................................. 32
18 Info window ............................................................................................................................................................................. 32
18.1 Factory reset.................................................................................................................................................................... 33
18.2 LOG - file.......................................................................................................................................................................... 33
19 Cleaning the scanner................................................................................................................................................................ 33
20 Moving the scanner to another location.................................................................................................................................. 35
21 Product and safety information ............................................................................................................................................... 36
22 Disposal .................................................................................................................................................................................... 36
23 Troubleshooting ....................................................................................................................................................................... 37
23.1 The scanner is unresponsive ........................................................................................................................................... 37
23.2 Device cannot be found................................................................................................................................................... 37
23.3 Forgot your password...................................................................................................................................................... 37
23.4 Power button light is steady red ..................................................................................................................................... 37
23.5 Download does not start automatically when exporting USING THE WEB DOWNLOAD EXPORT PLUGIN..................... 37
23.6 Scan quality is bad or has other issues............................................................................................................................ 37
24 Certifications and patents........................................................................................................................................................ 38
25 Customer care and support...................................................................................................................................................... 39
26 Manufacturer information ....................................................................................................................................................... 39

Ocus®40 MGU-00002 User Guide version 7.0
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©2022 Grundium. All rights reserved.
6-8G, 33720 Tampere, Finland
©2022 Grundium. All rights reserved.
GRUNDIUM OCUS®40 MGU-00002 USER GUIDE
Note: This user guide is for Ocus®40 MGU-00002 with software version 7.0 onwards. User guides for older software versions are
available at: https://www.grundium.com/d/MGU-00002_UserManuals/
1SALES PACKAGE CONTENTS
oOcus®40 scanner (MGU-00002)
oTransportation pin
oProtective cover
oPower supply and mains cable
oQuick guide
oDelivery Package
2TO USE THE OCUS®40 SCANNER, YOU ALSO NEED
oComputer or tablet with internet browser
oInternet connection
oGrounded mains outlet (recommended to use UPS device in critical operations)
It is recommended to use the latest available browser version. The functionality of Ocus®40 has been verified with latest
versions of these browsers:
oGoogle Chrome
oMozilla Firefox
oApple Safari
3INTRODUCTION TO THE OCUS®40 WHOLE SLIDE IMAGE SCANNER
The Grundium Ocus®40 MGU-00002 is a professional imaging instrument for digitizing microscope slides with sharpest image
quality in the business. Integration-ready and very easy to use, the Ocus®40 enables both local and remote use anywhere in the
world. Its excellent quality-to-price ratio and small footprint makes the Ocus®40 attainable to practically any establishment.
Ocus® technology has been granted U.S. Patent No. 10.341.551, 10.564.408 and 10.628.698.
Ocus® design has been granted U.S. Patent No. D872789.
Important Notice: The scanner generates a sequence of flashing lights when capturing the overview (macro) image of the
slide. Take this into account in case you are sensitive to blinking lights.

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4TECHNICAL SPECIFICATIONS
Numerical aperture 0.75
Resolution, microscope 40X 0.25 µm/pix
Resolution, overview 10 µm/pix
Depth of focus 1 µm
Focusing Fully electronic
Image sensor 12 Mpix
Slide capacity 1
Slide format 75 x 25 mm
Scan speed, 15 x 15 mm ~3 mins
Connectivity 1 GigE, 802.11 ac WLAN
Image formats TIFF, SVS, SZI
W x D x H (cm) 18 x 18 x 19
Weight (kg) 3,5 kg
Illumination Koehler LED
Internal Storage 500 GB, net capacity may vary
Input voltage (scanner) 12 VDC (max. 4 A)
Input voltage (power supply) 100-240 VAC 50-60 Hz
Ingress protection IP20
Impact protection IK06
Operating temperature +15 to +40 degrees Celsius (+59 to +104 Fahrenheit)
Operating humidity 0-95% RH, non-condensing
Operating altitude Max. 2000 m

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5BEFORE YOU START
Check the delivery package for damage. If you notice any damage on the case or the scanner, contact primarily your distributor
or [e-mail].
Remove the transportation support pin from the bottom of the scanner by turning the pin counterclockwise. Remember to
handle the scanner carefully to avoid dropping or damaging it and avoid leaving fingerprints on the glass surfaces or lenses while
removing the pin.
Image 1. Remove the transportation support pin by turning it counterclockwise.
Place the scanner on a flat surface and make sure there is at least 10 centimeters (4 inches) of free space around it.
Tip: Store the transportation support pin for possible later use. To ensure safe transportation, screw the transportation support
pin back in before moving the scanner to another location. Do not overtighten the pin, turning it until it stops is enough.
Note: Ocus scanner is a delicate instrument and not designed to withstand by itself stress from shipping/transportation –careful
packing is required. (See full packing instructions in section 20).

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6SCANNER PARTS
Image 2. Scanner parts.
1. Power button
2. Objective
3. Cover plate
4. X-Y-stage
5. Lever
6. Slide retainer
7. Slide support glass
8. Overview camera

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6.1 SCANNER CONNECTORS
Image 3. Scanner connectors.
1. Kensington Security Slot
2. USB connector
3. Power supply connector. Use only the power supply delivered with the scanner
Important notice: If there is any damage in the mains cable or the power supply, do not use the device
4. Network cable connector

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6.2 POWER BUTTON LIGHTS
Light Explanation
Green breathing Scanner is switched off. Power cable is connected.
Green steady Scanner is in Idle mode and connected to the Internet with remote/router access.
Green blinking Scanner is in live view mode, scanning, or exporting.
Yellow steady Scanner is in Idle mode and connected to the Internet without remote/router access.
Yellow blinking Scanner is starting up or shutting down.
Yellow rapid blinking Scanner is performing file system check to the integrated hard drive.
Red steady Scanner is in error state.
Red blinking Scanner is switched on and having no connection to the Internet.
Blue steady Scanner’s WLAN access point is on.
Purple steady Scanner is unregistered and has access to the Internet.
Purple blinking Scanner is unregistered and does not have access to the internet.
7FIRST USE
1. Register the scanner.
As a first step, the scanner needs to be registered in Grundium cloud (https://www.grundium.net). This is done via a
computer or a mobile device that has internet connection. These steps do not require the Ocus scanner to be powered
on. During the registration, a new user account can be created, or user can login with an existing one. During the
registration, the scanner is assigned to an existing Ocus team, or a new team can be created. See section 7.3 for
registration instructions.
2. Connect the scanner to the network using ethernet cable, or setup the ForOcus hotspot using a mobile device (see
section 8.1). Power on the Ocus scanner. Once the light is steady green, or steady yellow, using your end device (a
computer or a tablet is recommended) login to https://www.grundium.net with your user credentials, select the Ocus
team, and the Ocus scanner to operate it for the first time.
The wired (ethernet) connection is recommended, and the ForOcus mobile hotspot is recommended as the backup
connection.
Note: When starting up the scanner for the first time, an internet connection is required for the Scanner to obtain the
registration information from Grundium.net Cloud. After that, it is possible to use the scanner temporarily even without an
Internet connection, by utilizing the access point mode, (see section 8.1), but the feature set will be limited.
Important notice: To keep the security certificates up to date, the scanner must be connected to Internet at least once in
every 2 months –this is mandatory for secure connection between the scanner and the browser.

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Image 4. Label example with a serial number, SSID and a password.
Note: For the first use, the scanner requires that the network has a DHCP server providing IP address. If the use of static IP is
required, this can be done after the first time use in device settings.
7.1 SETTING UP THE NETWORK FIREWALL CONFIGURATION BASED ON THE MAC-ADDRESS
If the network you use has a firewall, make sure that the scanner is allowed to make requests to Grundium Cloud using the
outgoing connection to the Internet (TCP ports 80 & 443 for use within same network and optionally TCP port 471 for use from
remote network). If the firewall uses a MAC filter, you can find the MAC address of the scanner on the label at the bottom of the
scanner. Also, traffic between devices in the network must be allowed.
•Port TCP/443 must be open for outbound requests from the scanner to Grundium cloud *.grundium.net (use
*.grundium.net instead of IP address).
•Port TCP/443 must be open for outbound requests from the user’s computer to Grundium cloud *.grundium.net (use
*.grundium.net instead of IP address).
•Port TCP/443 must be open for traffic between the computer and scanner when in the same VLAN or separate VLANs.
•Your network must be setup to allow an external DNS (in this case the DNS service provided by Grundium cloud) to
provide name to IP resolution for internal IP addresses. This setup will provide the best user experience.
Optional:
To allow your users to access Ocus also from an outside network (e.g., from home in absence of VPN or from another
institution’s network): in addition to the above for internal use, allow the scanner to make outbound requests via TCP/471
to *.grundium.net (use *.grundium.net instead of IP address).

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7.2 CREATING USER ACCOUNT
1. Open the browser in your computer or tablet and type the following in the browser’s address field:
https://www.grundium.net
2. If you already have a user account to Grundium, login with your account details and move directly to chapter 7.3.
Image 5. Login to Grundium cloud.
3. If you do not have the account yet, click Register a new user to create a new account and then login.
4. When registering a new user, enter your email address and click Add a new account. Read and Accept Terms and
Conditions. Verification email will be sent to address you have registered. Check your email and copy the verification
code to the line and click Continue.
Note: Verification code is valid 72 hours or until it has been used successfully.
Image 6. Enter your email and click “Add a new
account”.
Image 7. Add verification code that has been sent to your
email.

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5. Enter your name and create a password, then click Confirm.
Image 8. Enter your name and password.
6. After registering is done, login to the system with your email address and password (see image 5).
You now have completed the user registration process.
7.3 REGISTERING A NEW OCUS SCANNER
1. Open the browser in your computer or tablet and type the following in the browser’s address field:
https://www.grundium.net
2. Sign in with your user account. (If you do not have an account, see section 7.2 “Creating user account”).
3. Click Register a new device. (See image 9).
4. Enter the serial number of your Ocus®40 scanner. The number is printed on the label in the Quick guide and at the
bottom of the scanner. Click Register when ready. (See image 10)
5. Select existing team from the dropdown menu or add a new team by clicking “ADD TEAM”. After entering a valid team
name click “+”. Assigning the Ocus scanner to a team allows the registered team members to access and control the
scanner.
Note: Name of the team needs to be in lower case and without spaces.
6. Select a region from the dropdown menu. (See image 11).
Note: It is important to select region geographically closest to your own country, because it defines the used server and
WLAN/Wi-Fi parameters specific to your country.
7. The password can be found on the label in Quick guide or at the bottom of the scanner.

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8. Click Continue after all required details have been entered.
Image 9. Register a new Ocus Scanner.
Image 10. Type the serial number of your Ocus®40 scanner.
Image 11. Team, region, and Ocus Scanner password are required information when registering a new Ocus scanner.
Note: After the registration, the Ocus scanner must be switched on and connected to the Internet for it to obtain the
registration information. (See section 7.4 and 7.5)

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7.4 CONNECTING THE SCANNER USING AN ETHERNET CONNECTION
It is highly recommended to use a wired network (ethernet) connection with the Ocus scanners to maximize data transfer
speed and stability.
1. Attach the power cable to the scanner and plug the cable in a wall outlet. The power button shows a breathing green
light.
2. Connect one end of the network cable to the scanner and the other end to the Ethernet connector for your network,
which provides connection to the Internet.
3. Press the power button. The power button flashes yellow. Once the scanner is switched on and ready to be used, the
power button shows a steady green or yellow light. If this is the case, skip to 8.1 Logging in to the scanner.
If the light turns blinking red, the scanner could not connect to the Internet.
oContact your IT department and verify if the network firewall rules have been configured (see section 7.1
“setting up the network firewall configuration based on the MAC address”).
oIf the firewall rules have already been set up, but the connection still fails, contact customer support:
[e-mail]
7.5 CONNECTING THE SCANNER USING A MOBILE HOTSPOT
If you have no access to ethernet network, as a secondary option, it is possible to use a Mobile Hotspot connection.
When ethernet cable is disconnected, and the Ocus scanner is not connected to a Wi-Fi network, the Ocus scanner
can automatically connect to a mobile hotspot / Wi-Fi network that has the following configuration:
Type: WPA-PSK
Name / password: “ForOcus_XYYYYY” (e.g., ForOcus_100123 if MGU-00001-000123, the serial number, and the
password can be found both in the bottom label of the scanner, or from the Quick Guide).
Note: Disconnect ethernet cable if connected.
Note: Mobile hotspot connection can be used temporarily to configure the scanner to connect to another Wi-Fi.
Note: It is not recommended to use 5GHz Wi-Fi band for the ForOcus hotspot. Ocus scanner does not support all
latest allowed 5GHz channels and it is possible that if the hotspot happens to be using one of these unsupported
channels, Ocus will not find the hotspot.
Note: If an iPhone is used to create the mobile hotspot, please turn OFF the iPhone hotspot’s “max compatibility”
mode, to enforce the iPhone to only utilize the 2.4GHz band.
Note: If there is no access to a device that can be used to create a mobile hotspot, please contact your technical
support.
Note: The ForOcus password cannot be changed.

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7.6 CONFIGURING A WIFI- CONNECTION
After the scanner has been connected to the internet, and it has obtained the registration information, a Wi-Fi connection can
be configured. This can be done while the Ocus Scanner is connected to the internet.
1. Open the browser in your computer or tablet and type the following in the browser’s address field:
https://www.grundium.net
2. Sign in with your user account. (If you do not have an account, see section 7.2 “Creating user account”.
3. Go to Settings.
4. On the network tab of the settings page, click on WLAN.
5. From the list of available networks, choose your network.
6. Click “Edit”
7. On the password popup, enter your network password, and click “Save”.
8. After the password popup has closed, click “Connect”.
The Ocus Scanner is connected to the chosen network when a “Connected” text appears next to the signal strength icon.
8LOGGING IN TO THE SCANNER
8.1 LOGGING IN TO THE SCANNER WITH INTERNET CONNECTION
This connection method works when the power button light is steady green or steady yellow.
Note. If the light is steady yellow, the end device used to operate the Ocus scanner needs to be connected to the same
network (VLAN) as the Ocus scanner, or routed connection must be allowed by the network administrator. (See section
7.1 “Setting up the network firewall configuration based on the MAC-address”).
1. Open the browser on your computer or tablet and go to https://www.grundium.net
2. Enter your e-mail address and password and click Login. (See image 12).
3. Select your team and the scanner you want to use, then click Connect to device. (See image 13).
Image 12. Log in to the scanner by giving your e-mail address
and password.
Image 13. Select your team and scanner from the list.

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8.2 LOGGING IN TO THE SCANNER USING THE OFFLINE MODE (ACCESS POINT MODE)
Once registered and after being used for the first time, Ocus scanners can be temporarily used in offline mode, for
example in a situation when a network connection is not available. This is done by connecting a Wi-Fi capable computer
or tablet to a Wi-Fi access point provided by the scanner.
To enable the Offline Mode:
oTo activate the Offline Mode access point while the Ocus scanner is powered on, press, and hold the power
button for 2-3seconds and then release.
oWhen the WLAN access point mode is activated, Ocus scanner establishes a WLAN network, where end devices
can be connected. Light on power button turns steady blue.
To connect an end device to the Ocus Scanner’s Offline Mode access point Wi-Fi SSID:
1. Open the WLAN/Wi-Fi settings on your computer or tablet and connect to WLAN/Wi-Fi access point provided by
the canner (WLAN/Wi-Fi name/SSID and password can be found on the label on the bottom of the Ocus Scanner
or in the quick guide, see image 4).
2. Make sure your computer is not connected to another network at the same time.
3. Open the browser in your computer or tablet and go to http://www.grundium.net
4. Type your e-mail address and password and click Login (See image 12).
When the Ocus scanner is restarted, the access point will automatically turn off.
Note: All other network connections are disabled while the access point is activated.
Note: Only one end device can be connected to the Ocus access point at once.
Note: WLAN settings are not available when operating the Ocus scanner in access point mode.
Note: Before it is possible to log in to the Ocus scanner while it is connected with Direct WLAN / Wi-Fi connection (Access
Point Mode), the Ocus Scanner needs to be registered to a team, and connected to the internet with a network
connection that allows the scanner to connect to the Grundium cloud. (See section 7 “First use”).

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9SCANNING
Important notice: Both in local and remote use, remember to keep at least 10 centimeters (4 inches) of free space around the
scanner. Do not touch the scanner when the stage is moving.
1. On your computer or tablet, navigate to Grundium.net, select Microscope view, click Eject slide tray, or Change
Slide.
Image 14.For inserting a slide into scanner click Eject slide tray.
2. Push the lever underneath the cover plate left to open the slide retainer (See image 15).
Image 15.Open the slide retainer and place the slide in the scanner.

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3. Place the slide in the scanner so that the label is on the right. Push the lever right to secure the slide.
4. Click New scan to take an overview image. (See image 16).
5. Set the region of interest to be scanned using the Add scan area button (See image 19).
6. Click Scan to scan the defined scan area.
Image 16. Start taking an overview image by selecting New
Scan.
Image 17. Zooming options.
Image 18. Auto focus sliders in the live view window.
7. Zoom out, click Add and select one or more areas you want to scan. To adjust the areas further, drag the borders of the
areas. Estimated scan time is shown on bottom left corner of the UI.

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Image 19. Navigator window.
8. Click Scan to start the scanning. The remaining scan time is shown on screen and once the scan is completed, the
scanned areas are marked with gray outlines in the overview image, and you can zoom into them.
Tip: The image is saved automatically in the scanner’s hard drive. If you want to give the image a specific name, type the name in
the File name field.
Tip: You can use the scanner in live view for quick viewing of details on a slide. The image can be panned by dragging the image
with mouse or fingertip. Live view can be activated by clicking Live view and full screen mode can be entered by clicking .
You can also take a snapshot image of the live view by clicking Save image. To zoom in and out on the specimen, use your
mouse scroll, or click +, - or 5x/10x/20x/40x quick buttons next to the zoom bar on display (see image 17).
Tip: Understanding how the scanner’s focusing system works will help to achieve better results faster. With vast majority of
sample types, it is easiest and fastest to just select a scan area and click Scan. In this case, the scanner will point the objective in
the center of the selected scanning area and seek focus from that location.
Tip: User can manually set focus using live view before scanning. The manually selected focus position is used as the starting
point for scanning. To manually set the focus, disable autofocus and user the sliders to set the focus. (See image 18).
Tip: Scanner’s electronic fine and coarse focus can be adjusted with the sliders on the right side of the live view image. If you use
a mouse with roller wheel, the roller will move the focus when mouse cursor is on top of the slider. The fine focus is much more
precise than the coarse focus but is limited in range. Clicking Seek will search the optimal position for coarse focus. Clicking AF
next to the slider activates the automatic fine focusing mode, where the fine focus will be continuously kept in optimal position.
Tip: You can find a measurement tool under the zooming options. (See image 17).
Tip: To quickly remove extra areas from the selected scanning area, click Trim all. The success of trimming depends on
the sample, so always confirm the trimming result visually.
Note: Ocus 40 optics has been designed for 0.17mm cover slip thickness. As high NA objectives are very sensitive to
variation in cover slip thickness, best results can be achieved using precision cover slips. Scanning with different thickness
slips or even without a slip is possible but resulting image quality will be degraded.

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9.1 SCAN MODE
There are four scan modes to choose from.
Image 20. Scan mode, and scan mode settings can be selected in Configure window.
•Normal - Default scanning mode.
oNo adjustments
▪Offset slider is visible, but adjusting the slider is disabled.
•Offset - User can adjust the scan layer offset.
The following can be set in scan mode view:
oUser can set the offset of the point of focus in comparison to normal scan mode result
oOffset interval reset can be done by clicking reset button
•Optical Sections - User can select the number of optical sections and their offset.
The following can be set in scan mode view:
oThe amount of scan layers (optical sections)
oInterval of optical sections
oOffset of the optical sections stack