Installation & Setup
Compatible Cameras
The table below displays which cameras are compatible to the software.
Compatible ZEISS Axiocams
|
Camera |
Connection |
|---|---|
|
Axiocam 105 color |
USB 3.0 |
|
Axiocam 202 mono |
USB 3.0 |
|
Axiocam 203 mono |
USB 3.0 |
|
Axiocam 208 color |
USB 3.0 |
|
Axiocam 212 color |
USB 3.0 |
|
Axiocam 305 color / mono |
USB 3.0 |
|
Axiocam 503 color / mono |
USB 3.0 |
|
Axiocam 506 color / mono |
USB 3.0 |
|
Axiocam 512 color / mono |
USB 3.0 |
|
Axiocam 702 mono |
USB 3.0 |
|
Axiocam 705 color / mono |
USB 3.0 |
|
Axiocam 712 color / mono |
USB 3.0 |
|
Axiocam 807 color / mono |
2x USB 3.0 |
|
Axiocam 820 color / mono |
2x USB 3.0 |
Compatibility of Windows Versions to Machine Learning and AI Features
ZEN core allows you to use certain machine learning and AI functionality, e.g. semantic segmentation and denoising (via the respective Intellesis functionality) as well as the use of AI models for instance segmentation.
The following table illustrates CPU and GPU usage for ZEN Toolkit AI, ZEN Toolkit 2D, and ZEN Toolkit Material Apps:
|
Windows 10 version 1607 (build 14393), e.g. Windows 10 Enterprise LTSB 2016 |
Windows 10 version 1809 (build 17763), e.g. Windows 10 Enterprise LTSC 2019 |
Windows 10 version 21H2 (build 19044), e.g. Windows 10 Enterprise LTSC 2021 |
Windows 11, version 24H2 (build 26100), e.g. Windows 11 Enterprise LTSC 2024 |
|
|---|---|---|---|---|
|
ZEN Toolkit AI |
CPU fallback for semantic segmentation and denoising. |
Additional GPU support for semantic segmentation and denoising. |
||
|
ZEN Toolkit 2D ZEN Toolkit Material Apps |
CPU fallback for semantic segmentation. |
Additional GPU support for semantic segmentation and instance segmentation using CPU. |
Additional GPU support for instance segmentation. |
|
When using instance segmentation models trained on arivis Cloud for image segmentation in ZEN Toolkit 2D or ZEN Toolkit Material Apps, an installation of Docker is necessary. Depending on your Windows and Docker version, the functionality can be limited to only run on CPU instead of GPU. The following tables illustrate which Docker and operating system version you need if you want to use the functionality also with GPU, and if you need to use Hyper-V or WSL.
To install Docker Desktop, you can use the ZEISS Microscopy Installer, with the exception of older Windows versions, for which you need to install an older version of Docker Desktop directly from the Docker website, see table below.
|
Windows 10 version 1607 (build 14393), e.g. Windows 10 Enterprise LTSB 2016 |
Windows 10 version 1809 (build 17763), e.g. Windows 10 Enterprise LTSC 2019 |
Windows 10 version 21H2 (build 19044), e.g. Windows 10 Enterprise LTSC 2021 |
Windows 11, version 24H2 (build 26100), e.g. Windows 11 Enterprise LTSC 2024 |
|
|---|---|---|---|---|
|
Docker version for instance segmentation |
not supported |
Version ≤ 4.24.2 |
Current version available with the ZEISS Microscopy Installer |
|
|
WSL/Hyper-V |
not supported |
Hyper-V |
WSL 2 |
|
|
ZEN Toolkit 2D |
No instance segmentation possible. |
Instance segmentation using CPU. |
Additional GPU support for instance segmentation. |
|
|
ZEN Toolkit Material Apps |
No instance segmentation possible. |
Instance segmentation using CPU. |
Additional GPU support for instance segmentation. |
|
Changes to the Operating System
NOTICE
Installation of software, hardware drivers, changes to operating system settings or other system interference beyond the actions needed to operate the software are always in the responsibility of the customer, because the potential impact cannot be estimated.
The following modifications have, in our experience, no effects on the functionality of the PC system:
- Network integration
- Installation of security software/antivirus software (highly recommend if your PC is attached to a network)
- Logon as Domain Users in an Active Directory environment (possibly with local administrator privileges if user needs to install software)
- Installation of standard software (e.g. Microsoft Office)
- Installation of printers
- Windows automatic updates and third-party software updates (Windows Service Packs are to be considered different)
- Information about allowed Windows service packs can be found in the corresponding system requirements for Windows.
Effects of following modifications cannot be estimated:
- Modifications in the Windows operating system
- Implementation of group policies and scripts
- Installation of third-party software with hardware support
- Installation of third-party software for generating large data rates (such as backup software) due to possible performance problems of the simultaneous operation of Fast Acquisition Systems
- Storage of data on network drives by redirecting folder structures (e.g. there can occur performance problems in case of Fast Acquisition systems or limitation of the available data storage capacity (disk quota))
If problems occur, the system can be restored to the state of delivery by a ZEISS service technician.
Installing ZEN core
NOTICE
- The installation of ZEN core and other components is performed using the ZEISS Microscopy Installer. Download the ZEISS Microscopy Installer in the ZEISS Portal from the Download Center under https://portal.zeiss.com/download-center/softwares/mic.
- Do not install an older ZEN core version over a newer ZEN core version. If ZEN core is already installed on your PC, uninstall the current version first.
- Depending on your PC configuration, the system requests an optional restart at the beginning of the installation.
- In exceptional cases, the system requests a restart at the end of the installation. If this is the case, a message will be displayed. This restart is required for the successful camera driver installation. You may postpone the restart until all components selected in the ZEISS Microscopy Installer are installed. After restart of the computer, reopen the ZEISS Microscopy Installer to install remaining components.
- In case of installing ZEN core on a SEM system, make sure that SmartSEM is not running when installing ZEN core.
- You have read the chapter Configure security software attentively.
- You have opened the ZEISS Microscopy Installer with admin rights and you are logged in.
- Your system is connected to the Internet.
- You have selected (default setting) the online installation, see ZEISS Microscopy Installer manual. If your system is not connected to the Internet, also see ZEISS Microscopy Installer manual.
- Open the Install tab, and on the left, select ZEN core with the respective version number (e.g. 3.12).
- The following dialog is displayed.

- On the right side, activate all components you want to install.
Always install the MTB when your system is connected to hardware. Select ZEISS hardware drivers > ZEISS Micro Toolbox (MTB). For updates of ZEN core Visioner 3.1 or 3.2 to higher versions, also install the MTB.
Note that if the 3rd party Python Tools are not installed, the following functionality will not work: Intellesis, Intellesis Object Classification, and Intellesis Denoising. Additionally, you need the 3rd party Python Tools to run a model trained by one of these modules.
In the Tools and accessories group, check which of the sample images are relevant for your modules: For TCA, TCA Small Sample Images (ZEN core) must be installed. Otherwise, the TCA workflows with loaded image will not work. The NMI Big Sample Images (ZEN core) are necessary when analyzing images in "real" sample size. The TCA Object Classification Images (ZEN core) should be installed if the AI Toolkit is licensed. - If Docker Desktop is not installed, you cannot use containerized features like AI models for instance segmentation. For installation information, see Installing Docker Desktop with ZEISS Microscopy Installer.
- Activate I agree to the Terms and Conditions of the selected software and click Install.
- The selected components are downloaded and installed. A progress bar shows the progress of the installation.
- In case a software product or a software component requires a reboot, a message appears informing you that you need to reboot your computer.
- Click Close to exit the ZEISS Microscopy Installer.
Installing Docker Desktop with ZEISS Microscopy Installer
Installation Not Possible for Existing .exe Versions of Docker
If you want to install Docker Desktop with the ZEISS Microscopy Installer but already have a Docker Desktop version that was installed with an .exe file, for example from Docker directly, the installation is not possible.
- You first have to uninstall the version manually. Note that this uninstallation deletes existing Docker images!
The ZEISS Microscopy Installer allows you to install Docker Desktop for your software application. Docker Desktop is only needed when you want to use containerized features like AI models for instance segmentation. For additional information and possible requirements, see Requirements for Docker Desktop. The ZEISS Microscopy Installer installs Docker Desktop for WSL2.
- Your system is connected to the Internet.
- You have opened the ZEISS Microscopy Installer with admin rights and you are logged in.
- You have selected (default setting) the online installation, see ZEISS Microscopy Installer manual.
- Open the Install tab.
- The available products are displayed.
- On the left, select ZEN core with your respective version number.
- The available components and tools for installation are displayed on the right side.
- On the right side, activate Docker Desktop.
- The component is selected for installation.
- Activate I agree to the Terms and Conditions of the selected software and click Install.
- The selected components are downloaded and installed. The status is displayed in the ZEISS Microscopy Installer.
- After successful installation, close the ZEISS Microscopy Installer and restart your PC to complete the installation.
- After the restart of your computer the installation was successful.
Installing ZEN Word Add-In
This Add-In enables you to create customized report templates in Microsoft Word, which you use in ZEN core to collate and export examination results into a Microsoft Word document in a predefined way.
- Microsoft Office 2016 or higher is installed.
- You have read the chapter Configure security software attentively.
- You have opened the ZEISS Microscopy Installer with admin rights and you are logged in.
- Your system is connected to the Internet.
- You have selected (default setting) the online installation, see ZEISS Microscopy Installer manual.
- Select Install tab > ZEN Office Add-In > ZEN Office Add-In components.

- Activate ZEN Word Add-In and I agree to the Terms and Conditions of the selected software, and click Install.
- The download starts. After downloading, the installation starts. A progress bar indicates the process.
- The following dialog is displayed.

- Click Install.
- The Welcome to the InstallShield Wizard dialog opens.

- Click Next.
- The License Agreement screen is displayed.
- Select I accept the terms in the license agreement, and click Next.
- The Customer Information dialog is displayed.
- Enter a user and the company name, and click Next.
- The Ready to Install the Program dialog is displayed.
- Click Install.
- The Installing ZEN Office AddIn dialog is displayed. The software will be installed now. You are informed when the installation is finished.
- After the installation the Setup completed dialog is displayed.

- Click Finish.
The Add-In is installed on your system and activated in Microsoft Word. The next time you start Microsoft Word, the new ribbon ZEN Report Templates is available, which enables you to create your own report templates or to modify existing ones.
Installing TCA with two digital cameras mounted to a manual dual adapter
The following instruction helps setting up the tiles region acquisition with the Axiocam 705 pol using both cameras.
The dual-camera support for TCA is approved for the following combination of digital cameras: Axiocam 705 pol and Axiocam 305 color or Axiocam 705 color.
The image orientation must be harmonized for both cameras to ensure the correct setting for tiles region acquisition and the correct lateral alignment of the particles. The settings are dependent on the microscope hardware and the MTB configuration of the stage.
- Attach the Axiocam 705 pol on top and the Axiocam 305 color / 705 color on the side of the dual adapter.
- Add both digital cameras to one MTB configuration.
- Rotate the Axiocam 705 pol and the digital color camera on the corresponding C-mount adapter to achieve for each a parallel camera-to-stage orientation.
- Select the Axiocam 705 pol in Maintenance > Select Active Camera or via the Select Camera tool in any of the acquisition workbenches.
- Define in Free Mode a manual scaling for Axiocam 705 pol, for all objectives and if zoom objectives are available, in addition for a minimum of 5 zoom magnification levels.
- Select, if required, the correct image rotation for Axiocam 705 pol in 2D-Acquisition > Extended Camera > Model Specific > General > Orientation for correct tiles region acquisition without stitching.
- For the validation define a tiles region with the large cross in the center of the particle test slide and acquire a small tiles region to verify correct tiles image acquisition without stitching.
- Select the digital color camera in Maintenance > Select Active Camera or via the Select Camera tool in any of the acquisition workbenches.
- Define a manual scaling for the digital color camera, for all objectives and if zoom objectives are available, in addition for a minimum of 5 zoom magnification levels.
- Adjust the image rotation for the digital color camera in 2D-Acquisition > Extended Camera > Model Specific > General > Orientation so that in camera live mode a centered particle or object has the same orientation independent which camera is selected.
- To align the zoom factor for Axiocam 705 color and Axiocam 705 pol, change the default setting for Axiocam 705 color in Extended Camera > Mode section > Live Speed drop down list to High Res.
Installing Remote API Client (for SEM systems)
To enable communication between SmartSEM and ZEN core, the RRemote Client has to be installed on the SEM system as well. After the ZEN core software is installed, install the RRemote Client.
- You have read the chapter Configuration of Security Software attentively.
- Your system is connected to the Internet.
- You have opened the ZEISS Microscopy Installer with admin rights and you are logged in.
- You have selected (default setting) the online installation, see ZEISS Microscopy Installer manual.
- You have closed SmartSEM and EM Server.
- Open the Install tab.
- On the left, activate ZEN core with the respective version number.
- The available components and tools for installation are displayed on the right side.
- On the right side, activate SmartSEM Remote API.
- Activate I agree to the Terms and Conditions of the selected software.
- Click Install.
- The download starts. The progress is displayed in the installer.

- After the download, the installation starts. Several installation dialogs are displayed, but no action is required. Wait until the different windows have disappeared. After the installation procedure you can check the configuration with the tool RConfigure (open from Windows Start menu).

- You have successfully installed the Remote Client on your SEM system. You can test the program with the Desktop-App SmartSEM API Test.
Creating a Desktop Shortcut to Start a Specific ZEN core (EM) Profile
If you want to have the possibility to start ZEN core directly with a certain profile, you can create a specific desktop shortcut.
- You have installed ZEN core.
- Open the Windows file explorer and navigate to the folder where ZEN core is installed. The default is C:\Program Files\Carl Zeiss\ZEN core.
- Right click ZENcore.exe and drag and drop it to the desktop with pressed right mouse click.
- A context menu is displayed.
- Select Create shortcuts here.
- A shortcut is created on the desktop.
- Right click on the shortcut and select Properties from the context menu.
- The properties window is displayed.
- On the Shortcut tab, go to Target.
- The path of the exe file is displayed, e.g. C:\Program Files\Carl Zeiss\ZEN core\ZENcore.exe
- Change this path by adding a space, /ProfileId= and the respective ID of the profile. For information, see the table below.
- The path is changed, e.g. to C:\Program Files\Carl Zeiss\ZEN core\ZENcore.exe /ProfileId=ZenCore.LM.Starter.
- Click OK.
- The properties window closes and the changes are saved.
- You have created a shortcut for a specific profile of ZEN core. Starting the software by clicking this shortcut directly starts the respective profile.
Profile IDs for ZEN core & ZEN core EM
|
Profile |
Profile ID |
|---|---|
|
ZEN analyzer |
ZenCore.LM.Analysis |
|
ZEN core |
ZenCore.LM.Core |
|
ZEN core SEM |
ZenCore.LM.SEM |
|
ZEN core starter |
ZenCore.LM.Starter |
|
ZEN core Visioner |
ZenCore.LM.Visioner |
|
Crossbeam |
Crossbeam |
|
EVO |
EVO |
|
FE-SEM |
FE-SEM |
|
Volutome |
Volutome |
Backing Up and Restoring Settings
NOTICE
Risk of Data Loss
The Manage ZEN Settings tool allows you to delete the settings of your application, even if you have not backed them up before, which results in data loss.
- Back up your settings before deleting to prevent data loss. Alternatively, contact your local Zeiss service representative before using this tool.
Limitation for Data Backup, Deletion and Restoration
Note that only the data for the current windows user will be saved or deleted. If you have a system with several users you have to do this for every windows user!
Although they are backed up, license and MTB files will not be restored automatically with this software tool.
You can manage (backup, restore and delete) application settings with the Manage ZEN Settings tool. This includes application data, user profiles, user documents (like calibration files), license and MTB data, as well as logging data.
- Use the ZEISS Microscopy Installer to install the Manage ZEN Settings tool. It is available in the Tools and accessories section of your application installation. For general information, also refer to the ZEISS Microscopy Installer manual.
- The tool is available on your PC.
- Open a file explorer and go to C:\Program Files\Carl Zeiss\ZEN Tools\ManageZENSettings.
- The folder displays the .exe file for the application.
- Double click ManageZENSettings.exe.
- You might be prompted execute the tool with administrative privileges. If so, confirm.
- The Manage ZEN Settings tool opens.

- Click Back Up ZEN Settings.
- The backup is created and placed in the defined/default folder.
- To restore settings, open the dropdown below Choose a ZEN Settings Back Up to restore and select the entry of the backup. Afterwards, click Restore ZEN Settings.
- The settings are restored.
- If you want to back up and/or delete settings, click on the respective buttons in the application window.
- To open the current folder for backups, click Open the current Back Up folder.
- A file explorer opens at the location, where backups are currently saved.
- To change the folder, open the dropdown below Choose a ZEN Settings Back Up to restore and select Change Back Up folder.
- A file browser opens.
- Select the folder for the backups and click Select Folder.
- The file explorer closes and the folder is changed.
ON THIS PAGE
- Installation & Setup
- Compatible Cameras
- Compatibility of Windows Versions to Machine Learning and AI Features
- Changes to the Operating System
- Installing ZEN core
- Installing Docker Desktop with ZEISS Microscopy Installer
- Installing ZEN Word Add-In
- Installing TCA with two digital cameras mounted to a manual dual adapter
- Installing Remote API Client (for SEM systems)
- Creating a Desktop Shortcut to Start a Specific ZEN core (EM) Profile
- Backing Up and Restoring Settings