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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

Other, compatible cameras

Camera

Notice

PrimoStar HD

USB only, not via network connection

Primovert HDcam

USB only, not via network connection

Hamamatsu: Orca Flash 4.0 V3 CL/USB3.0, Orca Flash LT USB3.0, Orca Fusion, Orca Fusion BT

Roper Photometrics: Prime 95 B, 95B 22mm, Prime BSI, Prime BSI Express

PCO: edge 5.5 CL, edge 4.2 CHLS USB3.0, edge 4.2 bi, edge 4.2 CL, edge 4.2 LT

Compatibility of Windows Versions to Machine Learning and AI Features

ZEN 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 Bio Applications:

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 Bio Applications

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 Bio Applications, 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
For version 4.24.1, use https://desktop.docker.com/win/main/amd64/123237/Docker%20Desktop%20Installer.exe

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 Bio Applications

No instance segmentation possible.

Instance segmentation using CPU.

Additional GPU support for instance segmentation.

Changes to the Operating System

NOTICE

Blue circular sign with a centered white exclamation mark

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

NOTICE

Blue circular sign with a centered white exclamation mark
  1. The installation of ZEN 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.
  2. Do not install an older ZEN version over a newer ZEN version.
  3. If ZEN is already installed on your PC, during installation the current version will be uninstalled first.
  4. Depending on your PC configuration, the system requests an optional restart at the beginning of the installation.
  5. The system requests a restart at the end of the installation. This restart is required for the successful camera driver installation. You can 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.
  6. In case of installing ZEN on a SEM system, make sure that SmartSEM is not running when installing ZEN.
  1. You have read the chapter Configuration of Security Software attentively.
  2. Your system is connected to the Internet.
  3. You have opened the ZEISS Microscopy Installer with admin rights and you are logged in.
  4. You have selected (default setting) the online installation, see ZEISS Microscopy Installer manual.
  1. Open the Install tab.
  2. The available products are displayed.
  3. On the left, select ZEN with the respective version number.
  4. The available components and tools for installation are displayed on the right side.
  5. On the right side, activate all components you want to install.
  6. If the 3rd party Python Tools are not installed, the machine learning based Intellesis functionalities will not work. This also includes their use in other parts of the software, like the neural networks in certain Bio Applications.
  7. 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.
  8. If you want to use functionality with systemwide Docker containers for the Spatial Biology toolkit, you need to activate the respective entry to install the containers.
  9. Activate I agree to the Terms and Conditions of the selected software and click Install.
  10. The selected components are downloaded and installed. The status is displayed in the ZEISS Microscopy Installer.
  11. After successful installation, close the ZEISS Microscopy Installer and restart your PC to complete the installation.
  1. After the restart of your computer the installation was successful. Start the software by clicking on the ZEN icon on your desktop.
  2. If you install ZEN on a computer for a SEM system, continue with Installing Remote API Client (for SEM systems).

Installing Remote API Client (for SEM systems)

To enable communication between SmartSEM and ZEN, the RRemote Client has to be installed on the SEM system as well. After the ZEN software is installed, install the RRemote Client.

  1. You have read the chapter Configuration of Security Software attentively.
  2. Your system is connected to the Internet.
  3. You have opened the ZEISS Microscopy Installer with admin rights and you are logged in.
  4. You have selected (default setting) the online installation, see ZEISS Microscopy Installer manual.
  5. You have closed SmartSEM and EM Server.
  1. Open the Install tab.
  2. On the left, activate ZEN with the respective version number.
  3. The available components and tools for installation are displayed on the right side.
  4. On the right side, activate SmartSEM Remote API.
  5. Activate I agree to the Terms and Conditions of the selected software.
  6. Click Install.
  7. The download starts. The progress is displayed in the installer.
    ZEISS Microscopy Installer window showing 'Installation is in progress', 'Download finished', and 'Installing: 10 %'
  8. 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).
    RConfigure dialog showing Client Port 8070, Client IP 127.0.0.1 and Server Port 8093, Server IP 127.0.0.1
  1. You have successfully installed the Remote Client on your SEM system. You can test the program with the Desktop-App SmartSEM API Test.

Installing MATLAB for Correlative Array Tomography

If you have bought the CAT Module (Correlative Array Tomography) the installation of MATLAB Runtime is mandatory on both computers (SEM and LM system). Proceed as follows:

  1. You have read the chapter Configuration of Security Software attentively.
  2. Your system is connected to the Internet.
  3. You have opened the ZEISS Microscopy Installer with admin rights and you are logged in.
  4. You have selected (default setting) the online installation, see ZEISS Microscopy Installer manual.
  1. Open the Install tab.
  2. On the left, activate ZEN with the respective version number.
  3. The available components and tools for installation are displayed on the right side.
  4. On the right side under Third Party Tools, activate MATLAB Runtime with version number 2015b 9.0.
  5. Activate I agree to the Terms and Conditions of the selected software and click Install.
  6. The download of the necessary files starts.
  7. After the download, a WinZip Self-Extractor window opens and the files are extracted.
    WinZip Self-Extractor titled MCRInstaller.exe displaying 'Extracting MATLAB Runtime R2015b for installation.'
  8. After the extraction, MATLAB Compiler Runtime Installer opens.
    MATLAB Runtime Installer dialog stating 'This application will install MATLAB Runtime.' with MATLAB logo and Next/Cancel buttons
  9. Click Next.
  10. The License Agreement dialog is displayed.
    License Agreement dialog showing The MathWorks license text and question 'Do you accept the terms of the license agreement? Yes No' with Next and Cancel
  11. Accept the License Agreement by activating Yes, then click Next.
  12. The Folder Selection dialog is displayed.
    Folder Selection dialog showing installation path 'C:\Program Files\MATLAB\MATLAB Runtime' with Browse and Restore Default Folder buttons
  13. Click Next to install to the default folder.
  14. The Confirmation dialog is displayed.
    Confirmation dialog listing Installation folder 'C:\Program Files\MATLAB\MATLAB Runtime\v90', size 1.626 MB and product MATLAB Runtime 9.0
  15. Click Install.
  16. The software is installed and the progress is displayed in the installation dialog.
  17. After installation the Installation Complete dialog is displayed.
    Installation Complete window with text 'Installation is complete.' MATLAB Runtime R2015b logo and Finish button
  18. Click Finish.
  1. You have successfully installed the MATLAB Runtime that is necessary for the working with the CAT module.
  2. After successful installation of all components, the ZEISS Microscopy Installer displays the respective status. You can now also close the ZEISS Microscopy Installer, or click Back if you want to install other software.

Backing Up and Restoring Settings

NOTICE

Blue circular sign with a centered white exclamation mark

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.

  1. 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.

  1. 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.
  2. The tool is available on your PC.
  3. Open a file explorer and go to C:\Program Files\Carl Zeiss\ZEN Tools\ManageZENSettings.
  4. The folder displays the .exe file for the application.
  5. Double click ManageZENSettings.exe.
  6. You might be prompted execute the tool with administrative privileges. If so, confirm.
  7. The Manage ZEN Settings tool opens.
    Manage ZEN Settings dialog with BackUp and Restore buttons and a backup selection dropdown
  8. Click Back Up ZEN Settings.
  9. The backup is created and placed in the defined/default folder.
  10. 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.
  11. The settings are restored.
  12. If you want to back up and/or delete settings, click on the respective buttons in the application window.
  13. To open the current folder for backups, click Open the current Back Up folder.
  14. A file explorer opens at the location, where backups are currently saved.
  15. To change the folder, open the dropdown below Choose a ZEN Settings Back Up to restore and select Change Back Up folder.
  16. A file browser opens.
  17. Select the folder for the backups and click Select Folder.
  18. The file explorer closes and the folder is changed.

Creating a Desktop Shortcut to Start a Specific ZEN Profile

If you want to have the possibility to start ZEN directly with a certain profile, you can create a specific desktop shortcut.

  1. You have installed ZEN.
  1. Open the Windows file explorer and navigate to the folder where ZEN is installed. The default is C:\Program Files\Carl Zeiss\ZEN 2\ZEN 2 (blue edition).
  2. Find and right click ZEN.exe and drag and drop it to the desktop with pressed right mouse click.
  3. A context menu is displayed.
  4. Select Create shortcuts here.
  5. A shortcut is created on the desktop.
  6. Right click on the shortcut and select Properties from the context menu.
  7. The properties window is displayed.
  8. On the Shortcut tab, go to Target.
  9. The path of the exe file is displayed, e.g. C:\Program Files\Carl Zeiss\ZEN 2\ZEN 2 (blue edition)\ZEN.exe
  10. Change this path by adding a space, /ProfileId= and the respective ID of the profile. For information, see the table below.
  11. The path is changed, e.g. to C:\Program Files\Carl Zeiss\ZEN 2\ZEN 2 (blue edition)\ZEN.exe /ProfileId=ZenBlue.LM.Lite.
  12. Click OK.
  13. The properties window closes and the changes are saved.
  1. You have created a shortcut for a specific profile of ZEN. Starting the software by clicking this shortcut directly starts the respective profile.

Profile IDs for ZEN

Profile

Profile ID

ZEN celldiscoverer

ZenBlue.LM.CellDiscoverer

ZEN Desk

ZenBlue.LM.Desk

ZEN Image Processing

ZenBlue.LM.ImageProcessing

ZEN lite

ZenBlue.LM.Lite

ZEN lattice lightsheet

ZenBlue.LM.muSpim

ZEN pro

ZenBlue.LM.Pro

ZEN SEM

ZenBlue.LM.SEM

ZEN slidescan

ZenBlue.LM.SlideScan

ZEN system

ZenBlue.LM.System

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