Installation & Setup

Minimum System Requirements	Recommended System Requirements
Intel® CPU with 6 cores, 3.0 GHz clock frequency (e.g. Intel® Core® i5-12500 CPU)	Intel® Xeon® CPU with 12 cores, 3.2 GHz clock frequency (e.g. Intel® Xeon® W5-3425)
16 GB RAM	64 GB RAM
Graphics adapter with support for resolutions of at least 1920 x 1200, 32 Bit true color, DirectX® 12.0 or higher (e.g. integrated Intel® UHD Graphics 670 or dedicated graphic card NVIDIA® RTX A1000 8GB)	Graphics adapter with support for resolutions of 3840 x 2160 Pixel (“4K”), 32 Bit true color, DirectX® 12.0 (or higher), OpenGL® 4.5 (or higher) (e.g. dedicated graphic card NVIDIA® RTX A4000 16 GB)
Hard drive 1 x 512 GB SSD NVMe and 1 x 8 TB HDD SATA 6Gb/s	Hard drive 1 x 2 TB SSD NVMe and 2 x 12 TB HDD SATA 6Gb/s (configured as 12 TB RAID 1)
2 x USB 2.0 and 2 x USB 3.0	4 x USB 2.0 and 2 x USB 3.0
Monitor: 24" TFT display, vertical resolution 1200 pixels at least	Monitor: 27" TFT display, vertical resolution 1440 pixels at least
	PCIe interface: 2 available PCI Express x8 Gen2 slots for camera interface cards
Microsoft® Windows® 10 x64 Professional or Enterprise, no special customer adapted versions. Windows® 10 version must be (at least) 1607 (build 14393), e.g. Windows® 10 Enterprise LTSB 2016. Microsoft® Windows® 11 x64 Professional or Enterprise, no special customer adapted versions. Windows® 11 version must be (at least) 24H2 (build 26100), e.g. Windows 11 Enterprise LTSC 2024. Recommendation: Windows® 10 resp. Windows® 11 should be updated to the latest build version before installing ZEN. Windows N editions do not support basic media functionality, so that they cannot be used for the ZEN application. Reference: https://learn.microsoft.com/en-us/windows/release-health/release-information https://learn.microsoft.com/en-us/windows/release-health/windows11-release-information The following toolkits and functions require (at least) Windows 10 version 1809 (build 17763), e.g. Windows® 10 Enterprise LTSC 2019: ZEN Deconvolution Toolkit fallback solution: run on CPU. ZEN Toolkit 2D can use CPU and GPU for semantic segmentation and CPU for instance segmentation. For older Windows versions instance segmentation cannot be used. For semantic segmentation only CPU is supported. ZEN Toolkit Bio Applications can use CPU and GPU for semantic segmentation and CPU for instance segmentation. For older Windows versions instance segmentation cannot be used. For semantic segmentation only CPU is supported. Hamamatsu Camera driver. No fallback solution, i.e. Hamamatsu cameras will not work. The following toolkits and functions require (at least) Microsoft® Windows® 10 version 21H2 (build 19044), e.g. Windows® 10 Enterprise LTSC 2021: ZEN Toolkit 2D can use CPU and GPU for instance segmentation trained with arivis Cloud. ZEN Toolkit Bio Applications can use CPU and GPU for instance segmentation trained with arivis Cloud. For more information on the compatibility of Machine Learning and AI Features, see Compatibility of Windows Versions to Machine Learning and AI Features. Processing functions that run on the GPU require NVIDIA driver version 566.03 or higher. Drivers for NVIDIA graphics cards in our workstations should also be downloaded from hp website (not from NVIDIA) e.g. for hp Z8 G5 workstation: https://support.hp.com/us-en/drivers/swdetails/hp-z8-fury-g5-workstation-desktop-pc/2101236624/swItemId/vc-339200-1

For software resp. system operation, the user must be logged on with at least user privileges. For the software installation procedure, the user must be logged on with an account owning local administrator rights.

For specific hardware requirements of microscope systems or software modules please refer to the corresponding system or module description.

See also

• Compatibility of Windows Versions to Machine Learning and AI Features

Without Airyscan 2	With Airyscan 2
HP Z2 G9 Workstation	HP Z8 G5 Workstation
Intel® Core™ i5-12500	Intel® Xeon® W5-3425
64 GB RAM	128 GB RAM
NVIDIA® T1000	NVIDIA® RTX™ A4000

Without Airyscan 2	With Airyscan 2
HP Z8 G5 Workstation	HP Z8 G5 Workstation
Intel® Xeon® W5-3425	Intel® Xeon® W5-3425
64 GB RAM	128 GB RAM
NVIDIA® RTX A1000 8GB NVIDIA® RTX™ A5000 (for Lightfield 4D)	NVIDIA® RTX™ A4000 NVIDIA® RTX™ A5000 (for Lightfield 4D)

For some functionality, you additionally need the software Docker Desktop on your PC to be able to use it. This includes the download and use of dedicated AI models, for example for instance segmentation. You can install Docker Desktop with the ZEISS Microscopy Installer. For details about Docker Desktop, refer to their documentation at https://docs.docker.com/desktop/, and for system requirements see https://docs.docker.com/desktop/install/windows-install/. Also note the following special conditions:

• For Windows 10 Enterprise LTSC 2019 (version 1809), docker version 4.24.2 or lower is required and not provided with the ZEISS Microscopy Installer. To download version 4.24.1, use https://desktop.docker.com/win/main/amd64/123237/Docker%20Desktop%20Installer.exe.
• If you work with Docker on a system with multiple Windows users, always sign out of your Windows account to initiate a shutdown of Docker when you have finished your work. Otherwise the other users may have problems using Docker.
• Docker containers from arivis Cloud are not shared between different Windows user accounts and may need to be re-downloaded to be available to other users.

Docker requires that BIOS-level hardware virtualization support is enabled and can either run with Hyper-V or with WSL2. We recommend using WSL2 if possible. WSL (short for Windows Subsystem for Linux) is a feature of Microsoft Windows that allows you to use of a Linux environment within Windows. For WSL2, the WSL2 feature has to be installed and activated. For more information, see the system requirements linked above and https://docs.docker.com/desktop/features/wsl/. WSL2 provides improvements to file system sharing and boot time, and Docker Desktop uses the dynamic memory allocation feature in WSL2 to improve the resource consumption.

If you do not or cannot use WSL2, the resources allocated to Docker are not automatically managed by Windows and might not be big enough in certain instances. In such a case, you can also adapt the resource allocation manually, see Adapting the Resource Allocation for Docker Desktop Manually. Additionally, Docker Desktop has experimental features that are activated by default, which can lead to an increased resource consumption, for example disk space. Such features can also be deactivated manually, see Deactivating Experimental Docker Features.

Hyper-V is Microsoft's hardware virtualization product which lets you create and run a software version of a computer, called a virtual machine. For Hyper-V, you have to activate Hyper-V and Containers Windows features. Using Hyper-V can negatively affect system performance.

Hyper-V System Performance Disclaimer

If Hyper-V is enabled in Windows, be aware that this might affect the overall PC system performance and, therefore, could lead to longer processing times or to reduced acquisition performance in the software. Enabling the BIOS level hardware virtualization does not influence the system performance and can be left switched on.

Hardware Recommendations:

• ZEISS MidRange Workstation
• 64 GB RAM or more (32 RAM dedicated to Docker Desktop)
• For the use of AI models the recommended hardware configuration is 8GB GPU and 64GB RAM. Only NVIDIA GPUs and the CPU are supported.

1. Start Windows Explorer and navigate to the 'zeiss' user directory.
   
2. Select Pictures and open the Properties menu via right mouse click.
   
3. In the Location tab click Move... and change the destination location to D:\zeiss\pictures.
4. Close the dialog with OK and answer the occurring message with Yes and Replace file at destination.
5. Change the path for the Documents and Desktop folder in the same way.

Note the following:

• The folder D:\zeiss\Desktop must be created manually (via New folder).
• Changes can be undone by clicking Restore Default.

To ensure correct installation, we recommend to perform the following settings:

• Restore point
• Set a restore point for the possibility to roll back the system in the case problems occur. It also is possible to ask the local ZEISS support team to create an image of the main drive of the PC before the security software is installed and setup by the customers IT department.
• Lower security rules
• Set the security rules from 'high' to 'low'. Refer to the respective operating instructions of your security software on how to set the security rules.
• Disable security software
• In rare cases, you may need to disable the security software completely. Make sure that you enable the security software after installation. Refer to the respective operating instructions of your security software on whether to enable or disable the security software.

To ensure the optimal operation on Windows, we recommend you to perform the following settings after the installation:

• Exclude program files from virus scanning
• Exclude the following files from virus scanning. Refer to the respective operating instructions of your security software on how to exclude files from virus scanning.
• ZEN.exe
• ZENService.exe
• ZISProtocolServer.exe
• MTBconfig.exe
• Configuration tool.exe
• AimApplication.exe
• CZCanCheck.exe
• CZCansrv.exe
• System_Maintenance_Tool.exe
• Exclude specific file extensions from virus scanning
  Exclude files with the following file extensions from virus scanning. Refer to the respective operating instructions of your security software on how to exclude file extensions from virus scanning.
• *.czi
• *.zvi
• *.zishm
• *.lsm
• *.zmbi
• Exclude ZEN specific folders from virus scanning
  Under Help > About ZEN > Show ZEN Information > Folders you can see the program specific folders for ZEN. Refer to the respective operating instructions of your security software on how to exclude folders from virus scanning.

To ensure correct operation of the software it is necessary to ensure that the security software on your computer is not blocking the program. For full functionality you should have made ​​the following settings:

• You have disabled the security software during installation or reduced the security settings.
• You have excluded the entire application, the defined paths or relevant files from virus scanning.

 

In case your ZeissPy installation is failing due to an Ordinal242/MKL-load-failed error, the reason might be that you have some 3rd-Party application installed which modified the System32 folder. During the installation, a warning message will be displayed and inform you about dlls that are in the System32 folder. For a potential solution, take the following steps:

1. Remove files from the System32 folder.
2. Set a new environment variable

In case you run into import or runtime issues in the context of externally trained neural networks, go to https://pypi.org/project/czmodel/ for information on model and compatibility requirements.