ZEN 3.5 (Blue Edition) - Installation Guide

Installation Guide
ZEISS ZEN 3.5 (blue edition)

ZEISS ZEN 3.5 (blue edition)
Original Manual
Carl Zeiss Microscopy GmbH

Carl-Zeiss-Promenade 10
07745 Jena
Germany
microscopy@zeiss.com
www.zeiss.com/microscopy
Carl Zeiss Microscopy GmbH

ZEISS Group
Kistlerhofstr. 75
81379 München
Document Name: ZEISS ZEN 3.5 (blue edition) Installation Guide

Revision: 1
Language: en-US
Effective from: 10/2021
© 2021 Without the prior written consent of ZEISS, this document or any part of it must neither be translated nor
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Content ZEISS
Content
1 System Requirements .................................................................... 4
1.1 ZEISS Microscopy Software......................................................................... 4

1.2 LSM 900 .................................................................................................... 4
1.3 LSM 980 .................................................................................................... 5
1.4 LSM 800 .................................................................................................... 5
2 Changes on the operation system ................................................. 7
3 How to separate operating system and user data ......................... 8
3.1 Setting up storage locations ....................................................................... 8

3.2 Moving default directories.......................................................................... 10
4 Configure security software .......................................................... 12
4.1 Before installation ...................................................................................... 12

4.2 After installation......................................................................................... 12
4.2.1 Default folders............................................................................ 13
4.2.2 Temporary files........................................................................... 14
4.2.3 System specific folders................................................................ 14
4.3 Summary.................................................................................................... 14
5 Installing ZEN ................................................................................ 16
6 Installing Remote API Client (for SEM systems) ............................. 20
7 Installing MATLAB......................................................................... 22
8 Sharing a folder for Direct Processing ........................................... 26
8.1 Looking up the IP address of your computer .............................................. 30

8.2 Connecting computers via cable ................................................................. 31
9 Compatible cameras ...................................................................... 32
10 Troubleshooting ............................................................................ 33
10.1 Fixing a failing ZeissPy installation (Ordinal242/MKL-load-failed error) ........ 33

10.1.1 Removing files from the System32 folder.................................... 33
10.1.2 Setting a new environment variable............................................ 33
10.2 Fixing runtime or compatibility issues for externally trained neural net-
works......................................................................................................... 33
Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 3

1 System Requirements | 1.1 ZEISS Microscopy Software ZEISS
1 System Requirements
1.1 ZEISS Microscopy Software
Minimum System Requirements Recommended system requirements

Intel® CPU with 6 cores, 3.3 GHz (e.g. Intel® Intel® Xeon® CPU with 4 cores, 3.8 GHz
Core® i5-10600 CPU) (e.g. Intel® Xeon® Gold 5222)
16 GB RAM 64 GB RAM
Graphics adapter with support for resolutions Graphics adapter with support for resolutions
of at least 1920 x 1200, 32 Bit true color, Di- of 3840 x 2160 Pixel (“4K”), 32 Bit true color,
rectX® 12.0 or higher (e.g. integrated Intel® DirectX® 12.0 (or higher), OpenGL® 4.5 (or
UHD Graphics 630 or dedicated graphic card higher) (e.g. dedicated graphic card NVIDIA
NVIDIA Quadro P1000 4GB) Quadro RTX4000 8 GB)
Hard drive Hard drive

1 x 512 GB SSD NVMe and 1 x 8 TB HDD 1 x 512 GB SSD NVMe and 2 x 6 TB HDD
SATA 6Gb/s SATA 6Gb/s (configured as 6 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 Monitor: 27" TFT display, vertical resolution
1200 pixels at least 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 ver-

sions.
Windows N editions do not support basic media functionality, so that they cannot be used for
the ZEN application.
The user must be logged on with at least user privileges. For the software installation proce-
dure local administrator rights are required.
For specific hardware requirements of microscope systems or software modules please refer to
the corresponding system or module description.
1.2 LSM 900
Without Airyscan 2 With Airyscan 2

Intel® Core i5-6500 4-core 3,2 GHz Intel® Xeon® CPU with 4 cores
Microsoft® Windows® 10
HP Z240 or newer HP Z6G4 (highly recommended with Airyscan

2 Multiplex Mode)
32 GB RAM 64 GB RAM
NVIDIA Quadro P4000 (highly recommended

with Airyscan 2 Multiplex Mode)

1 System Requirements | 1.3 LSM 980 ZEISS
1.3 LSM 980
Without Airyscan 2 or ELYRA With Airyscan 2 or ELYRA

Intel® Xeon® CPU with 4 cores Intel® Xeon® CPU with 8 cores
HP Z840 or Z6G4
32 GB RAM 64 GB RAM (96GB recommended)
4 or 8TB hard disk space configured as RAID 10
Microsoft® Windows® 10
NVIDIA Quadro P400 (only for monitors up to NVIDIA Quadro P4000 (or M4000 upgrade)
27")
RAID 10 HDD
10 Gbit Ethernet Adapter recommended
1.4 LSM 800
Minimum System Requirements Recommended System Requirements

Intel® Core i5-6500 4-core 3,2 GHz Intel® Xeon® E5-2643 4-Core 3.0 GHz
Intel® C236 chipset Intel® C602 chipset
16 GB DDR3-RAM 64 GB DDR3-RAM
Graphics interface PCIe Express x16
Graphics adapter NVIDIA CUDA capable NVIDIA CUDA capable graphics card support-
graphics card supporting resolutions up to ing resolutions up to 4K, e.g. NVIDIA Quadro
4K, e.g NVIDIA Quadro K2200 , 32-bit true M4000, 32-bit true color, DirectX 11.0 or
color, DirectX 11.0 or higher higher
Monitor 27" TFT , vertical resolution 1200 Monitor 30" TFT, vertical resolution 1440 pix-
pixels at least els at least
Hard disk Hard disk

1 x 128 GB SSD and 1 x x 256 GB SSD and
1 x 4 TB SATA 3.0 Gbit/s4 4 x 2 TB SATA2 (configured as 4 TB RAID 10
DVD-ROM DL drive (compatible with dual hard drive)
layer media) DVD-ROM DL drive (compatible with dual
layer media)
2x free PCIe x4 2x free PCI Express x8 Gen2
Trigger-Board and Signal Distribution Box
1 x FireWire IEEE 1394a interface 2 x FireWire IEEE 1394a interface
2 x serial interface (COM1 – COM2)
4 x USB 2.0, 2 x USB 3.0 interfaces
Microsoft® Windows® 7 SP1 x64 Professional or Ultimate or

Microsoft® Windows® 10 x64 Enterprise (not for Trigger board)
No special customer adapted versions

1 System Requirements | 1.4 LSM 800 ZEISS
Minimum System Requirements Recommended System Requirements

The user must be logged on as a member of the local 'User' group
For the software installation procedure local administrator rights are required
The hardware requirements of modules can be higher

2 Changes on the operation system ZEISS
2 Changes on the operation system

NOTICE
Installation of software, hardware drivers, changes to operating system settings or other sys-
tem interference beyond the actions needed to operate the software are always in the respon-
sibility of the customer, because the potential impact can not be estimated.
The following modifications have, in our experience, no effects on the functionality of

the PC system:
§ Network integration possible
§ 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 re-
quirements.
Recommended settings
Windows 10
§ When installing updates under settings select 'Current Branch for Business'.
Effects of following modifications can not 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 Sys-
tems
§ Storage of data on network drives by redirecting folder structures (e.g. there can occur perfor-
mance problems in case of Fast Acquisition systems or limitation of the available data storage
capacity (disk quota))
Info
If problems occur, the system can be restored to the state of delivery by a ZEISS service techni-
cian.

3 How to separate operating system and user data | 3.1 Setting up storage locations ZEISS
3 How to separate operating system and user data

The following guide shows how to move the standard folders for documents, images and the
desktop from drive C:\ (Operating System) to drive D:\ (User Data). This prevents images and
documents from being stored on the small system drive. The access rights and restrictions are re-
tained. If additional Windows user accounts are created, it is recommended to use this procedure
for them as well.
§ Use of drive C: for operating system, programs, swap file (pagefile.sys, SWAP)
§ Use of drive D: for user data (images, documents,...)
The description is exemplary for the user 'zeiss'. The settings are already pre-configured ex works
for the Workstation Premium (Order number 410203-9911-000 ) and Workstation Compact
(410201-9911-000)
3.1 Setting up storage locations
1. In the Windows Start menu go to Settings > System > Storage > Save locations.

3 How to separate operating system and user data | 3.1 Setting up storage locations ZEISS
2. Change the settings for New documents and New photos and videos to DATA (D:) and
click Apply.

3 How to separate operating system and user data | 3.2 Moving default directories ZEISS
3.2 Moving default directories
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\pic-
tures.
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.

3 How to separate operating system and user data | 3.2 Moving default directories ZEISS
§ The resulting directories in the software are:

4 Configure security software | 4.1 Before installation ZEISS
4 Configure security software

The following section explains how to configure your security software for installation and opti-
mum operation of the software properly.
Info
The term security software combines all programs which protect your computer from viruses,
unwanted interventions, etc.. This includes virus scanners, firewalls and intrusion detection sys-
tems. If you do not adapt the security settings there can be problems while installing or run-
ning the software. The following topics will show you how to avoid problems with the security
software and adapt the settings correctly.
4.1 Before installation
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 be-
fore 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 en-
able the security software after installation. Refer to the respective operating instructions of your
security software on whether to enable or disable the security software.
4.2 After installation
To ensure the optimal operation on Windows, we recommend you to perform the following set-
tings after the installation:
§ Exclude ZEN 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 / ZENCore.exe
– ZENService.exe
– ZISProtocolServer.exe
– MTBconfig.exe
– Configuration tool.exe
– AimApplication.exe
– CZCanCheck.exe
– CZCansrv.exe
– System_Maintenance_Tool.exe
§ Exclude ZEN specific file extensions from virus scanning
Exclude files with the following file extensions from virus scanning. Refer to the respective op-
erating instructions of your security software on how to exclude file extensions from virus
scanning.
– *.czi
– *.zvi

4 Configure security software | 4.2 After installation ZEISS
– *.zishm
– *.lsm
– *.zmbi
§ Exclude ZEN specific folders from virus scanning
Under About ZEN ... > Show ZEN Information > Folders you can see the program specific
folders. Refer to the respective operating instructions of your security software on how to ex-
clude folders from virus scanning.
Fig. 1: Program specific folders
4.2.1 Default folders
In the following table you can see the folders to which the captured images will be stored per de-
fault.
Operating system Folder / path

Windows 10: Pictures and
%USERPROFILE%\Pictures and
C:\Users\{user name}\Pictures
Change default ZEN image folder

Under File | Export/Import | Export or under File | Save as change the folder you want to store
your images into.
Change default folder for automatic image storage and continuous image acquisition
(camera streaming)
Under Tools | Options | Saving | Auto Save Path set your desired path/folder.
Change default folder for images on your operating system

§ In Windows 10 in the context menu of Pictures.

4 Configure security software | 4.3 Summary ZEISS
4.2.2 Temporary files

Windows 10 %TEMP% or
%LOCALAPPDATA%\temp or
C:\Users\{user name}\AppData\Local\Temp
Change default folder for temp files

1. Define an appropriate path for the TEMP environment variable (user context).
2. Define the environment variable SWAP indicating a corresponding path.
For Windows 10 this has the following paths or folders that you must exclude from virus scan-
ning:

Windows 10 (en) C:\Users\{user name}\Pictures
Windows 10 (en) C:\Users\{user name}\AppData\Local\Temp
Windows 10 (en) %TEMP%
Windows 10 (en) %SWAP%
4.2.3 System specific folders
If you are using a ZEISS PC system, the location of your images is predefined. The table below
show the system specific folders for the following ZEISS Microscopy High-End and Mid-Range
work stations:
§ Microscopy Workstation High-End GPGPU - 410203-9910-000

§ Microscopy Workstation HighEnd - 410203-9909-000
§ Microscopy High-End Workstation - 410203-9908-000
§ Microscopy Workstation Mid-Range - 410202-9902-000
§ Microscopy Mid-Range Workstation - 410202-9901-000
§ Microscopy Workstation Compact - 410201-99010-000
§ User PC Compact Smartpoof - 410211-9002-000
Operating system Folder / Path

Windows 10 D:\Users\{user name}}\Pictures
Default: %SystemDrive%\Users
Modified: D:\Users
4.3 Summary
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 fol-
lowing settings:
§ You have disabled the security software during installation or reduced the security settings.

4 Configure security software | 4.3 Summary ZEISS
§ You have excluded the entire application, the defined paths or relevant files from virus scan-
ning.

5 Installing ZEN ZEISS
5 Installing ZEN
NOTICE
4 Do not install an older ZEN version over a newer ZEN version.
4 If ZEN is already installed on your PC, during installation the current version will be unin-
stalled first.
4 If the system requests a restart at the beginning of the installation (depends on your PC
configuration) you need to agree. Otherwise the installation will not continue.
4 The system requests a restart at the end of the installation. This restart is required for the
successful camera driver installation.
4 In case of installing ZEN on a SEM system, make sure that SmartSEM is not running when
installing ZEN.
Prerequisite ü You have read the chapter Configure security software attentively.
ü You have opened the ZEISS Microscopy Installer with admin rights.
ü Your system is connected to the Internet.
ü You have selected (default setting) the online installation, see ZEISS Microscopy Installer
manual.
1. Open the Install tab.
2. On the left, activate ZEN (blue edition) with the respective version number.
à The available components and tools for installation are displayed on the right side.
3. On the right side, activate all components you want to install.
4. Activate I agree to the Terms and Conditions of the selected software.
5. Click Install.
à The language selection dialog is displayed.
6. Select the installation language from the dropdown list and click OK.
à Depending on your system configurations, additional pre-installation steps can be neces-
sary before you can continue installing the software. If the message dialog appears
which tells you to install missing requirements, we recommend to install all the listed re-
quirements and reboot your computer, when asked.

à After the installation of all required system components and after the download of all
necessary files, the ZEN InstallShield Wizard opens.
7. Click Next to start with the installation.

à The License Agreement dialog is displayed.
8. Select I accept the terms in the license agreement and click Next.
à The Destination Folder dialog is displayed. Here you can select an alternative installa-
tion folder. We recommend to leave the default folder settings untouched.
9. Click Next to install the software to the default folder or click Change to select a different
folder.

à The Custom Setup dialog window is displayed.
10. You can leave the default settings and click Next. If you do not want to install a certain
feature, simply deactivate it in the dropdown menu.
NOTICE! If you install ZEN on a SEM system, deactivate the feature MTB 2011.
à The Local ZEISS Apeer Prerequisite dialog is displayed.
11. Read the information and decide if you want to use the local Apeer functionality and
download the necessary Docker tool.
12. Click Next.
à The Ready to Install the Program dialog is displayed.
13. Click Install.
à The installation dialog is displayed. The software will be installed now.
à During installation several messages can appear. Also the 3rd party Python Tools will
be installed, which needs some extra time.
If the 3rd party Python Tools are not installed, the machine learning based Intellesis
modules will not work. This also includes the use of their functionality in other parts of
the software, like the neural networks in certain BioApps.
14. Click I accept the agreement and click Next.
15. Read the Information message attentively before you continue with the installation and
click Next.
à The Destination Location dialog is displayed.
16. We recommend to leave the default folder settings untouched and click Next.
à The Select Components dialog is displayed.
17. Select GPU-disabled, if you do not have a GPU or your GPU does not fulfill all minimum re-
quirements (see next step).
18. Select GPU-enabled, if your system fulfills the following requirements:
à NVIDIA GPU with CUDA Compute Capability 3.0 or higher. You can find a list of sup-
ported cards under https://developer.nvidia.com/cuda-gpus.
à Make sure that the latest drivers are installed. You can download them under https://
www.nvidia.de/Download/index.aspx.

à Alternatively, the install medium is additionally shipped with a set of ISV-certified NVIDIA
drivers located under Other\HP Drivers.
19. Click Install to continue with the 3rd party software installation.
à After the installation the dialog for completing the ZEISS Python setup wizard is dis-
played.
20. Click Finish.
à The installation of the ZEN software continues.
à After the installation, the InstallShield Wizard Completed dialog is displayed.
21. Click Copy License Files to copy the license files automatically from the supplied USB stick
to your computer.
22. Exit the Copy License File dialog first and then click Finish.
23. Connect the included dongle to a free USB port.
24. Close the ZEISS Microscopy Installer and restart your PC to complete the installation.
After the restart of your computer the installation was successful. Start the software by clicking on
the ZEN blue icon on your desktop.
If you install ZEN on a computer for a SEM system, continue with the next chapter.

6 Installing Remote API Client (for SEM systems) ZEISS
6 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.
Prerequisite ü You have read the chapter Configure security software [} 12] attentively.
manual.
ü You have closed SmartSEM and EM Server.
2. Activate ZEN (blue edition) > Tools and accessories > SmartSEM Remote API.
4. Click Install.
à The download starts. The following dialog is displayed:

6 Installing Remote API Client (for SEM systems) ZEISS
à 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 instal-
lation 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.

7 Installing MATLAB ZEISS
7 Installing MATLAB
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:
Prerequisite ü You have read the chapter Configure Security Software attentively.
manual.
2. On the left, activate ZEN (blue edition) with the respective version number.
à The available components and tools for installation are displayed on the right side.
3. On the right side under Third Party Tools, activate MATLAB Runtime.
5. Click Install.
à The download of the necessary files starts.
à After the download, aWinZip Self-Extractor window opens and the files are extracted
à After the extraction the MATLAB Compiler Runtime Installer opens.
6. Click Next.

à The License Agreement dialog is displayed.
7. Accept the License Agreement by activating Yes.

8. Click Next.
à The Folder Selection dialog is displayed.
9. Click Next to install to default folder.

à The Confirmation dialog is displayed.
10. Click Install.

à The software is installed and the progress is displayed in the installation dialog.

à After installation the Installation Complete dialog is displayed.
11. Click Finish.

You have successfully installed the MATLAB Runtime that is necessary for the working with the
CAT module.

8 Sharing a folder for Direct Processing | ZEISS
8 Sharing a folder for Direct Processing

This step by step guide gives instructions on how to create a shared folder for the Direct Process-
ing module in ZEN (blue edition).
You need an imaging system with its workstation (called acquisition computer) and for process-
ing you need a high-end workstation (called processing computer) with a P6000 card (M/P4000
or M6000 works too) running the newest NVIDIA driver. Both computers need the software ver-
sion ZEN (blue edition) 3.0 or higher.
Computer connection
The processing computer must be connected to the acquisition computer via ethernet connection.
It works best to have both workstations equipped with a 10 GB ethernet card. A 1GB Ethernet is
fine as well, just make sure to not create very large images and deactivate Follow acquisition in
ZEN when acquiring larger images. For details on how to connect your computer in a network,
ask your local IT department. For some basic information, see also Connecting computers via ca-
ble [} 31].
IP Addresses
This is not strictly necessary, but knowing the IP Addresses is the safest way to troubleshoot net-
working issues, so we recommend to check this in any case. It is easiest to network the comput-
ers if both have the same login credentials, e.g. Username = ZEISS, password = zeiss. The comput-
ers can only network with each other if a password is set for both logins. For a description of how
to look up the IP address of your PC, see Looking up the IP address of your computer [} 30].
Also note down the computer names. You can find those when you right click the This PC in the
explorer and select Properties
Creating a shared folder on the processing computer

You have to make your processing PC discoverable in your network and create a shared folder.
Prerequisite ü You are on the processing computer.

1. Click on Windows start menu > Settings > Network & Internet > Status > Network
and Sharing Center.
à The Network and Sharing Center opens.

2. Click Change advanced sharing settings.

à The Advanced sharing settings window opens.
3. Turn on network discovery for your network.

4. Click Save changes.
5. Open the Windows Explorer and create a folder where both data and communication be-
tween both ZENs should happen, e.g. “D:\direct processing”.
6. Right click on the folder and select Properties.
7. Go to the Sharing tab.
8. Click Advanced Sharing.

à The Advanced Sharing dialog opens.
9. Activate Share this folder.

10. Click Permissions.
11. The Permissions dialog opens.
12. To give access to specific groups or people, click Add.

à The Select Users, Computers, Service Accounts, or Groups dialog opens.
13. If you want to change which accounts you can add, click Object Types to open a dialog to
select different types.
14. If you want to change the (network) location, click Locations to open a dialog to select the
location.
15. In the text field, enter the user or group name you want to give access to and click Check
Names.
à If the name exists, it is verified. In case there is no (exact) match, or in case there are mul-
tiple matches, a dialog opens where you can refine your search or select the right user/
group.
16. Click OK.
à The Select Users, Computers, Service Accounts, or Groups dialog closes and the
user/group is added to the list on the Permissions dialog.
17. Select the user(s)/group(s) and activate the checkboxes for the permissions you want to give
them to this folder.
18. Click OK to confirm all changes in all dialogs.
You have created a shared folder on the processing computer. You can now setup the access to
the folder on the acquisition computer.
Accessing the shared folder from the acquisition computer

On the acquisition computer, you need to map the folder from the processing computer to a drive
letter.
Note: You could also do this by directly accessing the folder via the IP address, however, it is bet-
ter to use the Windows mapping function as this enables some caching mechanisms which make
the connection more reliable.
Prerequisite ü You are on the acquisition computer.

1. In Windows Explorer, open the Network location.
2. Select the processing computer. Here you might need the computer name you noted down
before.
3. Select the shared folder of the processing computer.
4. On the top of the Windows explorer, click Easy access and select Map as drive from the
dropdown menu.
à The Map Network Drive dialog opens.
5. Select the respective Drive for the Folder.
à A log in screen opens.

8 Sharing a folder for Direct Processing | 8.1 Looking up the IP address of your computer ZEISS
6. Enter the credentials of the processing computer.
7. Click OK.
8. Click Finish.
à The folder is mapped to your acquisition PC. The result will look something like this:
You are now ready to setup the connection of the two computers in ZEN. Please refer to the re-
spective chapter in the software manual or the online help, which is accessible by pressing the F1
button.
8.1 Looking up the IP address of your computer
1. In the Windows search, enter cmd.

2. Select Command Prompt.

8 Sharing a folder for Direct Processing | 8.2 Connecting computers via cable ZEISS
à The Command Prompt window opens.

3. Type in ipconfig/all and press Enter.
You can now see information for the network configuration of your computer. There you can
look up the IP address of your computer. You have to make sure to select the correct Ethernet
port, as ZEISS workstations usually have at least two. If only one is connected, this is the one
which shows an IP address.
8.2 Connecting computers via cable
We recommend connecting the PCs in a network by using i.e. a rooter. In case a rooter cannot be
used and two PCs are connected via a cable, consider the following remarks:
1. Establish a network by cable.

à By default, a network/connection is established.
2. As a test, check the IPs of the computers and ping each other.
3. In case this fails, check the ethernet adapter and enable DHCP. Also check firewall notifica-
tions/settings.
à Ports used by ZEN are open by default, but could be blocked by various reasons (IT, Win-
dows, firewall).
4. If a port is blocked. try to set another port in the ZEN options for Direct Processing (see also
the help for ZEN).
5. You can also test more than one ethernet adapter by pinging the PCs.

9 Compatible cameras ZEISS
9 Compatible cameras
The table below reveals, which cameras are compatible to the ZEN (blue edition) software.
Compatible ZEISS Axiocams
Camera Connection
Axiocam 105 color USB 3.0
Axiocam 202 mono USB 3.0
Axiocam 208 color USB 3.0
Axiocam 305 color / mono USB 3.0
Axiocam 702 mono USB 3.0
AxioCam MRc/MRm Rev. 3 FireWire A
AxioCam MRc5 FireWire A
AxioCam HRc/HRm Rev. 3 FireWire A
AxioCam ICc1 FireWire B
AxioCam ICc5 FireWire B
Axiocam ERc5s Rev. 2 USB 2.0
Other, compatible cameras
Camera Notice
PrimoStar HD USB only, not via network
connection
Primovert HDcam USB only, not via network

connection
Andor: iXon3 888 Ultra/Live USB 3.0, iXon3 897 Ultra/Live USB
3.0
Hamamatsu: Orca Flash 4.0 V3 CL/USB3.0, Orca Flash LT

USB3.0, Orca Fusion, Orca Fusion BT, Image EM X2 512, Image
EM X2-1K
Roper Photometrics: Evolve 512, Evolve 512 Delta, 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

10 Troubleshooting | 10.1 Fixing a failing ZeissPy installation (Ordinal242/MKL-load-failed error) ZEISS
10 Troubleshooting
This chapter contains information on how to tackle common problems while installing ZEN (blue
edition).
10.1 Fixing a failing ZeissPy installation (Ordinal242/MKL-load-failed error)
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 [} 33].
2. Set a new environment variable [} 33]
10.1.1 Removing files from the System32 folder
1. Open the Windows File Explorer.

2. Go to C:\Windows\System32.
3. Search for any MKL- or libiomp related files and rename them by adding a .bak to the file-
name.
4. Observe if any other software application breaks.
5. If an application fails, try to move the DLL files alongside the .exe of the breaking software
to another folder. If it works again, you can keep things in the moved state.
6. Check whether the error is gone and ZeissPy can be installed.
If this does not solve the problem, you can also try Setting a new environment variable [} 33].
10.1.2 Setting a new environment variable
1. In the Windows search, enter Environment Variable.

2. Click the search entry Edit the system environment variables.
à The System Properties dialog opens.
3. On the Advanced tab, click Environment Variables.
à The Environment Variables dialog opens.
4. Click New.
5. In the New User Variable dialog, set the Variable name to
CONDA_DLL_SEARCH_MODIFICATION_ENABLE and for Variable value enter 1.
6. Click Ok to close the New User Variable dialog.
7. Click Ok to close the Environment Variables dialog.
8. Click Ok to close the System Properties dialog.
9. Check whether the error is gone and ZeissPy can be installed.
10.2 Fixing runtime or compatibility issues for externally trained neural networks
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.

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1
Modifications reserved.
Carl Zeiss Microscopy GmbH phone: +49 3641 64 3161

Carl-Zeiss-Promenade 10 fax: +49 3641 64 3439
07745 Jena info.microscopy@zeiss.com
Germany www.zeiss.com/microscopy

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Installation Guide

ZEISS ZEN 3.5 (blue edition)

Carl Zeiss Microscopy GmbH

Carl Zeiss Microscopy GmbH

Document Name: ZEISS ZEN 3.5 (blue edition) Installation Guide

1.1 ZEISS Microscopy Software......................................................................... 4

2 Changes on the operation system ................................................. 7

3 How to separate operating system and user data ......................... 8

3.1 Setting up storage locations ....................................................................... 8

4 Configure security software .......................................................... 12

4.1 Before installation ...................................................................................... 12

5 Installing ZEN ................................................................................ 16

6 Installing Remote API Client (for SEM systems) ............................. 20

8 Sharing a folder for Direct Processing ........................................... 26

8.1 Looking up the IP address of your computer .............................................. 30

9 Compatible cameras ...................................................................... 32

10.1 Fixing a failing ZeissPy installation (Ordinal242/MKL-load-failed error) ........ 33

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 3

Minimum System Requirements Recommended system requirements

Hard drive Hard drive

PCIe interface: 2 available PCI Express x8

Microsoft® Windows® 10 x64 Professional or Enterprise, no special customer adapted ver-

1.2 LSM 900

Without Airyscan 2 With Airyscan 2

HP Z240 or newer HP Z6G4 (highly recommended with Airyscan

NVIDIA Quadro P4000 (highly recommended

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 4

1.3 LSM 980

Without Airyscan 2 or ELYRA With Airyscan 2 or ELYRA

32 GB RAM 64 GB RAM (96GB recommended)

4 or 8TB hard disk space configured as RAID 10

10 Gbit Ethernet Adapter recommended

1.4 LSM 800

Minimum System Requirements Recommended System Requirements

Intel® C236 chipset Intel® C602 chipset

Graphics interface PCIe Express x16

Hard disk Hard disk

2x free PCIe x4 2x free PCI Express x8 Gen2

Trigger-Board and Signal Distribution Box

1 x FireWire IEEE 1394a interface 2 x FireWire IEEE 1394a interface

2 x serial interface (COM1 – COM2)

4 x USB 2.0, 2 x USB 3.0 interfaces

Microsoft® Windows® 7 SP1 x64 Professional or Ultimate or

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 5

Minimum System Requirements Recommended System Requirements

The hardware requirements of modules can be higher

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 6

2 Changes on the operation system

The following modifications have, in our experience, no effects on the functionality of

Effects of following modifications can not be estimated:

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 7

3 How to separate operating system and user data

3.1 Setting up storage locations

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 8

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 9

3.2 Moving default directories

1. Start Windows Explorer and navigate to the 'zeiss' user directory.

§ The folder D:\zeiss\Desktop must be created manually (via New folder).

Installation Guide ZEISS ZEN 3.5 (blue edition) | en-US | Rev.1 10