Installation GuideZEN 2.5 (blue edition) -...

Installation Guide

ZEN 2.5 (blue edition)

2

Carl Zeiss Microscopy GmbH

Carl-Zeiss-Promenade 10

07745 Jena, Germany

[email protected]

www.zeiss.com/microscopy


Königsallee 9-21

37081 Göttingen

Germany

Effective from: 04 / 2018

© Jena 2018 by Carl Zeiss Microscopy GmbH - all rights reserved

This document or any part of it must not be translated, reproduced, or transmitted in any form or by any means, electronic or mechanical, including

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The use of general descriptive names, registered names, trademarks, etc. in this document does not imply, even in the absence of a specific

statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Software programs will

fully remain the property of ZEISS. No program, documentation, or subsequent upgrade thereof may be disclosed to any third party, unless prior

written consent of ZEISS has been procured to do so, nor may be copied or otherwise duplicated, even for the customer's internal needs, apart from

a single back-up copy for safety purposes.

ZEISS reserves the right to make modifications to this document without notice.

Content

Installation Guide ZEN 2.5 (blue edition) | V1.0 en 04/2018 3

1 System Requirements ZEN (Widefield Systems) 4

1.1 ZEN lite 4

1.2 ZEN pro/desk 4

1.3 ZEN system 5

2 System Requirements LSM 800 7

2.1 ZEN lite 7

2.2 ZEN system 7

3 System Requirements CAT Module 9

3.1 ZEN SEM (SEM systems) 9

3.2 ZEN system / pro (LM system) 9

4 Changes on the operation system 11

5 Configure security software 13

5.1 Before installation 13

5.2 After installation 135.2.1 Default folders 155.2.2 Temporary files 155.2.3 System specific folders 16

5.3 Summary 17

6 Installing ZEN 18

7 Installing the Remote API Client (SEM systems) 22

8 Installing Matlab 26

9 Compatible cameras 30

1 System Requirements ZEN (Widefield Systems) | 1.1 ZEN lite

4 Installation Guide ZEN 2.5 (blue edition) | V1.0 en 04/2018

1 System Requirements ZEN (WidefieldSystems)System Requirements ZEN (Widefield Systems) |

1.1 ZEN lite

Minimum System Requirements

Intel® Core™ i5-4670 4-Core 3.0 GHz

Intel® Q87 chipset

4 GB DDR3-RAM

Graphics Adapter 1920 x 1200 Resolution, 32-bit true color, 4GB RAM, DirectX11.0 or higher

Monitor 20" TFT 1600 x 1200

Hard disk 250 GB SATA 3.0 Gbit/sDVD-ROM DL drive (compatible with dual layer media)

1 x FireWire IEEE 1394a interface

2 x USB 2.0, 2 x USB 3.0 interface

Microsoft® Windows® 7 SP1 x64 Professional or Ultimate or Microsoft® Windows® 10 x64 Enterprise (not for Trigger board)No special customer adapted versions

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

System Requirements ZEN (Widefield Systems) |

1.2 ZEN pro/desk

Minimum System Requirements Recommended SystemRequirements

Intel® Core™ i5-4670 4-Core 3.0GHz

Intel® Xeon® E5-2643 4-Core 3.0GHz

Intel® Q87 Chipset Intel® C602 Chipset

8 GB DDR3-RAM 16 GB DDR3-RAM

Graphics interface PCIe x16

1 System Requirements ZEN (Widefield Systems) | 1.3 ZEN system


Minimum System Requirements Recommended SystemRequirements

Graphics adapter 1920 x 1200resolution, 32 bit true color, DirectX11.0 or higher

NVIDIA CUDA capable graphics cardsupporting resolutions up to 4K , 32bit true color, DirectX 11.0 or higher


Hard disk 250 GB SATA 3.0 Gbit/s

DVD-ROM DL drive (compatible withdual layer media)

Hard disk1 x 128 GB SSD and2 x 2TB SATA2 (configured as 2 TBRAID 1 hard drive)

1x free PCI Express x8 Gen2 2x free PCI Express x8 Gen2

2x FireWire IEEE 1394a interface card

2 x serial interface (COM1 and COM2)

2 x USB 2.0, 2 x USB 3.0 interface 4 x USB 2.0, 2 x USB 3.0 interface





System Requirements ZEN (Widefield Systems) |

1.3 ZEN system

Minimum SystemRequirements

Recommended System Requirements

Intel® Xeon® E5-2643 4-Core 3.0 GHz

Intel® C602 chipset


Graphics interface PCIe Express x16

1 System Requirements ZEN (Widefield Systems) | 1.3 ZEN system




Graphics adapter NVIDIACUDA capable graphicscard supportingresolutions up to 4K, e.gNVIDIA Quadro K2200 ,32-bit true color, DirectX11.0 or higher

NVIDIA CUDA capable graphics card supportingresolutions up to 4K, e.g. NVIDIA Quadro M4000,32-bit true color, DirectX 11.0 or higher

Monitor 24" TFT ,vertical resolution 1200pixels at least

Monitor 30" TFT, vertical resolution 1440 pixels atleast

Hard disk 1 x 128 GB SSD and 2 x 2 TB SATA 3.0 Gbit/s(configured as 2 TB RAID1 hard drive)DVD-ROM DL drive(compatible with duallayer media)

Hard disk 1 x x 256 GB SSD and4 x 2 TB SATA2 (configured as 4 TB RAID 10 harddrive)DVD-ROM DL drive (compatible with dual layermedia)

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





2 System Requirements LSM 800 | 2.1 ZEN lite


2 System Requirements LSM 800System Requirements LSM 800 |

2.1 ZEN lite

Minimum System Requirements

Intel® Core™ i5-4670 4-Core 3.0 GHz

Intel® Q87 chipset

4 GB DDR3-RAM

Graphics Adapter 1920 x 1200 Resolution, 32-bit true color, 4GB RAM, DirectX11.0 or higher


Hard disk 250 GB SATA 3.0 Gbit/sDVD-ROM DL drive (compatible with dual layer media)

1 x FireWire IEEE 1394a interface

2 x USB 2.0, 2 x USB 3.0 interface





System Requirements LSM 800 |

2.2 ZEN system



Intel® Xeon® E5-2643 4-Core 3.0 GHz

Intel® C602 chipset


Graphics interface PCIe Express x16

2 System Requirements LSM 800 | 2.2 ZEN system




Graphics adapter NVIDIACUDA capable graphicscard supportingresolutions up to 4K, e.gNVIDIA Quadro K2200 ,32-bit true color, DirectX11.0 or higher

NVIDIA CUDA capable graphics card supportingresolutions up to 4K, e.g. NVIDIA Quadro M4000,32-bit true color, DirectX 11.0 or higher

Monitor 24" TFT ,vertical resolution 1200pixels at least

Monitor 30" TFT, vertical resolution 1440 pixels atleast

Hard disk 1 x 128 GB SSD and 2 x 2 TB SATA 3.0 Gbit/s(configured as 2 TB RAID1 hard drive)DVD-ROM DL drive(compatible with duallayer media)

Hard disk 1 x x 256 GB SSD and4 x 2 TB SATA2 (configured as 4 TB RAID 10 harddrive)DVD-ROM DL drive (compatible with dual layermedia)

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





3 System Requirements CAT Module | 3.1 ZEN SEM (SEM systems)


3 System Requirements CAT ModuleSystem Requirements CAT Module |

3.1 ZEN SEM (SEM systems)

System Requirements

SEM Imaging PC, Core i5, 1394b, SSD

Graphics card: AMD FirePro 3D V4900, 1GB DDR5

RAM: 32 GB (4x 8GB), DDR3-1600

Harddisk:

1st drive: SSD Sandisk X210, 128 GB

2nd drive: Seagate 1000 GB 7k SATA3

Chassis: Chenbro PC617 based (closed side, USB3 front). color: black (with silverfrontbezel)

PSU: Seasonic SSP-450RT (450W) ATX 80+ Gold

Mainboard: DFI HD631-Q87 (on board: 2x Ethernet, Intel Chipset GPU, 6 COMports)

Operating System: Windows® 7 Ultimate EN English. 64 Bit for Embedded(Service Pack 1)(installation medium supplied for 32 Bit and 64 Bit system)

CPU: Intel® i5-4570S, Haswell

Firewire 1394b: IOI Technology, FWB-PCIE1X20 2x 1394b external screwlockconnectors

DVD drive: LG GH-24NS SATA

Ethernet ports: 2x Ethernet on board (1x for internal system network, 1x forcustomer network)

Serial ports: 6x RS232, on rear panel and slot brackets (onboard)

USB ports: USB 2.0: 4x on rear side / USB3 6x on rear side, 2x Frontpanel(supplied by PCIe add-on card)

System Requirements CAT Module |

3.2 ZEN system / pro (LM system)

System Requirements

HP Z840 Workstation

3 System Requirements CAT Module | 3.2 ZEN system / pro (LM system)


System Requirements

CPU: 2 x Intel® Xeon E5-2623v3 4-Core 3.0 GHz 10 MB / 1866 MHz

Chipset: Intel® C612

Memory: max. 256 GB RAM *

Memory Expansion Slots: 16 x DDR4-RAM Module / 2133 MHz ECC

PCI Express and PCI Connectors: 3 x PCI Express Generation 3 x16 (1 x used forgraphics interface) 2 x PCI Express Generation 3 x8 1 x PCI Express Generation 3x4 1 x PCI Express Generation 2 x1

Graphics interface: AMD® FirePro W5100 4GB graphics (4 x Display Port 1.2a,max. resolution 4096 x 2160 pixel)

Hard Drives: 4 x 2 TB SATA 7200 upm (configured as 4 TB RAID 10 hard drive)

Optical Storage: DVD +/- RW recorder for rewriteable media

Drive Bays: 6

I/O Controller: 2 channels of SATA 6.0 GB/s, 4 channels of sSATA 6.0 GB/s and8 channels of Serial Attached SCSI (SAS) 6.0 GB/s

Network Controller: Dual integrated 10/100/1000 LAN interface

I/O: 1 x serial, 8 x USB 3.0 (4 x front, 4 x rear), 2 x USB 2.0 (2 x rear), PS/2 forkeyboard and mouse

Certifications & Declarations: CE, CSA, UL, FCC

Power Supply: 110 - 240 V / 50 - 60 Hz / 1125 W with country specific plug

Chassis Dimensions: (H x W x D): 444 x 203 x 525 mm

Rescue kit

* Windows® 7 x64 is supporting max. 192 GB RAM

4 Changes on the operation system



INFO

Installation of software, hardware drivers, changes to operating system settingsor other system interference beyond the actions needed to operate the softwareare always in the responsibility of the customer, because the potential impactcan not be estimated.

The following modifications have, in our experience, no effects on thefunctionality of the PC system:

¢ Network integration possible

¢ Installation of security software / antivirus software (highly recommend if yourPC is attached to a network)

¢ Logon as Domain Users in an Active Directory environment (possibly with localadministrator 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 ( WindowsService Packs are to be considered different).

Information about allowed Windows service packs can be found under Systemrequirements.

Recommended settings

Windows 7

Allow option "Check for updates but let me choose whether to download andinstall them". That prevents, for example, aborting time series experiments if anautomatic restart is performed after an automatic update.

Windows 10

Choose what updates are installed “Current Branch for Business”.

Effects of following modifications can`t 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 asbackup software) due to possible performance problems of the simultaneousoperation of Fast Acquisition Systems



¢ Storage of data on network drives by redirecting folder structures (e.g. therecan occur performance problems in case of Fast Acquisition systems orlimitation of the available data storage capacity (disk quota))

If problems occur, the system can be restored to the state of delivery by a ZEISSservice technician.

5 Configure security software | 5.1 Before installation


5 Configure security softwareThe following section explains how to configure your security software forinstallation and optimum operation of the ZEN (blue edition) software properly.

INFO

The term security software combines all programs which protect your computerfrom viruses, unwanted interventions, etc.. This includes virus scanners, firewallsand intrusion detection systems. If you don`t adapt the security settings therecan be problems while installing or running the software. The following topicswill show you how to avoid problems with the security software and adapt thesettings correctly.

Configure security software |

5.1 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 caseproblems occur. It also is possible to ask the local ZEISS support team to createan image of the main drive of the PC before the security software is installedand setup by the customers IT department.

¢ Lower security rules

Set the security rules from "high" to "low". How you set the security rules,refer to the respective operating instructions of your security software.

¢ Disable security software

In rare cases, you may need to disable the security software completely. Makesure that you enable the security software after installation. How to disable orenable the security software, refer to the respective operating instructions ofyour security software.


5.2 After installation

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

¢ Exclude ZEN program files from virus scanning

Exclude the following files from virus scanning. How to exclude files from virusscanning, refer to the respective operating instructions of your securitysoftware.

– ZEN.exe / ZENCore.exe

– ZENService.exe

5 Configure security software | 5.2 After installation


– ZISProtocolServer.exe

– MTBconfig.exe

– Configuration tool.exe

– AimApplication.exe

– CZCanCheck.exe

– CZCansrv.exe

– System_Maintenance_Tool.exe

¢ Exclude ZEN specific file extensions from virus scanningExclude files with the following file extensions from virus scanning. How toexclude file extensions from virus scanning, refer to the respective operatinginstructions of your security software.

– *.czi

– *.zvi

– *.zishm

– *.lsm

– *.zmbi

¢ Exclude ZEN specific folders from virus scanningUnder About ZEN ... | Show ZEN Information| Folders you can see theprogram specific folders. How to exclude folders from virus scanning, refer tothe respective operating instructions of your security software.

Fig. 1: Program specific folders



5.2.1 Default folders

In the following table you can see the folders to which the captured images will bestored per default.

Operating system Folder / path

Windows 7: My Pictures and

%USERPROFILE%\My Pictures and

C:\Users\{user name}\My Pictures

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 youwant to store your images into.

Change default folder for automatic image storage and continuous imageacquisition (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 7 in the context menu of My pictures.

¢ In Windows 10 in the context menu of Pictures.

5.2.2 Temporary files


Windows 7 /Windows 10

%TEMP% or

%LOCALAPPDATA%\temp or

C:\Users\{user name}\AppData\Local\Temp

Change default folder for temp files

¢ First, define an appropriate path for the TEMP environment variable (usercontext).

¢ Then define the environment variable SWAP indicating a corresponding path.



For Windows 7 and Windows 10 this has the following paths or folders that youmust exclude from virus scanning:


Windows 7 (en) C:\Users\{user name}\My Pictures

Windows 10 (en) C:\Users\{user name}\Pictures

Windows 7 & 10 (en) C:\Users\{user name}\AppData\Local\Temp

Windows 7 & 10 (en) %TEMP%

Windows 7 & 10 (en) %SWAP%

5.2.3 System specific folders

If you are using a ZEISS PC system, the location of your images is predefined. Thetable below show the system specific folders for the following ZEISS MicroscopyHigh-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 7andWindows 10

D:\Users\{user name}}\Pictures

Notice:

For Windows 7 the folder C:\Users was moved to D:\Users

by changing the registry keys:

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\ProfileList\ProfilesDirectory

Default: %SystemDrive%\Users

Modified: D:\Users

5 Configure security software | 5.3 Summary



5.3 Summary

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

¢ You have disabled the security software during installation or reduced thesecurity settings.

¢ You have excluded the entire application, the defined paths or relevant filesfrom virus scanning.

6 Installing ZEN


6 Installing ZEN

INFO

Do not install an older ZEN version over a newer ZEN version.

If ZEN is already installed on your PC, during installation the current version willbe uninstalled first.

In case of installing ZEN on a SEM system, make sure that SmartSEM is notrunning when installing ZEN.

Prerequisites ¢ You have read the chapter Configure security software [} 13] attentively.

¢ If you have inserted the product DVD into the DVD drive, the installation willstart automatically. After a short while you will see the installation screen.When automatic DVD playback has been deactivated on your computer,perform installation as follows:

Procedure 1 Click on Computer in the Windows start menu.

2 Double-click on the DVD-RW drive in the Devices with Removable Mediasection.

You will see folders and contents of the product DVD.

3 Double-click on the Setup.exe entry.

Depending on the security settings on your computer several warningmessages could appear. Ignore the messages or confirm with Ok.

After a short while you will see the installation screen with an overview of theinstallation menu.

4 Click on Install ZEN.

The language selection dialog window is displayed.

5 Select the installation language from the dropdown list and click on OK.

Depending on your system configurations additional pre-installation steps canbe necessary before you can continue installing the software. If the messagedialog appears which tells you to install missing requirements, we recommendto install all the listed requirements and reboot your computer, when asked.

6 Installing ZEN


After the installation of all required system components the ZEN InstallShieldWizard opens.

6 Click on Next to start with the installation.

The License Agreement dialog is displayed.

7 Select I accept the terms in the license agreement and click Next.

The Destination Folder dialog is displayed. Here you can choose an alternativeinstallation folder. We recommend to leave the default folder settingsuntouched.

8 Click on Next to install the software to the default folder or click on Change toselect a different folder.

The Customer Information dialog is displayed.

9 Enter a user name and the company name in the User Name andOrganization input fields and click on Next.

The Custom Setup dialog window is displayed. You can leave it by the defaultsettings and click on Next. If you don`t want to install a certain feature simplydeactivate it in the dropdown menu.

6 Installing ZEN


NOTICE If you install ZEN on a SEM system, deactivate the featuresZEN (black edition) and MTB 2011.

The Select File Association dialog is displayed.

10 Decide if you want to associate CZI files wether with ZEN blue or with ZENblack. This dialog is not available if you have deactivated wether ZEN (blueedition) or ZEN (Black edition) for installation. Then the file types are associatedwith the corresponding software automatically. Click on Next.

The Ready to Install the Program dialog is displayed.

11 Click on Install to install the software. Accept all occurring windows securitymessages with OK.

6 Installing ZEN


After the driver installation the InstallShield Wizard Completed dialog isdisplayed.

12 Click on Copy License Files to copy the license files automatically from thesupplied USB stick to your computer.

13 Click on Finish and connect the included dongle to a free USB port.

The installation was successful. Reboot your computer and start the software byclicking on the ZEN blue icon on your desktop.If you install ZEN on a computer for a SEM system, continue like described in thenext chapter.

7 Installing the Remote API Client (SEM systems)


7 Installing the Remote API Client (SEMsystems)To enable communication between SmartSEM and ZEN, the RRemote Client has tobe installed on the SEM system as well. The DVD contains the setup for RemoteAPIClient 5.4. If you need another version, cancel the installation and use the setupfiles from the SmartSEM DVD.

After having installed the ZEN software, you will be asked to install the RRemoteClient. Continue as described below:

Procedure 1 Close SmartSEM and EM Server.

2 Double click on the Installation file RClientInstaller.exe.


3 Click on the I Agree button.

The Destination Folder dialog is displayed.



4 Choose your destination folder and click on the Install button.

The software will be installed now. Different installation windows are displayedand it will take some time. Please wait until the different windows aredisappeared.



At the end the RConfigure dialog is displayed.

5 Check the automatic port setting: 8070 for client and 8080 for server.Correct if necessary.

6 Check that the Client IP and the Server IP are identical and change it ifnecessary. For systems with variable IP, it might be necessary to input thecomputer name instead of the IP.

7 Check that the client and server version are identical.

8 Click on the Apply button.



The Remoting Configuration Change dialog is displayed.

9 Click on the Ok button.

10 Click on the Finish button.

You have successfully installed the RRemote Client on your SEM system.

8 Installing Matlab


8 Installing MatlabIf you have bought the CAT Module (Correlative Array Tomography) theinstallation of MatlabRuntime is mandatory on both computers (SEM and LMsystem). Proceed as follows:

Procedure 1 Click on Computer in the Windows start menu.

2 Double-click on the DVD-RW drive in the Devices with Removable Mediasection. You will see folders and contents of the product DVD.

3 Go to the folder Other \ MatlabRuntime.

4 Double- click on the MCRInstaller.exe entry.

A WinZip Self-Extractor window opens and the files will be extracted

After the extraction the MATLAB Compiler Runtime Installer opens.

5 Click on Next button to start with the installation.

8 Installing Matlab



6 Accept the License Agreement by selecting the Yes radio button.

7 Click on the Next button.

The Destination Folder dialog is displayed.

8 Click on Next button to install to default folder.

8 Installing Matlab


The Confirmation dialog is displayed.

9 Click on the Install button.

The installation dialog is displayed. The software will be installed now.

After installation the Installation Complete dialog is displayed.

8 Installing Matlab


10 Click on the Finish button.

You have successfully installed the MatlabRuntime that is necessary for the workingwith the CAT module.

9 Compatible cameras


9 Compatible camerasThe table below shows, which cameras are compatible to the ZEN (blue edition)software.

Compatible ZEISS Axiocams

Camera Notice

Axiocam 105 / 305 / 503 / 506 / 512 / 702 color /mono

64 bit only

AxioCam MR Rev.1-2 / HR Rev.1-2

AxioCam MR Rev.3 / HR Rev.3 / HS

AxioCam MRc 5

AxioCam IC cameras (ICc1, ICm1, ICc5)

AxioCam ERc 5 s

AxioCam ERc 5 s Rev. 2 USB only, not vianetwork connection

Other, compatible cameras

Camera Notice

PrimoStar HD USB only, not vianetwork connection

Primovert HDcam USB only, not vianetwork connection

Andor: iXon3 888 Ultra USB3.0, iXon3 897 Ultra USB3.0

ELYRA systems only

Hamamatsu: Orca Flash 4.0 V3 CL/USB3.0, Orca FlashLT USB3.0, Image EM X2 512, Image EM X2-1K

Roper Photometrics: Evolve 512, Evolve 512 Delta,Prime

PCO: edge 5.5 CL, edge 4.2 CL/USB3.0


Carl-Zeiss-Promenade 10

07745 Jena, Germany

[email protected]

www.zeiss.com/microscopy


Königsallee 9-21

37081 Göttingen

Germany

ZEISS reserves the right to make modifications to this document without notice.

© Jena 2018 by Carl Zeiss Microscopy GmbH - all rights reserved

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