ZEISS ZEN Core Software User Guide

: June 6, 2024
: Zeiss

Table of Contents

Welcome
Starting the Software
Operating Modes
User Roles
Creating a Job Template
Running a Job
Performing a Free Examination
Archive
Documents / Resources
- Read User Manual Online (PDF format)
- Download This Manual (PDF format)

Quick Guide
ZEISS ZEN core

ZEISS ZEN core
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 core Quick Guide
Revision: 2
Language: en-US Effective from 12/2020
© 2020 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 photocopying, recording, or by any information or retrieval system. Violations will be prosecuted. 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 up-grade 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 backup copy for safety purposes. ZEISS reserves the right to make modifications to this document without notice.

Welcome

The ZEN core is the image acquisition and analysis software from ZEISS designed to support mainly industry & manufacturing markets. Its design and intuitive user interface help you examine samples quickly, easily, and reliably, especially in quality assurance environments. The software offers two main operating modes. In Free mode, you can configure and use the software freely to your personal needs. It is designed for expert microscopy users who exactly know what they want to do. The workflow-based approach of the Job mode is used for repeatable experiments.
1.1 Working with ZEN starter
You can use the software without any license. The software is then run as the free version called ZEN starter with limited functionality. Nevertheless, you can still perform many typical actions, for example:

Load and view existing microscope images
Acquire images (Manual EDF, Panorama)
Perform interactive measurements (reduced set of tools available)
Create reports

1.2 Job Mode and Free Mode
The ZEN core is designed to support two fundamental ways of using your microscope:

Working with jobs (creating, running, editing, and managing jobs) in Job Mode
Performing free examinations in Free Mode

Job Mode In the software, the term job refers to a collection of examination tasks. Jobs can be created to ensure that the same examination tasks are carried out each time the job is run, in the same manner, and with the same settings. Jobs are used mainly in routine quality control examinations where it is essential that identical examinations are performed for each sample.
Free Mode Free examinations can be used to inspect a sample quickly, easily, and flexibly without defining examination tasks. Typical use is to examine a faulty sample where the cause of the fault is unknown or for one-off examinations that will not be repeated. In such cases, only the examination results, reports and images need to be saved rather than the examination tasks.

Starting the Software

Prerequisite
The software and all required licenses have been installed.

Double click on the program icon on your desktop.
The software starts, and the login screen is displayed.
Click on the button of the application you want to work with.
The available applications depend on your licenses and system.
During the program start, the hardware settings will be initialized.
On the login screen, click on your name in the list of users, and enter your password. Click Login. If you forgot your password or don`t know your user name, contact the System Administrator or Supervisor. The Home Screen is displayed. You can start working with the software.

2.1 User Interface – Home Screen
The Home Screen is displayed after you log in. The available operating modes depending on your user role.

Title Bar including System Messages icon, Workspace Zoom and Help icon.
Operating Modes selection, see Operating Modes [} 7].

Operating Modes

ZEN core contains different operating modes that correspond to the different ways of working with the microscope. The modes that are available to you depend on your user role.

Icon	Mode	Description
Free Mode	Inspect a sample quickly, easily, and flexibly without defining

examination tasks.
| Job Mode| Run an examination on a sample according to the step-by-step tasks defined in the job template.
Also, define fixed examination steps to be performed each time a sample is examined.
| Manage Templates| Edit and manage templates in the archive:
§ Form templates
§ Report templates
§ Macro templates
§ Image analysis settings
§ Custom workbenches
§ APEER modules
§ Intellesis models
§ Standards technical cleanliness
| Browse Results| View and manage job results in the archive.
| Maintenance| Configure global settings, manage users, calibrate measurements etc.

User Roles

User management is an optional component. It is disabled by default. If user management is disabled, the user has all user rights at the same time. When user management is enabled, three types of user roles are defined initially in the software:

Administrator
Supervisor
Operator

The available modes and tasks you can perform in the software depend on your user role. User roles can be added and modified under Maintenance > User Management.

User Role	Tasks
Administrators	Administrators install and configure the software. This

includes:
Managing system settings
Managing users
Specifying the connected hardware in the Microscope ToolBox application (MTB)
Configuring and managing the archives.
Supervisors| Supervisors perform the following main tasks:
Creating job templates for the operators to run
Performing free examinations (Free Mode)
They are also able to perform the following tasks:
Running jobs
Managing jobs in the archive (running, editing, deleting)
Defining and evaluating job reports
Releasing Job Templates
Operators| Operators can only perform a limited number of tasks:
Searching for a job
Running a job
Browsing the job results
See also| User Interface – Home Screen [} 6]

Creating a Job Template

5.1 Introduction
This chapter only applies mainly to supervisors.
5.2 Workflow
One typical workflow when creating a job template can be summarized in the following figure. Each step represents one task in the job template and is represented with an icon in the Task List.

Select Job Mode and click on Create a new template and edit it.
Acquire an image
Use the microscope camera or load an image from the file system.
Process the image
enhance the image and configure which parameters can be modified, for example, adjust the brightness and specify that contrast can only be altered +/- 10%.
Analyze the image
Define the measurements to be performed and configure the accepted measurement tolerances. If desired, repeat steps 2 4.
Configure the input form
Select a form template and specify the metadata to be recorded (e.g. sample ID, current time) and how it is entered (manually, automatically).
Configure the report
Select a report template and configure how measurement results and metadata should appear in it.
Save the job
Specify a name for the job template and which users are allowed to run it.

5.3 Creating a New Job Template

The software is supplied with example job templates that you can configure to your requirements.
However, you can also create a new job template from scratch.

Prerequisite

You are logged in as a supervisor or you have sufficient privileges to create a job template
The Home Screen is visible

Open the Job Mode and click Create a new template and edit it.
Select the category of the first task to be performed, e.g. Acquisition.
Select the workbench for the first task to be performed and click + Add Task.
Alternatively, you can double-click the desired workbench.
The first task is displayed in the Task List and the corresponding workbench and tools are displayed in the Workbench Panel.
Continue with the steps described in the typical workflow.

See also

Specifying Tools for a Task [ 10]
Saving and Completing the Job Template [ 13]
Workflow [ 9]

5.4 Specifying Tools for a Task
For each task to be performed when the job is run, you can specify which tools are available to complete the task. For example, for a processing task, you can specify that only the White Balance tool and Gauss tool are available. This is done by adding and removing tools from the corresponding workbench so that only those required when running the job are included in the workbench.
Info
If a tool is required when running a job, it must be included in the workbench. However, if you do not want the operator to be able to change the values of the tool parameters you can lock or hide individual parameters. To hide the entire task from the operator, right-click it and apply the Run Silent option. The task is then executed but not visible to the operator when the job is run.
Adding tools
To add a tool to a workbench:

Select the workbench to which you wish to add a tool.
Click the Add tool button in the workbench header.
Select the desired tool.
The tools that are available depend on the current workbench.

Info
If you wish to add large numbers of tools to a workbench, it may be advisable to add another workbench of the same type and to distribute the tools across the two workbenches.
Removing tools
To remove a tool from a workbench:

Click anywhere within the tool.
Click Delete this tool.

If you remove a processing tool, the new processing result is not displayed until you click the corresponding icon in the Task List.
5.5 Locking and Hiding Parameters in Tools
When creating a job template you can specify the operator’s privileges for each parameter individually. The privilege is indicated by the following icons:

**** The parameter can be seen and changed by the operator
If the parameter can be changed by the operator, you can choose to limit the range of permitted values.
The parameter can be seen but not changed by the operator
Parameter is hidden from the operator (and thus cannot be changed)

To change the property of a parameter:
1. Click the icon until it has the desired state
The icon cycles between the three states in the above order.
If all the parameters in a workbench are hidden or locked, the corresponding task is performed automatically in the background when the job is run.
If you want an entire task to be performed automatically in the background without user interaction, you can use the Run Silent option. This overrides the settings of individual parameters within the task.

Right-click the icon of the task in the Task List and select Run Silent.
See also
Specifying Tools for a Task [ 10]

5.6 Applying an Image Processing Tool
ZEN core contains various image processing tools you can apply to your images. To apply an image processing tool, you must select the Image Processing workbench and add the desired tool (if not already available).
To add an image processing tool:
Prerequisite

You are logged in as a supervisor.
The Image Processing workbench is selected.

Open the Tool Overlay by clicking the + Add Tool button in the Workbench Area.
Double-click the desired tool in the Tool Overlay.
The categories help you find the tool you need for your job.

The tool is added to the Image Processing workbench. You can now adjust it as required for the job, add more tools, or remove tools you do not need.
If you are working in Create a new template and edit it within Job Mode and a branch in the Task List contains multiple processing workbenches, they are all applied, from left to right. The output of a processing workbench provides the input for subsequent processing workbenches.
The same holds for the tools within one processing workbench: the processing tools are applied from top to bottom and the output of a processing tool provides the input for the subsequent processing tool.
See also

Selecting Workbenches [ 21]
Specifying Tools for a Task [ 10]

5.7 Analyzing the image
Once you have acquired an image you can analyze its properties by performing various types of measurements. The measurement results can then be added to a report.
In Create Job Template mode you can specify which measurement tools are available when the job is run as well as tolerances (upper and lower limits for the measurement value).

Click Add Task | Measurement | Interactive Measurement | Add
à The four most common tools are visible in the Interactive Measurements tool. For further tools, click Add Tool.
Select a tool and click on the image to measure the sample.
To specify measurement tolerances click the icon.
Expected value: Typically the theoretical value contained in the CAD data or sample specification. Upper limit/Lower limit: Limits between which the measurement must lie, e.g. to fulfill quality control criteria.
Enter instructions about how to perform the task, for example, which part of the sample should be measured in the input field of the workbench.

5.8 Creating or Modifying a Form Template
Forms provide a simple way to add information to a job when it is run by an operator. If the available form templates in the Archive are not suitable for your purposes, you can create a new form template or modify an existing one. The Form workbench is selected.

To create a new form template, click the plus icon. +
To modify an existing form template, click the folder icon and select the desired form template.
Modify the form template as desired:
substepCustomize the layout (e.g. add or remove fields)
substepCustomize the properties of the fields
substepTranslate the form
When you are satisfied with the form template, click the Apply button to use the form template in your job template.

5.9 Configuring a Job Report
Reports enable you to collate all the information from your examination, e.g. images, measurement data and hardware setup, in a single document as a protocol of your examination.
Reports contain placeholders to enable you to collate the information easily. The placeholders also ensure that each time the job i run, the same information is added to the report.

Click Add Task | Reporting | Reports | + Add.
Click on the Folder button in the Add Templates tool.
Opens the Select Report Templates dialog.
Activate the checkbox of the desired report template, e.g. Report Form, and click the Select button.
Select the report template in the Add Template tool to display the available placeholders.
Click on the arrow in a placeholder, e.g. Image, and select the corresponding measurement information that you wish to add. You can add multiple items to a single placeholder.

5.10 Saving and Completing the Job Template
You can save a job template at any time during its creation. The Save Job Template dialog enables you to specify the following:

Job template properties (name and description)
Category to which the job template is assigned
Permissions (users that can run the job)

You can also modify the above in the Archive later. For each job, you can specify which users are allowed to run it. Typically, a group of users is specified, but you can also specify individual users. By default, a job can be performed by any user.
Prerequisite

You are in Create a new template and edit it within Job Mode.

Click the Save button.
In the General tab enter a meaningful Name and Description.
In the Security tab specify which users or user groups should be allowed to run the job.
By default, all users can run the job.

Running a Job

6.1 Introduction
This chapter applies to supervisors and operators.
6.2 Workflow
The following diagram shows an example of the workflow when running a job. Any steps where no interaction is required are performed automatically in the background.

Select the appropriate job for the sample.
Acquire an image of the region defined by the supervisor.
Process the image as defined by the supervisor.
Perform the analyses defined by the supervisor. You are automatically guided through the analyses and presented with the appropriate tool.
Repeat steps 2 – 4 for other areas of the sample as defined by the supervisor.
Check the information in the job report.
Save the job results.

6.3 Running a Job
Prerequisite

You are logged in as an operator.
You are on the Home Screen

Click on Job Mode.
Click the desired job in the list.
Click on Run.
Alternatively, you can double-click the desired job. The first step in the job is displayed (typically acquire an image). 4
To continue with the next step, click on Next.
When you have completed all the steps, click on Save and close.

If the job requires a different hardware configuration to your current setup, the system prompts you which components need to be changed. For more information about how to change components, see your microscope instruction manual.
6.4 Acquiring an Image
Acquiring an image is typically the first step when running a job. The image is acquired using the camera on your microscope.

Ensure you acquire the same area of the sample as the supervisor. à Follow any instructions added by the supervisor in the workbench panel.
If your microscope has a motorized stage, you can navigate the sample and adjust the focus using the software.
Otherwise, move the sample on the motorized stage by hand and focus manually. For more information, see your microscope instruction manual.
If your microscope has a motorized object revolver you can select the correct zoom level using the software.
Otherwise, select the correct objective by hand. For more information, see your microscope instruction manual.
If desired, adjust the acquisition parameters.
For more information about individual parameters, click.
Click Snap.
If you are not satisfied with the image, click Live and repeat the above steps.
When you are satisfied with the image, click Next.

6.5 Processing the Image
Image processing enables you to adjust the appearance of the image after it has been acquired, for example, to compensate for changes in brightness if the illumination changes between jobs. Typical processing actions include:

Brightness and contrast
Reduce noise and enhance contours
Adjust the size, rotation, and quality The tools that you can use, and thus the properties that you can alter, depend on what the supervisor has enabled in the job template.

Adjust the values of the parameters.
All processing tools are applied in one go, in the order displayed in the workbench
Repeat the above steps until you are satisfied with the resulting image.
For more information about individual parameters, click.
Click Next.

6.6 Performing an Interactive Measurement
Interactive measurements enable you to measure e.g. distances, angles, area, and intensities of pixels. All the measurements to be performed in the current image are displayed in the Center Screen Area at the locations specified by the supervisor.

Follow any instructions added by the supervisor in the workbench panel.
Drag each measurement to the correct location.
Click the measurement to move or resize it.
The corresponding handles for moving or resizing the measurement are displayed in the image.
Click Next.

If the supervisor specified an expected value and upper/lower limits for a measurement value (e.g. area or diameter), a corresponding color symbol in the Task Panel indicates whether your measurement result lies inside the expected limits (green) or outside the limits (red).
6.7 Creating a Report
Reports enable you to collate all the information from your examination in a single document. Typical information includes:

Images
Measurement data
Metadata (e.g. examination time, hardware setup)

Each report template contains placeholders for the above information to enable you to collate the information easily. The placeholders are usually filled automatically with the correct information. Depending on the settings applied when the job was created, you might be allowed to change the content of a placeholder.

Follow any instructions added by the supervisor in the workbench panel.
Check that all the information is included in the report (for example the correct images).
A preview of the report is displayed in the Right Tool Area.
To change the information in a placeholder, select the desired report template in the Add
Templates tool. à Various placeholders are listed in the Workbench Area.
Click the arrow icon in a placeholder and select the corresponding measurement information that you wish to add, for example, image, measurement result, etc.
You can add multiple items to a single placeholder. The report preview updates accordingly.
If you require a paper copy click Print Report.

6.8 Saving and Completing a Job
When you have completed the last examination task, you can save the job.

Check that you are satisfied with all your measurement results.
If you are not satisfied with a result, navigate back to the corresponding task and change the parameters accordingly.
To complete the job, click the Save button.
The measurement results are saved and a report is generated automatically.
Choose what you want to do next:
Repeat the same job with a new sample.
Return to the Home Screen.

Performing a Free Examination

7.1 User Interface – Free Mode
The following figure shows the typical user interface when working in Free Mode.

Workbench & Tool Area
Displays the added workbenches and tools.
Center Screen Area / Image Area
Shows the current image, measurements, and measurement results.
Results Table
Lists the results of all the measurements in the image. You can show/hide the table by clicking on the Show/Hide results table button.
Documents Area
Contains a list of all documents (images, measurement results, reports, and imported documents) within the examination. Click a document to display it and select it in the open task. Each time you apply a tool a new document is generated. Some document formats might not be supported within ZEN core, e.g. .txt or MS Excel files. A link is provided to open them externally.
Display Tab
Here, you can adjust how the image is displayed (i.e. Gamma value). For a detailed description, see the Display tab. Data Zone Tab Here, you can configure the display of additional hardware and acquisition data that are related to the acquired image. The data to be displayed can be configured under Maintenance | General Options | Documents | Image Data Zone Optional Data.
See also 2 Workflow [ 19]

7.2 Workflow
In Free Mode, there is no typical workflow. In this mode, workbenches can be used in any sequence.

Select Free Mode from the Home Screen.
Acquire an image.
Acquire an image using the camera or load an image from the file system.
Process the image.
Enhance the appearance of the image using various processing tools.
Analyze the sample.
If desired, repeat steps 2 4.
Save or export the images and analysis results.

Each time you apply a tool a new image is generated in the Documents Area. You can apply any number of processing or analysis tools in any order.
7.3 Documents
In Free Mode, user-created documents such as images, tables, forms, or reports are listed in the Documents Area. To have a good overview, the document’s name is displayed permanently and the full name is displayed when you hover over it. In the Documents area, you can open a document by clicking on it. If you use a tool, it is applied to the currently selected image (rather than the most recent image). The resulting image is added to the bottom of the Documents Area. From the context menu, you can also close, rename or save documents.
Renaming Documents in the Documents Area

In the Documents area, use the context menu to rename a document.
The name you give to the document will be displayed on the Data Zone tab. In the Documents Area, the image and the image name is displayed permanently. The full name is visible via mouseover.

Saving Documents in the Documents Area
You can save one document or multi-select documents to save them on a drive.

In the Documents Area, right-click into the document and select Save as. à The file browser opens.
Navigate to the directory, where you want to save the documents. à The name of the document is the default name of the document to be saved. It is the same name that is used in the Documents Area and on the Data Zone tab. Click OK
You can multi-select documents, right-click and select Save as. à The file browser opens.
To keep the documents names of each document, activate the Use names of Documents Area checkbox. If you deactivate the checkbox, all documents will have the name of the document to be saved on top in the Documents Area. For your overview, they are counted up. Check the name and type and change it, if necessary. If you have annotations in your image, you want to burn in, you can resize them between 1 and 1000000 % with the image.
Press [Enter] or click somewhere outside the document name to save the document.

Example:
1. There are two images in the Documents Area. They are called aaa and BBB.

Here, aaa is activated. The name is visible on the Data Zone tab.
2. Activate both images, and in one of them, right-click and select Save as. In the following dialog, do not activate the Use names of Documents Area checkbox. 3. Click Save.
7.4 Selecting Workbenches
In Free Mode, you can change which workbenches are displayed in the Workbench Area. To be able to use the tools within a workbench it must be selected. However, you can add or remove a workbench from the Workbench Area at any time without affecting the examination results. The order of the workbenches also does not affect the examination results. Remove any workbenches you do not require to reduce the number of workbenches displayed in the Workbench Area.
Adding workbenches – To add a workbench to the Workbench Area:

Click the Add Workbench button.
In the left pane, click the desired workbench category.
In the center pane, click the desired workbench.
A description of each workbench is displayed in the right pane.
Click + Add. Removing work- To remove a workbench from the Workbench Area: benches
1. Right-click the icon of the workbench.
2. Click Close workbench.

Info
The next time you start a free examination the workspace is displayed as you left it.
See also
Customizing Workspace [ 21] 7.5 Customizing Workspace
The Free Mode workspace always starts with the same workbenches displayed in the Workbench Bar as were used for the previous free examination.

If you have a set of workbenches that you commonly use for free examinations, you can simplify your work by adding them to the Workbench Bar.
Furthermore, if there are workbenches you rarely need, you can remove these from the Workbench Bar.
You can also modify existing workbenches by adding and removing tools.

By combining the above methods, you can configure the free examination workspace to your requirements.
See also
Selecting Workbenches [ 21] 7.6 Assigning Information to Report Placeholders
Reports enable you to summarize all the information from your examination in a single document. Typical information includes:

Images
Measurement data tables
Metadata (e.g. examination time, hardware setup)

Each report template contains placeholders for the above information to enable you to collate the information easily. The placeholders also ensure that each time the job is run, the same information is added to the report.
Prerequisite

At least one report template is listed in the Add Templates tool.

Select the desired report template in the Add Templates tool.
Various placeholders are listed below the list of templates and a preview of the report is displayed in the Center Screen Area.
Click the arrow icon in a placeholder and select the corresponding data that you wish to add, for example, an image or a table containing measurement results, etc..
As a rule, you can add a single item to each placeholder. The image placeholder is an exception: you can add multiple images to a single image placeholder. Therefore simply select multiple images from the list. The selected images are highlighted in grey.
The report preview updates accordingly.
Repeat the above step until you have added information to all the placeholders.
Click Create Report to create the document in the Documents Area.
You can export the report from the Documents Area by using the context menu.
If you require a paper copy of the template click Print Report.

7.7 Exporting Results
You can export images or measurements results, e.g. to publish them or to archive them on an external storage device.

Click Add Workbench and select the Output Documents category.
Select the Save File workbench and click Add.
Select the image to be exported, specify a filename in the Save Image tool, and click Apply.

Alternatively, you can right-click a document (such as an image or report) in the Documents Area and use the context menu to export it.