ZEN core

Imaging Software for Connected Microscopy in Material Laboratories

ZEN core handles more than just microscopy imaging. ZEN core is the most comprehensive suite of imaging, segmentation, analysis, and data connectivity tools for multi-modal microscopy in connected material laboratories.


Easy to Configure – Easy to Use

Benefit from an adaptive user interface tailored to the needs of industrial and research environments. ZEN core offers you configurable user management to specify users and roles. Whatever their level of experience, operators will learn the software quickly.

Advanced Imaging and Automated Analysis

ZEN core is the command center for automated imaging and analysis functions on compound light microscopes. By using built-in automated image acquisition routines, you benefit from the consistency of an advanced and repeatable workflow.

Infrastructure Solution for the Connected Lab

ZEN core provides the infrastructure for connected laboratory environments, linking ZEISS imaging and microscope solutions to a single, familiar GUI and keeping your valuable data together across instruments, laboratories, and locations.

One Interface for all ZEISS Microscopes in a Multi-user Environment

One Interface for all ZEISS Microscopes in a Multi-user Environment

From entry-level stereo microscopes to fully automated imaging systems, ZEN core provides a unified user interface for ZEISS microscopes and cameras. ZEN core enables the correlation of light and electron microscopy in multi-modal workflows and provides connectivity between systems, laboratories, and locations. 

  1. Microscope and camera control
  2. Data acquisition and analysis
  3. Correlative microscopy
  4. Post-acquisition analysis
  5. Automated intelligent segmentation
  6. Contextual analysis
  7. Integrated reporting
  8. Central data management
  9. Connectivity between systems, laboratories, and locations

User Management Designed to Assure Data Repeatability and Integrity

User Management Designed to Assure Data Repeatability and Integrity
  • Adaptive user interface tailored to the needs of industrial and research environments
  • Task-specific workbenches
  • Job Mode for repetitive tasks and customized workflows
  • Configurable user management to specify different user roles, like operator, supervisor, and lab manager
  • Combination of Job Mode with user management functions to assign inspection tasks to certain users and user groups

Materials Modules for Metallography Applications

Including material modules for the determination of grain sizes, phases and layer thicknesses as well as for the classification of graphite particles and non-metallic inclusion analysis, ZEN core provides all important metallographic applications under a uniform user interface.

Cast Iron Analysis

Depending on process parameters and chemical composition of the material, graphite particles in cast iron can occur in different shape and distribution. This influences the mechanical properties of the material.

Analyze the shape and size of graphite particles fully automatically. Obtain the spheroid number according to EN ISO 945-1: 2008 + Cor.1:2010. Determine the nodularity of vermicular graphite and examine the content of graphite particles in area percentage.

Cast Iron Analysis: Size and shape distribution
Cast Iron Analysis: Size and shape distribution

Grain Size Analysis

The size and distribution of grains are directly linked to the material properties. Quantify the crystallographic structure of your materialographic samples in accordance to international standards. Three evaluation methods allow you to characterize your material:

  • Planimetric method for automatic grain boundary reconstruction
  • Intercept method with a variety of different chord patterns to interactively recognize and count the intersections with grain boundaries
  • Comparison method for manual image evaluation with comparative diagrams
Grain Size Analysis: intercept method
Grain Size Analysis: intercept method

Multiphase Analysis

Any part of the material with a distinct crystal structure can be taken as a “phase”. Different phases are separated from one another by distinct boundaries. Distribution and orientation of phases affect the material properties like hardness, strength or elongation at break.
Analyze the phase distribution in your samples. Determine size, shape or orientation precisely and fully automatically. Use this distribution analysis to gain information about porosity of additive manufactured material.

Multiphase Analysis: result view with distribution of different phases
Multiphase Analysis: result view with distribution of different phases

Layer Thickness Measurement

Measure thickness of coatings and platings, or the depth of hardened surfaces in the cross section of a sample.

Evaluate complex layers systems either automatically or interactively. The module calculates the course of the measurement chords depending on the gradient present.

Get the results from your part in a clearly report containing images, sample data and measurement values, such as the maximum and minimum chord lengths, mean, and standard deviation.

Layer Thickness: automatic detection of a layer
Layer Thickness: automatic detection of a layer

Non-Metallic Inclusion Analysis (NMI)

Metallographic analysis of NMI is governed by industry standards that are supported by ZEN core which guides the user quickly and easily through the workflow, generating a report and inclusion gallery compliant with the standards.

Powerful inspection views and automated deformation axis detection features make analysis easy, intuitive and repeatable. With additional GxP functionality, ZEN core users are able to offer their customers full traceability and data integrity in NMI analyses, meaning that grade certification is auditable, particularly advantageous for customers in regulated industries.

NMI: Global Results view
NMI: Global Results view providing the option to toggle between inclusion types: oxides, sulfides, and artifacts.

Comparative Diagrams

Make your Wall Charts digital. Compare your sample under the microscope with comparative diagrams directly on your screen.

Choose between different schematic micrographs with specific characteristics. These change gradually from image to image and may relate to grain size, carbide precipitation in steel, or quality of sample preparation.

The module also provides a chart series creator to design your own comparison diagrams, e.g. for pass-/fail criteria in quality control or best target preparation images for your individual material microstructures.

Comparative Diagrams: compare the sample with standardized or customized wall charts
Comparative Diagrams: compare the sample with standardized or customized wall charts

Advanced Imaging and Analysis

Automation for Light Microscopes

ZEN core provides you with a wide range of choices for automated image acquisition:


Enhanced Depth of Field
Automatically acquire images with enhanced depth of field


Online Panorama
Acquire panorama images on coded and non-coded stages


Free-Form Tiles
Easily define stitching areas to create highly resolved images

ZEN Intellesis: Image Segmentation by Machine Learning

ZEN Intellesis is your software module for powerful machine learning segmentation of multidimensional images including 3D datasets. You can smoothly integrate multiple imaging modalities or achieve superior segmentation on any single image.

Images that had to be processed manually can now be analyzed automatically, by training ZEN Intellesis to segment them for you. Use your expertise to train the software and let ZEN Intellesis do the tedious segmentation.

You will also benefit from saving sample preparation time, as ZEN Intellesis can adapt to your sample preparation. Reproducibility is guaranteed as the stored analysis program can be re-used sample by sample, or re-trained to handle new samples.

Learn more about ZEN Intellesis

Segmentation model training Automated segmentation
Segmentation model training: The user labels a few regions just by painting them in to teach the system how to segment the image.
Automated segmentation: Once a segmentation model has been trained, it can be re-used, shared, and applied to a bundle of images.

ZEN Connect: Quality Data Put in Context

Organize and visualize different microscopy images and data from the same sample in their context, all in one place. For sample-centric analysis, ZEN Connect workflows enable you to get from a quick overview image to advanced imaging with multiple modalities. The correlations between the images at different scales can be seen and easily navigated. The interdependencies of the different datasets can be stored, exported and re-used in a Client Server Database. ZEN Connect also enables an integrated reporting across the connected images and datasets.

Learn more about ZEN Connect

ZEN Connect user interface: images at different scales can be easily navigated.
ZEN Connect user interface: images at different scales can be easily navigated.

Infrastructure Solutions for the Connected Laboratory

GxP Module: Secure and Compliant Microscopy Processes

The GxP module enables traceable workflows through seamlessly integrated microscopy hardware and software to meet the requirements of regulated industries. Every workflow available in ZEN core can be made GxP compliant.

  • User management
  • Audit trail
  • Release procedure of workflows
  • Electronic signatures, incl. countersign functionality
  • Checksum protection of process-critical data
  • Disaster recovery
GxP module: Electronic signature validation
GxP module: Electronic signature validation

Shuttle & Find: Correlative Microscopy

Correlative microscopy is a powerful technique for combining the complementary attributes of different microscopic techniques to obtain maximum meaningful information from parts or materials samples. Shuttle & Find is the ZEISS correlative microscopy interface, designed specifically for use in materials analysis and industrial QA.

  • Transfer samples between LM and EM systems faster than ever.
  • Relocate regions of interest automatically.
  • Improve efficiency and throughput.
  • Collect the maximum relevant information.
  • Take well informed material decisions.

Learn more about Shuttle & Find

ZEN Data Storage: Central Data Management in the Connected Laboratory

As digitization continues to improve microscopic investigations, you’re facing an ever-growing mass of images and data that needs to be managed, all the more so in multi-user laboratories. ZEN Data Storage enables you to separate image and data acquisition from post-acquisition works, making everyone in the lab work more efficiently in a number of ways:

  • Share instrument presets, workflows, data and reports with ease.
  • Access all data from different systems and locations.
  • Your analyses are quality assured and reproducible.
  • Perform multi-modal workflows and reap maximum information from your samples.
  • Help your IT department implement security and backups.
ZEN Data Storage: Central Data Management in the Connected Laboratory

Module Packages

Module Package Features & Applications Download

ZEN starter

  • Free basic version (no license necessary)
  • Extend this version with specific modules for your applications

ZEN  starter - Run ZEN core for free
Use this free microscope software to try out key features of the ZEN package.
learn more

ZEN core

  • Full control of motorized ZEISS microscopes
  • Advanced image acquisition, processing and analysis
  • Multi-modal workflows and database connectivity features

Release Notes for ZEN core Rel 3.3

Documentation of the CZI image format:
Learn more about the CZI format and request a free licence



Software Suite for Connected Microscopy in Material Laboratories

pages: 25
file size: 11683 kB

Application Note: ZEISS ZEN core

Fast Routine Investigation of Additive-manufactured Al-Si Samples

pages: 5
file size: 3302 kB

Application Note: ZEN core

Quality Inspection of Weld Connections

pages: 8
file size: 1531 kB

Detection, Quantification and Advanced Characterization of Non-metallic Inclusions in Steels

Detection, Quantification and Advanced Characterization of Non-metallic Inclusions in Steels. Description of NMI module in ZEN Core software.

pages: 10
file size: 1138 kB

In Situ Microscopy on the Melting and Cooling Behavior of an Al-Si 12 Alloy Using ZEISS ZEN core

pages: 6
file size: 2153 kB

Microscopy in Metal Failure Investigations

Determine the root cause of metal failure and learn about microscopy tool set for any metal failure investigation

pages: 8
file size: 4315 kB

ZEN 2 core Quick Guide

pages: 24
file size: 1702 kB

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