Software Suite for Connected Microscopy from the Materials Lab to Production

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.

Enjoy its highlights:

  • Easy to configure – easy to use. Benefit from an adaptive user interface.
  • Advanced imaging and automated analysis. Use built-in acquisition routines and take advantage of the consistency of repeatable workflows.
  • Infrastructure solution for the connected lab. Keep your data together across instruments, laboratories and locations.
German Design Award Winner 2022


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 segmentation
  6. Contextual analysis
  7. Integrated reporting
  8. Mobile Access
  9. Central Data Management
  10. Connectivity between systems, laboratories, and locations
  11. Interfaces for further analysis

User Management Designed to Assure Data Repeatability and Integrity

  • Create multiple user accounts with defined privileges and roles according to your needs.
  • Create and manage users directly in ZEN core – or connect to ActiveDirectory and reuse those user accounts.
  • Administrate all users efficiently using ZEN Data storage as a central hub for all your connected microscopes.
  • Protect access with passwords and leverage extensive capabilities to put password rules and expiration times in place.
User Management Designed to Assure Data Repeatability and Integrity

Perform Automated Segmentation, Contextual Analysis and Reporting

ZEN analyzer is your desktop version of ZEN core, designed for activities that can be done independently of the microscope. Your instrument is not blocked for post-processing tasks. Instead use it to run other experiments—anywhere, anytime, and with genuine efficiency.

  • The ideal solution for segmentation and analysis, as well as for reporting and creating job templates.
  • Offering remote access to ZEN Data storage.
  • Enables you to use all workbenches available in ZEN core giving full control of all data and templates, accessible from your desk.
Perform Automated Segmentation, Contextual Analysis and Reporting

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 clear 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

Linkam Stage Control

Observe materials under temperature.

Multi Channel Acquisition

Acquire images with multiple channels in one go automatatically, e.g. multiple fluorescent channels or just bright- and darkfield.

ZEN Intellesis Enables Image Segmentation by Machine Learning

Segmentation is one of the biggest challenges faced by today’s microscopists, but you can avoid errors and user bias by using machine learning for image segmentation.

ZEN Intellesis Segmentation
This software module provides powerful machine learning segmentation of multidimensional images including 3D datasets. It’s designed for smooth integration of multiple imaging modalities and for achieving superior segmentation on any single image.

  • Automatically analyze images that once had to be processed manually. Train a model to segment them for you.
  • Use your own expertise to train the software and let it do the tedious segmentation. Or import dedicated networks trained elsewhere (for example, on www.APEER.com)
  • Benefit from saving time in sample preparation as ZEN Intellesis Segmentation can adapt to your own preparation process. Reproducibility is guaranteed as the stored analysis program can be used again, sample by sample, or retrained to handle new samples.
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 Intellesis Object Classification

Sometimes segmenting objects like particles, inclusions or grains is straightforward, but it can still be hard to classify them further into different types. Even machine learning-based segmentation techniques may struggle in this case because they only take the appearance of pixels into account and are unable to consider derived properties of pixel clusters (objects) as well.

ZEN Intellesis Object Classification now offers an easy way to classify already segmented objects into subclasses. An object classification model can be trained to perform the classification automatically.

  • Instead of looking at individual pixels, the model uses more than 50 properties measured per object to distinguish them. These derived measurements include geometric and intensity-based features.
  • Since ZEN Intellesis Object Classification works on tabulated instead of image data, the classification process is much faster than segmentation by specifically trained deep neural networks.
  • In addition, the classification process is independent of the prior segmentation, whether it was done by classic thresholding or using machine learning.

Learn more about ZEN Intellesis

Object classification performed on standard nano- and microplastic particles (polystyrene (PS, light blue), polyethylene (PE, green), polyamide–nylon 6 (PA, dark blue), and polyvinyl chloride (PVC, red)) on a polycarbonate filter imaged with ZEISS Sigma. This correlative study combines the high resolution of an electron microscope with the analytical capabilities of a Raman microscope. The classification model is capable of distinguishing the different particle types based on their properties.

Infrastructure Solutions for the Connected Laboratory

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 Data Storage. Perform exportable line, angle and area measurements in the workspace within or across aligned images. 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.

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. ZEN core is the ZEISS correlative microscopy interface, designed specifically for use in materials analysis available on all ZEISS light- and electron microscopes with motorized stages.

  • 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 Correlative Microscopy for Materials Analysis

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.
  • Combine ZEN Data Explorer with ZEN Data Storage for mobile access to your data. This lets you use your tablet or smartphone to examine your results when you’re on the go.
ZEN Data Storage: Central Data Management in 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

Module Packages

Module Package Features & Applications Download / Learn More

ZEN core

  • Full control of motorized ZEISS microscopes

ZEN core 
Release Notes for ZEN core Rel 3.4

learn more about the CZI format and request a free licence

ZEN starter

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

try out key features of the ZEN package

ZEN analyzer

  • Desktop version of ZEN core
  • Data processing, analysis and reporting
  • Mulit-modal workflows and database connectivity features

learn more about the 60 day free trial ZEN analyzer



Software Suite for Connected Microscopy in Material Laboratories

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file size: 14957 kB

ZEISS Microscope Software for Your Routine Laboratory - Flyer

Get it done. Easy.

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Application Note: ZEISS ZEN core

Fast Routine Investigation of Additive-manufactured Al-Si Samples

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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 core - Application Note

Quantitative Structural Analysis of CFRP Components Using ZEISS ZEN core

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file size: 2036 kB

ZEN 2 core Quick Guide

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file size: 1702 kB

Obtenga imágenes. Sin complicaciones. - Flyer (Spanish Version)

Software de microscopía de ZEISS para la rutina de laboratorio

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file size: 1537 kB

ZEISS ZEN core (Italian Version)

La linea di software per microscopia connessa, dai laboratori di materiali alla produzione

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ZEN 2 core (Russian Version)

Краткое руководство

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file size: 3662 kB

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