ZEISS ZEN - Monitor with ZEN

ZEN Microscopy Software

Your Complete Solution from Sample to Knowledge

ZEN is the universal user interface you will see on every imaging system from ZEISS. For simple and routine works, ZEN leads you straight to result. For complex research experiments, ZEN offers the flexibility to design multi-dimensional workflows the way you wanted. No matter what microscopy task you have, you will find intuitive tools and modules to assist you:

  • Acquire images using smart automation
  • Process images with scientifically proven algorithms
  • Visualize big data by GPU powered 3D engine
  • Analyze images via Machine Learning-based tools
  • Correlate between light and electron microscopes
ZEISS ZEN - Smart Aquisition

Smart Acquisition

Make your most complex experiments a success

Operate every one of your devices with the same convenient interface. Smart Setup, the intelligent control center, will automatically generate the settings for you, regardless of the microscope types. Aiming for reproducible experiments? So long as you have one raw image from a previous acquisition, a simple click lets you replicate the exact experiment precisely. You will find plenty of other smart automation, some guide you for rare events detection, and others assist you with hardware calibration.

ZEISS ZEN - Quantitative Processing

Quantitative Processing

Obtain reliable and reproducible results

More than 180 image processing tools help you transform and manage your data. Simply search the keyword of your intended method, e.g., kymograph or deconvolution, ZEN will lead you straight to it. ZEN will read the metadata of the input image, then display only the logical processing steps, and optimize the default parameters automatically. You can even process images from other platforms using third-party import tools. With a dedicated workspace, you can also batch process multiple images with ease for quantitative and unbiased results.

ZEISS ZEN - Powerful Visualization

Powerful Visualization

Interact with your big data confidently

Quickly generate a huge 2D tile scan with multi-channels at high magnification, and smoothly zoom in and out with a simple mouse scroll, just like using a map application on your smartphone. Having 200 GB of cleared mouse brain data? Just load it in ZEN – you will be amazed by the speed and clarity of the various 3D rendering methods. Powered by arivis ImageCore technology and efficient use of system resources, you can view your large 3D images even on regular consumer hardware.

ZEISS ZEN - Effective Analysis

Effortless Analysis

Gain insight into your research efficiently

Image analysis is essential to extract meaningful information from your microscopy images, via digital tools of segmentation and registration. ZEN addresses this with the simple and modular Bio Apps. Each Bio App is optimized for one type of application, e.g., cell counting or confluency measurement, with tailored segmentation settings and streamlined data presentation. The wizard-based ZEN Image Analysis module guides you step by step to create your unique measurements.

ZEISS ZEN - Unique Correlative Microscopy

Unique Correlative Microscopy

Combine perspectives across scales and modalities

ZEN overlays, navigates, and organizes your multimodal data. Spending days painfully locating synapses between two special neurons for the ultrastructural information? You can substantially improve your efficiency by combining the large field of view of a widefield fluorescent microscope and the high resolving power of a field emission electron microscope. ZEN lets you quickly overview the whole slice with fluorescent markers, identifying and relocating ROIs for EM imaging.

ZEISS ZEN - Secure Storage

Secure Storage

Stay confident when dealing with complex data

ZEN stores each of your valuable experiments with all its metadata.

The .czi file format is Bio-Formats compatible and can be read directly by ImageJ, and much other third-party software. Export your data into OME-TIFF (Open Microscopy Environment) to further facilitate cross-platform image data exchange.

To manage massive amounts of data, ZEN provides a server-based central platform to store and organize your raw data and manage user access right; while ZEN Data Explorer grants browser-based access from anywhere.

The ZEN Toolkit Structure

Overview of the most important ZEN toolkits
Overview of the most important ZEN toolkits

Simplified Access to Endless Possibilities

ZEN software provides a comprehensive end-to-end solution for any microscopy user, continuously evolving to address emerging life science applications with added features, e.g., automated smart acquisition, intuitive image analysis, and cloud-based data management. However, the increased capabilities also make the ZEN ecosystem complex. With the ZEN Toolkit structure, you get simplified options that make the numerous capabilities more accessible. Tailor your ZEN installation with toolkits for acquisition, analysis, and special features according to the needs of your experiments.

ZEN Toolkits

  • Base
    Perform basic image acquisition of multi-channel fluorescence and time-lapse experiments with manual, coded, and motorized microscopes.

    Motorized Focus
    Acquire images of multi-channel fluorescence, time-lapse and z-stack experiments, with software autofocus, extended depth of focus processing, and direct processing.

    Acquire images of multi-channel fluorescence, time-lapse, z-stack, tile scan, and multi-position experiments with software autofocus, extended depth of focus processing, and direct processing.

    Acquire images of multi-channel fluorescence, time-lapse, z-stack, tile scan, multi-position, and confocal HDR experiments with software autofocus, extended depth of focus processing, direct processing, and colocalization analysis.

    Configure inhomogeneous acquisition experiments with a simple user interface, and perform adaptive and automated acquisition using image analysis or Python scripting tools.

  • 2D
    Employ extended image processing functions and perform automatic 2D image analysis guided by an intuitive software wizard.

    Employ extended image processing functions, visualize 3D/4D image stacks with advanced rendering tools, and perform 3D image analysis guided by an intuitive software wizard.

    Visualize and analyze 3D/4D data of unlimited size with the flexible pipelines and machine learning tools of the stand-alone Vision4D software platform.

    Segment, classify, and denoise images based on deep learning algorithms accessible through a dedicated user interface for training AI models.

    Acquire and correlate images from different instruments such as light and electron microscopes, with a sample-centric workspace and a dedicated file management system.

    Customize and automate image acquisition, processing, and analysis with a dedicated Python script editor for recording, debugging, and code completion.

    Molecular Quantification
    Acquire and analyze molecular dynamics using FRAP, FRET, and ratio imaging within a dedicated analysis workspace using the most established algorithms. 

    Intuitively enhance the resolution of 2D and 3D data down to 120 nm using 15 published deconvolution algorithms, powered by efficient multi-CPU/multi-GPU processing.

    Bio Apps
    Perform out-of-the-box cell counting, confluency measurement, spot detection, and gene/protein expression with AI-based segmentation and tailored result presentation.

Newest ZEN Release Highlights

Find out if you can benefit from the latest features available with the most current ZEN release.

  • Instance Segmentation
    Instance Segmentation

    Instance Segmentation Performance Gain​

    After optimizing the Deep Learning training performance in the previous version, this release now adds accelerated model employment. You will benefit from:

    • Better time-to-result for Instance Segmentation​
    • Faster inference also in Image Analysis Wizard, Bio Apps, and Guided Acquisition workflows

    Up to 90 %​

    Speed improvement for large 2D images, 3D data, and time series​

    Up to 3-fold​

    Faster segmentation of data sets with small objects​

    Up to 3-fold​

    Faster filtering of raw predictions​

    2-fold to 30-fold​

    Faster transfer of models to ZEN​
    As a user of the Bio Apps Toolkit, you can now analyze nuclear translocation of molecules
    As a user of the Bio Apps Toolkit, you can now analyze nuclear translocation of molecules

    New Addition to Bio Apps: Translocation​

    As a user of the Bio Apps Toolkit, you can now analyze nuclear translocation of molecules. The new method comes with:

    • Simple, one-step setups​
    • A dedicated result view including multi-well plate heatmaps​
    • The option to integrate advanced Deep Learning segmentation
      Parallel Lattice SIM Processing
      Parallel Lattice SIM Processing

      Parallel Lattice SIM Processing

      Lattice SIM processing has been implemented as a feature of Direct Processing. When performing SIM² processing workflows, you will benefit from:

      • Improved time-to-result​
      • Increased computational resources by parallel processing on a dedicated processing workstation​
      • Intelligent data compression for faster file transfers
        AI-based Live Denoising
        AI-based Live Denoising

        AI-based Live Denoising

        On widefield modalities, users of the AI Toolkit can now employ Noise2Void Deep Learning during Continuous Acquisition Mode. This enables:

        • Efficient live denoising with best-in-class algorithm​
        • Sample exploration with quality images under mild illumination settings​
        • Reduction of phototoxicity and bleaching
        • Instance Segmentation​

          Instance Segmentation​

          Instance Segmentation has received important updates that will boost your segmentation quality and time-to-result:​

          • ​Significant reduction of model training times​
          • Multi-channel Instance Segmentation models in ZEN Image Analysis​
          • Random object coloring for visualizing dense objects
          • Remote model download for systems with restricted internet access
          Lossless Compression​

          Lossless Compression​

          Fast, lossless compression with Zstd is now available as standard for image acquisition with ZEN. ​

          • ​With compression rates between 2X and 20X, you will benefit from fast file transfer rates and reduced data storage costs.
          • For effortless batch compression of existing data archives, use our free standalone tool CZI Shrink
          Direct Processing​

          Direct Processing​

          With this release, Direct Processing has received the following improvements:

          • Reduce the computational load on your acquisition system by running AI Denoising and Linear Unmixing (for LSM Spectral Imaging) on a remote workstation.
          • Direct Processing is now compatible with mixed mode acquisition on LSM systems and Celldiscoverer 7.​
          Connect Toolkit​

          Connect Toolkit​

          Your correlative imaging will benefit from the latest additions to the ZEN Connect toolkit:​

          • ​Dynamics Profiler is now integrated into the Connect workspace.​
          • Publication-ready screenshots can be created from multi-volume 3D data.​
        • Automatic ZEN Profile Selection​

          Automatic ZEN Profile Selection​

          Simplify your ZEN start-up​
          Start-up of ZEN with the appropriate profile has been further simplified. While ZEN configured itself based on available (partially complex) licenses in the past, it now directly accesses available MTB ZEN profiles to choose from.​

          Bigger data. Faster processing.​

          Large Data Handling​

          Bigger data. Faster processing.​
          With ever-increasing data sets, large data handling remains a key topic for microscope users. The ZSTD lossless compression can now be set as default for image acquisitions, leading to higher file transfer rates and optimized data storage. Furthermore, algorithms for maximum intensity projections, tiles stitching, and image pyramids generation have been significantly accelerated.​

          Stitching in Direct Processing​

          Stitching in Direct Processing​

          Faster and more automatable image pre-processing​
          The largely popular workflow tool Direct Processing has received another addition to its toolset. With ZEN 3.8 you will be able to include stitching directly into your automated acquisition workflows, while simultaneously benefit from performance gains by algorithm optimization and parallel processing.​

          Convallaria stem section acquired with ZEISS Axio Imager and segmented with Instance Segmentation​

          Instance Segmentation​

          The segmentation revolution continues…​
          Instance Segmentation is now available for annotation and training on the arivis AI cloud platform. Within ZEN, the Image Analysis Wizard and the Bio Apps Toolkit are ready for integrating this new AI functionality into your workflows. Instance Segmentation solves the problem of precisely separating objects even in close vicinity to each other, without relying on error-prone and limited watershed algorithms.​

        • Gain user flexibility and better use of workstation resources

          Floating Licenses

          Gain user flexibility and better use of workstation resources
          The introduction of Floating Licenses for ZEN and its toolkit packages expands the usage models in your institution. Where ZEN users were formerly restricted to a particular workstation, you are no longer limited and may now use your infrastructure resources much more flexibly.

          Zstandard metrics compared to other compression alternatives

          Zstandard metrics compared to other compression alternatives. 
          Source: https://engineering.fb.com/2018/12/19/core-data/zstandard/

          Image Compression by Zstandard

          Use the full potential of your imaging system
          Advanced imaging systems acquisition rates can easily outpace data storage speeds, thereby limiting large data experiments. ZEN is now equipped with lossless and fast Zstandard compression. Up to 20-fold compression ratios accelerate data storage and optimize data economy. Zstandard comes built-in with both the Direct Processing module and ZEISS Lattice Lightsheet 7 systems. It is also optionally available for any data in .czi format.


          Smart Acquisition Package

          Class selection for detailed scans: green-positive cells next to dark areas

          Smart Acquisition Package

          Class selection for detailed scans: green-positive cells next to dark areas

          Class selection for detailed scans: green-positive cells next to dark areas

          Smart Acquisition Package

          Improvements for Guided Acquisition workflows
          The Guided Acquisition module has been equipped with new features to perform even more complex Smart Imaging workflows. For this, it now comes with fully developed class selection in the Image Analysis Wizard and allows precise adjustments on how much detailed acquisitions should be run.

          Artificial Intelligence (AI) Readiness

          Artificial Intelligence (AI) Readiness

          Open Model architecture enables model exchange
          Deep Learning tools have become ubiquitously available in image analysis software, and the ZEISS software portfolio is no exception. To foster simple model exchange, ZEN and Vision4D are compatible with APEER Deep Learning and 3rd party models. Apply your favorite models in established workflows free of charge.


          • ZEN Microscopy Software

            Your Complete Solution from Sample to Knowledge

            File size: 5 MB
          • ZEN Data Storage and Data Explorer

            Smart data management in life sciences

            File size: 2 MB
          • ZEN 3D Toolkit

            Visualization and Analysis of 3D Volume Models

            File size: 1 MB
          • Quick Guide ZEN (blue edition)

            File size: 3 MB

        Visit the ZEISS Download Center for available translations and further manuals.

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