Digital Imaging for Light Microscopy

ZEN – ZEISS Efficient Navigation

Shortens the Path to Your Goal


ZEN - ZEISS Efficient Navigation is the single user interface you will see on all light microscopy imaging systems from ZEISS.

ZEN microscope software leads you simply and quickly to the result. At all times you see which options the system is making available to you and which step is appropriate to take next. Use ZEN imaging software to achieve scientific success: nothing diverts you from your goal - to document your results and reproduce them at any time.

As a result you save time, reduce training and support costs, and get faster answers to your questions.


Focus on What You Need

ZEN with Axio Observer

ZEN controls all light microscope systems from ZEISS, letting you operate all of your devices with the same convenient interface. ZEN arranges operating elements in a way that follows your work flow. Functions you use only rarely are hidden away, out of sight - but always there with a single click.

Select Fluorophore. Acquire. Done.


Smart Setup is the core of ZEISS ZEN microscope software – your intelligent control centre. Select the dye for your sample from the database with more than 500 dyes and ZEN automatically applies all necessary settings for your imaging system.

A Secure Format for Important Data

ZEN colocalization function

The security of your data gets top priority as ZEN stores each of your experiments with all its metadata. Using the new data format .czi from ZEISS you easily process even the huge amount of data you acquire with our fast 3D imaging systems. Alternatively, store your images as OME-TIFF, the image format specification of the Open Microscopy Environment, to facilitate cross-plattform image data exchange even including your valuable metadata.

Application Video


In this video, our imaging specialists present you the integrated "Light Path". With this interactive tool you see the status of all components of your system at a glance and control them with ease. All you need to do is place your sample under the microscope and select your desired light path. With the microscope software ZEN, working with a microscope has never been easier.


The Right Module for Every Application

Even in the basic version ZEN offers countless functions for day-to-day work with your microscope. Thanks to its modular concept, however, the software guarantees you other advantages too: you can tailor ZEN precisely to your requirements and only need to learn to work with the functions you actually need. You will find the optimal ZEN module for every task here.

Acquiring Images
Use ZEN to create meaningful microscope images. Give two-dimensional multichannel images additional depth of field, for example, or acquire temporal and spatial information together with your image.

ZEISS ZEN for Image Acquisition

Multi Channel

Multi Channel

With ZEN Multi Channel image acquisition module you create images with multiple channels. To do this, with widefield systems you combine any number of fluorescence channels with images in transmitted light, e.g. phase contrast, according to your requirements. A special feature here is that you can select your dyes from the integrated database. This already contains data sets for more than 500 fluorochromes and can be expanded as required.

For each fluorescence excitation wavelength, the relevant channel is acquired with the optimal exposure time. An independent exposure time and microscope setting can also be assigned to each channel. The advantage: you structure your experiments flexibly and perform even highly complex multichannel experiments simply.

Z Stack

Z Stack

ZEN Z Stack module helps you to acquire axial image stacks on your ZEISS microscope with motorized focus drive. The image acquisition program controls the Z-drive of your stand in precisely the right increments and synchronizes it with acquisition. ZEN can calculate the increments fully automatically, if required, or you can allocate them manually.

A special feature here is that from now on you create your Z Stacks with graphical support. This assistance is even available to you dynamically during acquisition. The size of your experiment, which is saved in a compact .CZI file, is limited only by the travel range of your system and the minimum increment.

Extended Focus

Extended Focus

With the Extended Focus module you generate images with extended depth of field from previously acquired Z-stacks. The ZEN module extracts sharply imaged details from existing images at different focus positions and combines them to create a new image. The advantage: you always have maximum depth of field in all regions of your images in transmitted light, reflected light and fluorescence contrast.

Tiles & Positions

Tiles & Positions

With the optional ZEN Tiles & Positions module and a motorized stage you scan your specimen automatically, making it possible to analyze large areas. A large, virtual overview image can be generated in this way from numerous individual images. This allows you to navigate over the specimen like a map and zoom easily into any regions of interest. Tiles & Positions and ZEN align the individual images precisely in relation to one another, providing the optimal basis for further analyses.

A special feature here is that a software wizard helps you to mark positions on multiwell plates, multi-chamber slides, slides and dishes interactively and locate them with a click of your mouse.

Experiment Designer

Experiment Designer

Would you like to plan complex experiments in advance, but retain complete control at all times? From now on ZEN will help you do this! Using the Experiment Designer module you will even be able to create images in several combined image dimensions with just a few clicks of your mouse, and after only a short training period. You plan combinations or repeats of your image acquisition tasks. such as time series, Z-stacks, tile/multiposition images and channels, in a clearly visualizable form using experiment blocks.

Repeated steps can be achieved very easily using loops, and pauses or interactions can be defined if your experiment extends over a long period and requires interactive intervention. The Experiment Designer supports an almost unlimited number of blocks in your experiments, which can naturally be saved and reloaded at any time. You plan, ZEN controls.

Time Lapse

Time Lapse

With the ZEN Time Lapse module for widefield systems you control your microscope, camera and imaging software from ZEISS. This allows you to document dynamic processes in your specimens with a compact image sequence. ZEN controls the exposure setting for your microscope here with millisecond precision. With the Time Lapse module, damage is no longer caused to specimens as a result of unnecessarily long exposure times – an important requirement for your quantitative analyses of living specimens.

Your most impressive images can be exported at any time into common video formats, such as AVI or MOV, for demonstrations and publications. The advantage: images are acquired with maximum speed and are only limited in size by the free space available on your hard drive.

Manual Extended Focus

Manual Extended Focus

With the Manual Extended Focus module you use ZEN to create images without being restricted by your microscope's depth of field. The software module extracts the sharp details at different focus positions from the interactively acquired Z-stacks and combines them into an image with maximum depth of field. Using the live image display, additional images can be added to the intermediate result.

The advantage: you always have maximum depth of field in all regions of your images. This even applies irrespective of the contrast technique used – whether transmitted light, reflected light or fluorescence, thanks to our wavelet algorithm.



With the Autofocus module for widefield systems you determine the optimal focus position for your specimen in transmitted light, reflected light and reflected light fluorescence. ZEN "learns" the ideal position during your everyday work on the light microscope and is therefore trained continuously with regard to correct focusing. No calibration procedure is required for this and the focus is recorded automatically for all objectives and contrast techniques.

The additional advantage for you: in the case of images that are acquired over time or at different positions, the system continually refocuses automatically.



This ZEN module is ideal if your specimens no longer fit into the image field. With Panorama you create high-resolution overview images from individual images. The software puts the images together with pixel precision. The advantage: even images that have been acquired offset from each other can be joined precisely using ZEN and Panorama. This means that important details from the individual images of your microscope specimen are recorded in a single image.

A special feature here is that you can use the live image as a 'joystick' and therefore acquire the individual images even more quickly.

Processing Images
With these powerful additional modules you can display fluorescence signals with even greater contrast or visualize image stacks in 3 dimensions. ZEN therefore creates the best possible conditions for your experiments and publications.

ZEISS ZEN for Image Processing



The Colocalization module can be used to unmix the overlapping signals of different fluorescence channels.
To do this, the ZEN software makes use of modern methods, such as the automated threshold value method of Costes et al. Meaningful results on the colocalization of proteins can be obtained as a scatter plot, image and data table.

If you only want to analyze certain areas of the image, you can simply mark the corresponding region directly in the image and scatter plot. Spectral Colocalization for ZEN then supplies the data both for the whole image and the selected regions.
Of course you can also export your measured values in CSV format and process them further using a spreadsheet.



Due to the optical properties of the microscope system, light from the areas above and below the focal plane also enters the image. This means that fine structures on the specimen can no longer be picked out.

It is precisely here that the 3D Deconvolution software module starts, by calculating out of focus light back to its place of origin. The distorted specimen structure unfolds and is displayed more sharply. This technique also reduces any image noise that may be present, making a decisive contribution to the first-class image quality of your image stacks and 3D models.



With 3Dxl you can display multi-dimensional image stacks in 3D. The ZEN module processes up to 8 different channels and works seamless with other image dimensions such as time (“4D”) or multiple tiles. Highlight is its ability to handle really large images (hundreds of gigabyte) efficiently and smoothly.

You can position a three-dimensional model interactively according to the view that you require and provide it with annotations, coordinates and scaled axes. It goes without saying that 3Dxl also provides you with tools for the interactive measurement of distances and angles. Would you like to present or publish the result afterwards? If so, simply export the images and animations into common image formats, such as TIF, JPG or AVI.

Analyzing and Interpreting Image Data
ZEN provides important information on your microscope specimens interactively or fully automatically. Besides size and volume information, this also includes detailed data on cell physiological processes

ZEISS ZEN for Image Analysis

Image Analysis

Image Analysis

Would you like to generate automatic measurement procedures simply yourself? The ZEN Image Analysis module makes it possible for you to do this, even without programming knowledge. With our measurement program wizard you tackle even complex measurement tasks yourself in just a few minutes. Once created, the programs are always available to be used for an unlimited number of images. You retain full control over the measurement process at all times.

Each step can be changed interactively before it is performed. Even processes that run automatically can be easily interrupted if necessary, allowing you to adjust the settings to your requirements. If desired, you can of course also use the Image Analysis module to export all your measurement data simply in the Excel-compatible CSV table format and process them further as you wish.

Interactive Measurement

Interactive Measurement

Measure microscopic structures interactively. Generate gray value profiles of cell organelles. Trace the contour of a cell nucleus with your mouse to determine its area. Count cells simply by clicking on them.

With the ZEN and the Interactive Measurement module you define yourself which of the 90 plus morphological parameters available are measured in your images. The Contour tool, for example, allows you to determine the area, diameter and perimeter of a cell simultaneously. You perform a comprehensive and precise analysis of the cell in a single operation, even in the online image. For each tool you can specify which measurement results you want ZEN to show in your image.

The Interactive Measurement module also enables you to present your measurement data impressively in the form of a table, list or graph. ZEN 2011 saves your measurements together with the image data in the new CZI file format. This means that you can export your measurement data at any time in Microsoft Excel-compatible CSV format for documentation or further analyses.

Open Application Development for ZEN
You have a special application that demands functionality beyond ZEN? Use the integrated OAD (Open Application Development) environment of ZEN (blue edition).

Join the OAD community

ZEN Open Application Development

With OAD you create your own macro solution based on the well-established Python language. Benefit from the simple access to a vital set of ZEN functions and the ability to include libraries such as the .Net Framework.

Join the OAD community to discuss macros and help other users to develop their ultimate solution in the ZEN OAD Forum.

Module Packages

ZEN: Your Flexible Choice of Components

Module Package

Features & Applications  

ZEN lite

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

ZEN desk

  • Supports offline analyses
  • Extend this version with modules for image processing and analysis

ZEN pro

  • Controls all ZEISS light microscopes except laser-based 3D imaging systems

ZEN system

  • Controls all ZEISS light microscopes including laser-based 3D imaging systems

Upcoming Features of ZEN!

Don’t miss out on the latest release and take advantage of new features and functions

Improvements have been made across many key areas of the software. On the one hand we have enhanced and added to new functions like Machine learning, 3D image analysis and data management. On the other hand we have optimised existing utilities and modules in terms of convenient use, features and speed.

Function Module / Featrue What's New


Welcome screen

Shortcuts to load a data, acquire an image, or create a Connect project, faster than ever
Stay updated with newsfeeds and hotfix release info

Triggered acquisition

Triggered acquisition is now optimized for online ratio metric experiments
Improved safety feature to avoid sample collision

Guided Acquisition

Focus map is now implemented for more accurate tile scan



Multi-GPU supported for faster results



Interactively visualize your 3D data and segmented results
Advanced bridge functionality to send your 3D data to Vision4D for deep dive analysis


3D image analysis

New module to segment and analyze your 3D data
Step-by-step wizard to guide you through the workflow
Interactive table available to sort, highlight, and export the segmented results


Use your own machine learning models (czmodel) for more reliable image segmentation
Batch analysis is now available for increased throughput
Improved usability for reduced learning curve

Intellesis and APEER

Intellesis now supports 3D image analysis
Artifical Neural Network (ANN) model are now supported


ZEN connect

Improved measurement functionalities


ZEN Data Storage

Auto-upload of images directly after acquisition

ZEN Data Exlporer

Extended metadata are now supported
Visualization of ZEN Connect projects is improved

Visit the ZEISS portal – access our download center.


ZEN Microscopy Software

Your Complete Solution from Sample to Knowledge

pages: 28
file size: 4580 kB

ZEN Data Storage and Data Explorer

Smart data management in life sciences

pages: 4
file size: 2289 kB

Quick Guide ZEN (blue edition)

pages: 22
file size: 3537 kB

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