ZEISS Efficient Navigation

ZEISS ZEN Digital Imaging for Light Microscopy

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 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
    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.


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.

ZEN Acquiring Images

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


ZEN Screenshot 2

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


ZEN Screenshot 3

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


ZEN Screenshot 4

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). 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 Package

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
  • (LSM 880, LSM 800, Cell Observer SD, Laser TIRF 3)


Register to download your copy of ZEN lite free of charge

Release Notes on ZEN 2.3 SP 1 (0.2 MB)

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

SR-DIP software for ZEN blue edition
Superresolution processing for bleach series data

How to use the SR-DIP
Important information SR-DIP
Install SR-DIP