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Zen2 Blue

Zen2 Blue

Zen2 Blue is your powerful yet simple digital imaging software solution for for all applications in light microscopy - from routine to research.  

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ZEN 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 Carl 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.

Focus on What You Need

ZEN controls all light microscope systems from Carl 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.

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 itsmodular 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.

Multi Channel

With ZEN Multi Channel image acquisition module you create images withmultiple 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.

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.


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

With the optional ZEN Tiles & Positions module and a motorized stage youscan 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.


Time Lapse

With the ZEN Time Lapse module for widefield systems you control your microscope, camera and imaging software from Carl Zeiss. This allows you todocument dynamic processes in your specimens with a compact image sequence. ZEN controls the exposure setting for your microscope here withmillisecond 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.


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.



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.



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.



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



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.


3D VisArt

With 3D VisArt you can display multi-dimensional image stacks as 3D volume models. The ZEN module processes up to 8 different channels and, besides the spatial image coordinates, also takes the time lapse informationrelating to your images into consideration.


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.


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.


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.