ZEN 3.7 Microscopy Software

The Complete Solution – from Sample to Insight

ZEN is the unified user interface for all ZEISS imaging systems. For simple and routine microscope tasks, let the ZEN software guide you directly to your goal. For complex research experiments, you can flexibly create multidimensional workflows with ZEN according to your needs. No matter what task you need to accomplish with your microscope, the intuitive tools and modules of ZEN support you at every step:

• Image acquisition with intelligent automation
• Image processing with scientifically supported algorithms
• Visualization of large datasets with GPU-based 3D engine
• Image analysis with machine learning tools
• Correlation of light and electron microscopes

Intelligent Image Acquisition

Successfully complete even highly complex experiments

Operate all your devices with a single user-friendly software. The intelligent control center "Smart Setup" automatically generates the right settings for you – no matter which type of microscope is used. Want your experiments to be reproducible? Simply use a raw image from previous captures: With a single click, the corresponding experiment is precisely replicated. In addition, ZEN offers many other intelligent automation features: Some guide you in finding rare events, others assist you in calibrating the hardware.

Quantitative Processing

Achieve reliable, reproducible results

More than 180 image processing programs facilitate the conversion and management of your data. Whether kymography or deconvolution – with ZEN, you can easily search and find processing methods using keyword search. ZEN simply reads the metadata from the imported images, displays only the relevant processing steps, and automatically optimizes the preset parameters. Tools for importing third-party files also allow you to import image data from other platforms. In addition, you can easily process multiple images in batches with a separate function area, thus generating unaltered quantitative results.

Powerful Visualization

Work confidently with large datasets

Generate a large 2D tile image with high magnification and multiple channels in no time, which you can smoothly zoom in and out of by simply scrolling with the mouse – like a map app on your smartphone. Have you received 200 GB of cleaned data while working on a mouse brain? Simply load it into the ZEN software and be amazed by the speed and detail of the various 3D rendering methods. With the arivis ImageCore technology and efficient use of system resources, even large 3D images can be displayed on ordinary devices.

Efficient Analyses

Gain insight into research data efficiently

Image analyses with tools for segmentation and alignment are essential for obtaining meaningful information from microscopy data. ZEN supports you with its simple, modular Bio Apps. Each Bio App is designed for a specific application, such as cell counting or confluence measurements, and offers individual segmentation settings as well as optimized data display. The ZEN Image Analysis module with wizard assistant guides you step by step through the creation of your individual measurements.

Unique Correlative Microscopy

Combine perspectives across different scales and modalities

ZEN overlays, navigates, and organizes multimodal data. Spending days painstakingly locating synapses between two specific neurons to determine ultrastructural information? You could work much more efficiently by combining the large field of view of a widefield fluorescence microscope with the high resolution of a field emission microscope. With ZEN, you can quickly survey the entire fluorescently stained section and identify and revisit areas of interest for electron microscopic imaging.

Secure Storage

Easily manage even complex data

ZEN saves each of your valuable experiments with all associated metadata.

The CZI format is compatible with Bio-Formats and can be read directly by ImageJ and many other third-party software products. For easy cross-platform exchange of image data, the files can also be converted to OME-TIFF (Open Microscopy Environment).

ZEN stores and organizes your raw data and manages user access rights on a central, server-based platform to facilitate the management of large datasets. With ZEN Data Explorer, access from any location via browser is possible.

Harnessing limitless possibilities more easily

ZEN software is the comprehensive solution for all microscope users. The software is continuously developed and equipped with additional features for new applications in the life sciences, including automated intelligent image acquisition, intuitive image analysis, and cloud-based data management. However, this wide range of features increasingly complicates the ZEN ecosystem. ZEN Version 3.6 therefore provides simplified options to better utilize the many functions of the software. Many ZEN modules have great synergy potential and are often combined in practice for specific applications. Building on this idea, we have compiled packages that include all important software functions: You now receive new module packages for acquisition, toolkits, and use cases tailored to your experiments. Compared to individual modules, the packages offer significant cost advantages, allowing you to get more value out of your investment.

Acquisition Packages

• Base: Basic image acquisition functions for multichannel fluorescence and time-lapse experiments with manual, encoded, and motorized microscopes.
• Motorized Focus: Image acquisition functions for multichannel fluorescence, time-lapse experiments, and Z-levels including the tools Software Autofocus, Extended Depth of Focus, and Direct Processing.
• Motorized: Image acquisition functions for multichannel fluorescence, time-lapse experiments, Z-levels, tile images, and experiments with multiple positions including the tools Software Autofocus, Extended Depth of Focus, and Direct Processing.
• Advanced: Image acquisition functions for multichannel fluorescence, time-lapse experiments, Z-levels, tile images, experiments with multiple positions, and confocal HDR experiments including the tools Software Autofocus, Extended Depth of Focus, Direct Processing, and the colocalization analysis function.
• Smart: Configure non-uniform acquisition experiments via a simple user interface and adaptive and automated acquisition creation with image analysis or Python script tools.