Discover New Insights by Connecting Information Across Dimensions

ZEN Connect for seamless data handling, simplified workflows and enriched insights into your samples.

Imagine the possibilities when you can easily combine multiple perspectives of a sample - across scales, across modes of acquisition and across contrast techniques - to provide answers to some of most complicated scientific questions. With ZEN Connect you can now bring a whole portfolio of imaging technologies - ZEISS or non-ZEISS together. Your multimodal data is automatically relocated and overlaid, and then stored in well-organized projects with intuitive image labels. As a result, you gain efficiency and effectiveness with intuitive data management, simplified workflows and limitless navigation.


Intuitive Data Management

Move away from location centric data structure to an entirely sample centric organization.
Gain from project based data storage and effortless image labeling. Get better control over your data structure even in complex experiment set-ups.

Simplified Sample Workflows

Use your standard sample formats without the need for special fiducials. Initiate your workflow with any microscope, analyze your full sample on a large scale, and identify specific areas of interest with the automatic overlay and relocation algorithm.

Limitless Navigation

Analyze data in a wider context connecting large field of view images with the highest resolution details. Work seamlessly with any file format in the open platform. Gain meaningful experiment results through fully connected information.

Application Examples

Live Cell Imaging

ZEN Connect has particular advantages for live cell imaging. Because cells are not continuously imaged on the microscopes in many scientific applications, several minutes or even hours of live cell imaging must be followed by longer reincubation or growth periods. The ZEN Connect workflow makes it fast and easy to repetitively return to the same areas in your sample.

Petri dish overview scan
Petri dish overview scan using a widefield microscope. The tiled images are used to align the sample to the next microscope.

After transferring the petri dish to the LSM, time series were taken through a complete 4D approach using time and z information to visualize the dynamics of the microtubules  


Connectomics research is becoming increasingly important in understanding brain function. To understand cellular details, increasing resolution of the analyzed areas is of major importance. ZEN Connect enables you to analyze your data in a wider context, connecting large fields of view imaged on a wide field system. In this way you will achieve the best possible resolution from specific regions of interest analyzed with LSM or even electron microscopes. With ZEN Connect, data are linked with their context at all times during your experiment.

Neuroscience 1
With ZEN Connect you analyze data in a wider context, connecting large fields of view imaged on a widefield system with higher resolution data single cells on a LSM.
Neuroscience  2
You gain a further increase of resolution by using Airyscan to achieve the best possible resolution of specific regions of interest analyzed with LSM or even electron microscopes.


Understanding immune responses on an ultrastructural level is of major importance in understanding infection processes. The formation of immunosynapses is a rare event which can only be statistically clarified using correlative approaches. ZEN Connect allows you to prescreen your sample on a widefield or LSM system and select regions of interest to analyze the cell biology ultrastructurally on the FE-SEM.

Immunology 1
Zebra fish immune cells prepared for electron microscopy. Ribbons of sections were placed on an ITO-coated cover slip.
Immunology  2
Cells of interest were preselected using widefield imaging and transferred to the SEM to re-shuttle the positions using ZEN Connect and Shuttle & Find.



Overlay and Organize Images From Any Source to Connect Your Multimodal Data

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ZEISS ZEN Connect Software

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