Acquire. Process. Visualize.
Analyze. Correlate. Store.

ZEN Microscopy SoftwareYour Complete Solution from Sample to Knowledge

zeiss.com/zenExperience the End-To-End
Microscopy Software›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

ServiceZEISS Efficient Navigation – ZEN, for short – is the universal user interface you
will see on every imaging system from ZEISS. No matter what microscopy task
you have, you will find intuitive tools and modules to assist you:
•
•
•
•
•
•

Acquire images using smart automation
Process images with scientifically proven algorithms
Visualize big data by GPU powered 3D engine
Analyze images via Machine Learning-based tools
Correlate between light-light or light-electron microscopes
Store raw data in a secure format locally or in the cloud

For simple and routine works, ZEN leads you straight to result. The universal
user interface lets you operate any ZEISS microscopes with the same g­ raphical­elements and workflows. You’ll save time and reduce costs for training and­support.
For complex research experiments, ZEN offers the flexibility to design multi-­
dimensional workflows the way you wanted. The “Optimal” buttons let you
quickly start with default parameters, and the “Show All” buttons open endlesspossibilities. You’ll never run out of ideas when designing experiments.
ZEN provides a comprehensive end-to-end solution for any microscopy user.
The wide selection of software modules brings you from sample to knowledge.
To simplify the options and make ZEN more accessible, the modules are grouped
into dedicated acquisition, toolkit and application packages according to theirintended use.

2

Acquire. Process. Visualize.
›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Smart Acquisition

Quantitative Processing

Powerful Visualization

Make your most complex experiments a success.

Obtain reliable and reproducible results.

Interact with your big data confidently.

ZEN controls all ZEISS imaging systems so you canAcquiring stunning microscopy images is just theAdvances in microscopy automation, camera

operate every one of your devices with the same

beginning of the experimental journey. More thantechnology, and light-sheet microscopy have fu-

convenient interface. As a researcher, you might

180 image processing tools, using transparent andeled the exponential growth of data size and the

not be familiar with all microscope components,

scientifically proven algorithms, help you transform

challenge of big data visualization. Using ZEISS

but you surely know your sample and the dyes

and manage your data. Simply search the keyword

Axioscan 7 slide scanner, you can quickly gener-

used. With “Smart Setup”, the intelligent controlof your intended method, e.g., kymograph orate a huge 2D tile scan with multi-channels at

center, simply search and select the dyes and ZEN

deconvolution, ZEN will lead you straight to it. Not

high magnification. The powerful ZEN pyramid

will automatically generate the settings for you,familiar with those processing settings? ZEN will

data structure enables you to smoothly zoom inregardless of the microscope types. Aiming forread the metadata of the input image, then display

and out of such 2D data with a simple mouse

reproducible experiments? So long as you have

only the logical processing steps, and optimize

scroll, just like using a map application on your

one raw image from a previous acquisition, athe default parameters automatically. You cansmartphone. Having 200 GB of cleared mouse

simple click lets you replicate the exact experi-even process images from other platforms using

brain data from ZEISS Lightsheet 7? Just load it inment precisely. And that’s just the start of ZEN’s

ZEN third-party import tools. With a dedicated

ZEN – you will be amazed by the speed and clarity

smart acquisition. You will find plenty of otherworkspace, you can also batch process multipleof the various 3D rendering methods. Powered

smart automation, some guide you for rare events

images with ease for quantitative and unbiased

by arivis ImageCore technology and efficient use

detection, and others assist you with hardware

results. With many of those processing tools in ourof system resources, you can view your large 3D

calibration.

free version, ZEN lite, you can comfortably carry on

images even on regular consumer hardware.

working on your laptops at home.

Sample courtesy of Wouter Masselink and Elly Margaret
Tanaka, IMP, Vienna

3Analyze. Correlate. Store.
›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Effortless Analysis

Unique Correlative Microscopy

Secure Storage

Gain insight into your research efficiently.

Combine perspectives across scales and modalities.

Stay confident when dealing with complex data.

Image analysis is essential to extract meaningful

The fascinating variety of microscopy imaging

Data security gets top priority as ZEN stores each

information from your microscopy images, via

technologies allows observing the same speci-of your valuable experiments with all its metadata

digital tools of segmentation and registration.

men faster, deeper, longer, and at a greater level(476 entries and counting). The proprietary .czi

However, building a specific image analysis work-of detail from different perspectives. Imagine thefile format is comprehensive, easy-to-work-with,flow that adapts to one’s application is not an easy

possibilities for answering your scientific questions

big data-supported, yet open. It is Bio-Formats

task. It requires knowledge of image processing,when you combine these images from multiple

compatible and can be read directly by ImageJ,

and the ability to assemble a series of operations.

instruments, ZEISS or third-party. ZEN Connect isand many other third-party software. With a

ZEN addresses this imbalance with the simple

your unique correlative microscopy solution thatsingle click, you can also export them into OME-

and modular Bio Apps. Each Bio App is optimized

overlays, navigates, and organizes your multimodal

TIFF, the image format specification of the Openfor one type of application, e.g., cell counting or

data. Spending days painfully locating synapses

Microscopy Environment, to further facilitate

confluency measurement, with tailored segmenta-

between two special neurons for the ultrastructural

cross-platform image data exchange. Managing

tion settings and streamlined data presentation.

information? You can substantially improve yourmassive amounts of data in your facility?

Needing to build a special workflow? The wizard-

efficiency by combining the large field of view of

ZEN Data Storage provides you a server-based

based ZEN Image Analysis module guides you stepa widefield fluorescent microscope, and the highcentral platform to store and organize yourby step to create your unique measurements. You

resolving power of a field emission electron micro-

raw data and manage user access right; while

can also integrate our machine learning-based

scope. ZEN Connect lets you quickly overview theZEN Data Explorer grants user browser-based

segmentation tool, Intellesis, into the workflow forwhole brain slice with fluorescent markers, identify-­access from anywhere.

the easy and accurate analysis of noisy images.

ing and relocating ROIs for EM imaging.

Courtesy of G. Eichele, Department of Genes and Behavior,
Max Planck Institute for Biophysical Chemistry, Göttingen

4

What’s New: ZEN 3.6 Highlights›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

New Packaging Structure

ChannelTime

Z Stack

Extended Focus

Tiles & Positions

Software Autofocus

Simplified access to endless possibilities
ZEN software provides a comprehensive end-to-end solution for any microscopy user, continuously evolving to address emerging life science applications
with added features, e.g., automated smart acquisition, intuitive image analysis, and cloud-based data management. However, the increased capabilities
also make the ZEN ecosystem complex.
With ZEN version 3.6, you get simplified options that make the numerous­capabilities of the software more accessible. Many ZEN modules show greatsynergy and have been frequently combined to get your specific job done.
­Using that as the guiding principle, we have consolidated all the powerfulsoftware functionalities into a simple set of acquisition, toolkit, and application packages tailored to your experiments. The packages come with a substantial price saving compared to the individual modules, so you can get morevalue for your investment.
N See page 7 for an overview of the simplified ZEN structure.

Example of Motorized Acquisition Package (additionally including Direct Processing)
The Motorized Acquisition Package will fulfill all your needs for flexible multi-dimensional image
acquisition: multi-channels, time series, z-stacks, tiles, multi-positions, and the combination of anyof the above dimensions. Additional tools of software autofocus, direct processing, and extended
depth of focus provide extra creativity when designing your next experiments.

5

What’s New: ZEN 3.6 Highlights›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

AI Denoising is the latest addition to the AI Toolkit package. It is based on

Raw low-SNR image

the popular Noise2Void Deep Learning algorithm. It comes with a dedicated
ZEN training environment and is extremely easy to use, all you need is thenoisy input image. Trained models can be re-applied to an unlimited number ofimages with a dedicated IP function. The algorithm is GPU-compatible, whichmakes it reasonably fast, but can also run on CPU, if needed. The method
especially performs when applied to low signal-to-noise imagery of any kind,light microscopy as well as electron microscopy – well suited for dealing withdifficult imaging conditions such as weak staining or phototoxicity problems.
Simplified workflows make parameter setup (for background subtraction and

Low-SNR image + AI Denoising

image smoothing methods) obsolete. Combine AI Denoising with other analysis tools and get improved results of adjacent segmentation or object classification methods.
APEER, the Deep Learning platform for microscope image analysis, is also
becoming more and more convenient to use, which is simultaneously goodnews for ZEN. Seamlessly import trained models into the Intellesis Segmentation tool to make full use of the modern Annotation and Training Pipeline in

Reference high-SNR image

APEER. Conveniently annotate difficult data sets to semantic and instance segmentation –without any need for expensive hardware. Options for overlappingclasses, on-the-fly predictions for iterative user interaction and clean documentation of all data sets and training runs make this tool a joy to work with.

Convolaria, acquired with ZEISS Axio Imager 2
A short acquisition time (5 ms) results in a noisy raw image (upper section), but the signal-to-noise
ratio (SNR) can be improved significantly by AI Denoising post-processing (center section).
A high-SNR image is shown as reference (lower section).

6

Your Simple and Affordable ZEN Packages›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Instrument

Base Software

Manual Microscopes

Motorized Microscopes

ZEN lite

Laser-Based Systems

ZEN *ZEN Desk **Acquisition Packages

Base Acquisition

Motorized Focus
Acquisition

Motorized
Acquisition

Advanced Acquisition

Smart Acquisition ***Toolkit Packages

Application Packages

Special Features

2D Toolkit

3D Toolkit

Vision4D Toolkit ****AI Toolkit

Connect Toolkit

Developer Toolkit

Deconvolution Toolkit

Molecular Quantification
Toolkit

Peripheral Device Drivers

LSM Plus

Airyscan & jDCVPhoton Counting,
FCS and RICS

Sample Navigator

Lightsheet &Lattice Lightsheet

Correlative Array
Tomography

EM Processing

Bio Apps* Includes Base Acquisition Package; ** No device control and acquisition features; *** Requires 2D Toolkit Package; **** Sold as a stand-alone software

7

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Panorama

Manual Extended Focus

APEER On-site Basic

Generate precise, high-resolution overview

Generate images manually with no limit on depth

Use APEER modules fully integrated in ZEN:

­images from manually-acquired individualof field:• Use public and private APEER modules to en-

2D images:• Extract sharp details from individual images at• Acquire overlapping individual multi-channel
images interactively and combine them to forma panorama image on microscopes with an
encoded or motorized stage.
• 3D panorama images can be acquired onstands with a motorized Z-drive.
• Live Panorama: ZEN automatically takes images

various focus positions and combine them into
an image with extended depth of field.
• Works with images acquired interactively.
­Images can be added to the intermediate result

able additional processing and analysis features
and workflows in ZEN incl. Python scripting.
• Remote execution within your local IT infrastructure is supported• Customized and open-source image analysis

via a time interval function or key function

functions in ZEN, provided via APEER• Wavelet algorithm allows use in transmitted• Further ZEN integration of processing andlight, reflected light and fluorescenceanalysis via APEER On-site Advanced moduleand stitches them during sample navigation.
Contact us: apeer-solutions@zeiss.com

Included in: ZEN lite (free)Included in: ZEN lite (free)Included in: ZEN lite (free)8

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Measurements

Data Storage Client

Spectral Unmixing

Perform interactive measurements:

Get access to the connected laboratory solution

Extract single fluorescence dyes from strongly• Morphological parameters of interactively

ZEN Data Storage:

overlapping multi-channel or Lambda stack data:• Centralized storage and flexible concurrent• Widefield multi-channel acquisition anddefined contours: area, orientation angle,
perimeter, diameter, center of gravity, radius ofcircle with equal area, shape factor, boundingbox, projections, etc.
• Intensity values for rectangles and contours• Free configuration of all interactive measure-­access for your images and data
• Central, intelligent data management including
access management and sharing of data
• Centralized user management with role-based
permissions

ment tools displays desired parameters in• Separation of image acquisition and analysis

tables, lists or graphs• Web-based access to the data from anywhere• Interactive measurement in online images

via the included ZEN Data Explorer• ZEN Data Explorer smartphone and tablet app

LSM Lambda stack acquisition• Export and import of single component reference spectra• Interactive mode: user-selection of regions• Fully automatic mode with Automatic Component Extraction (ACE)• Weighted unmixing for channels with low
signal-to-noise ratio• Residual channel calculation

available for Apple and Android

Included in: ZEN lite (free), ZEN, ZEN desk

Included in: ZEN, ZEN desk

Included in: ZEN, ZEN desk

9

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Third Party Import

Direct Processing

Extended Focus

Import third-party microscopy images into ZEN:

Perform time-consuming image processing tasks

Generate images with no limitation of depth• Third-party images in native format including

simultaneously during image acquisition:of field:• Deblurring for fast and easy 2D background• Extraction of the sharp details from individual

extraction of relevant metadata• Metadata extraction depending on the originalformat (powered by Bio-Formats)removal with truly quantitative output­images at various focus positions, combination• Processing methods: deconvolution, Airyscan

into an image with high depth of fieldprocessing, raw convert, denoising, unsharp• Processing of already acquired Z stacks

mask• Wavelet algorithm allows use in transmitted light,• Pipelines to set up sequences of image process-reflected light and fluorescenceing functions• Remote processing to maximize computational
resources during acquisition.
• Instantaneous side-by-side comparison of raw
and processed data

Included in: ZEN desk, Connect Toolkit

Included in: ZEN desk, Motorized Acquisition,

Included in: ZEN desk, Motorized Acquisition,

Advanced Acquisition

Advanced Acquisition

Sample courtesy of H. Braun, LSM Bioanalytik GmbH,­Magdeburg

10ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Colocalization

Multi-Channel

Time Lapse

Quantify colocalization in two channels:

Acquire fluorescence and transmitted light images

Acquire images over a period of time:• The gray value pixel distribution is displayed in

in independent channels:• Images acquired at maximum possible speed

two channels with the help of a scatter plot

• Technically unlimited number of independent• Definition of intervals between images, total

with four quadrants. Link scatter plot, image

channels for reflected light and transmitted

and data table.

light techniques• Draw multiple regions into the image. Data

• Fully automatic generation of the required

table shows measured values dynamically for

microscope setting for a channel with theboth - the entire image and the individual­possibility of adjusting the setting manually forregions.

the channel• Display and export 17 measured values in adata table that can be exported for further
analysis.

• Independent exposure times and shading­corrections for each channel• Simultaneous acquisition of two channels using­acquisition duration and number of time points• Acquisition can be interrupted to analyze
already acquired images or change experimentparameters.
• Experiment size limited only by free space on
the hard drive• Time series can be started and stopped­manually, at fixed times, after a waiting period
or by input (trigger) signal.

two synchronized cameras

Included in: ZEN desk, Advanced Acquisition

Included in: Base Acquisition, ZEN

Included in: Base Acquisition, ZEN

Click here to view this video

11

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Z stack

Software Autofocus

Tiles & Positions

Acquire Z stacks with the help of a motorized

Determine the optimum focus position of theGenerate precise, high-resolution images throughfocus drive:

specimen:

automatic scanning of predefined regions and• Definition of the Z stack in first and last or• For transmitted light, reflected light and fluo-

positions of a sample:

center mode
• Z stack limited only by the travel range of thesystem and minimum increments• Optimum Distance button sets the correct
increment to satisfy the Nyquist criterion.
• Integrated Z-drive backlash compensation for
maximum precision• Z stack can be acquired at relative or absolute
focus positions in the experiment.

rescence• Calibration-free operation for all objectives andfilter sets
• Quality, search area, and sampling rate adjustment of the autofocus to the application• Automatic Autofocus activation during the experiment at defined time intervals and channels
and at predefined tile positions or individual
positions• Regions of tile images and individual positions
can be combined freely• Automatic scanning with a motorized stage• Overlapping individual images can be combined into an overview image using “stitching”
algorithms• Predefined or customized multi-well plates,
multi-chamber slides, slides and dishes• Focus Strategy Wizard for best focusing results

Included in: Motorized Acquisition, Advanced

Included in: Motorized Acquisition, Advanced

Included in: Motorized Acquisition, Advanced

Acquisition

Acquisition

Acquisition

12

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

HDR-Confocal

Guided Acquisition*

Experiment Designer

High dynamic range imaging by automatic

Perform targeted acquisition of objects of interest

Configure inhomogeneous acquisition experi-

acquisition and merging of images with different

fully automatically:ments:

excitation intensities:• Save time and storage space by focusing the• All experiment dimensions supported: time

• Single-click operationacquisition on objects of interest only

series, Z stacks, tile images, channels• Automate your workflow comprising of• Operation via a simple graphical interface using

weak and bright objects within the same image

overview scan, object detection via auto-

four different types of experiment blocks along• Automatic triple scan with increasing excitation

mated image analysis, and high-resolution,a timeline: Acquisition, Execute, Pause and• Optimal representation of the morphology ofintensity and processing on the fly

multi-­dimensional image acquisition for eachdetected object• Customize focusing strategies for both overview scan and detailed acquisition• Automatically save all images, tables and­settings in one folder for easy access and reuse

Included in: Advanced Acquisition

Included in: Smart Acquisition

Sample courtesy of F. Tatin, Cancer Research, London

Sample courtesy of Dr. L. Lim, Katholieke Universiteit, Belgium* requires Image Analysis

Interaction blocks• Synchronous or asynchronous control of hardware actions during the experiment• Definition of a number of iteration loops• Powerful processing functions to extract or fusemultiblock images

Included in: Smart Acquisition

13

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Experiment Feedback*

Image Analysis

Advanced Processing & Analysis*

Experiment Feedback (also known as conditional

Create automated measurement programs guided

Extend the processing functions and perform

or adaptive experiment) allows the definition of

by an intuitive software wizard:

feedback experiments:

specific rules and actions to be performed during• Flexible class and subclass definition• Add more collections of image processing

an experiment:• Objects selection either by a few reference• Change the course of the experiment depending on the current system status or the natureof the acquired data on runtime

objects, by automatic thresholding, or based onmachine learning• Refine results with object separation and filters• Integrate tasks such as data logging or starting• Measure geometric and intensity features ofan external application (e.g., Python or MAT-

individual objects or in the entire image

LAB) directly into the experiment• The feedback script uses Python and ZEN specific commands• Examine results at one glance using interactive
plotting, with a direct link between images,
tables and graphs• Export results for further analysis.

Included in: Smart Acquisition* requires Image Analysis; is part of Advanced Processing &Analysis

Included in: 2D Toolkit

functions: Edges, Arithmetics, Morphology,
Segmentation, Binary• Adaption and modification of running experiments using Python scripts• Access to results from the online image analysis
during the experiment runtime• Access to the current system status• Data Logging or starting of external applications like Python, Fiji or MATLAB directly fromwithin the imaging experiment

Included in: 2D Toolkit, 3D Toolkit* requires Image Analysis

14

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

3D Visualization*

Advanced 3D Visualization*

3D Analysis

Visualize 3D and 4D image stacks:This module introduces the Tomo3D viewer:

Enable analysis of 3D image objects:• Display of 3D volume models using efficient ray• Rendering of up to three 2D and one 3D view• Integrated with Image Analysis Wizard

tracing technology, even for large data
• Display of up to six channels and time series• Rendering methods: Transparency, Volume,
Max Intensity Projection, Surface, Mixed, withup to three clipping planes• Visualization of dense structures, such as EM,
XRM and dense fluorescent data
• Send to arivis Vision4D with saved settings andsample pipelines for easy 3D analysis

panes together• Ray-casting-based volume rendering with transparency, volume and maximum intensity modes• Flexible channel-wise adjustment of 3D view,
background color and lighting• The position of the three orthogonal 2D viewpanes are synchronized with the 3D view
• Navigation through the sample and projection
views via colored cut lines• Compatible with various segmentation methods: threshold-based, Intellesis segmentation,
APEER semantic segmentation• 3D morphological operations for post-processing• Multi-class object table for display, quantification, and .csv export of object features, including 3D parameters• Sorting and publication-grade visualization of
objects with different transparency modes• Generate animations

Included in: 3D Toolkit

Included in: 3D Toolkit

Included in: 3D Toolkit* powered by arivis

Courtesy of H. Reuter, Leibniz-Institute on Aging –Sample courtesy of William Okafornta, Core Facility CellularF­ ritz-Lipmann-­Institut e.V. (FLI), Germany* powered by arivis

Imaging (CFCI), TU Dresden

15

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

ServiceIntellesis Segmentation

Intellesis Object Classification

Intellesis Denoising

Machine-learning algorithms to segment images:

Classify segmented objects with Machine Learning:

Apply Noise2Void-based image denoising:• Train a simple image segmentation model or• Training environment with class assignment• Improve signal-to-noise ratio of images

import pre-trained deep neural networks.

• Compatible with objects obtained by conven-• Suitable for fast frame-rate, low-phototoxicity,• Support of any multi-dimensional datasets
including tiles, Z stacks or multi-channel images

tional or Intellesis segmentation• Support of any multi-dimensional datasets• Compatible with most common image formats

including tiles, Z stacks or multi-channel images

such as CZI, OME-TIFF and imported third-party• Compatible with most common image formats

formats from other vendors• Fully integrated with the ZEN Image Analysis
pipeline and scripting interface• Open-Source PyPi package to enable usage ofexternally trained networks inside ZEN

such as CZI, OME-TIFF and imported third-party
formats from other vendors• Well-established open-source machine-learning

low-photobleaching or low-staining intensity
experimental conditions• Deep Learning training and inference completelyfrom within ZEN• Unsupervised algorithm for training basedon raw input, no additional reference images
neededalgorithms, powered by Python, TensorFlow,• No parameter setup necessary

ONNX, Scikit-Learn, and Dask

• Runs on any CPU, but also GPU-compatibility
for acceleration

Included in: AI Toolkit

Included in: AI Toolkit

Included in: AI Toolkit

Noisy

Denoised− Quality+ Quality+ Long-term Imaging+ Long-term Imaging+ Sample Viability+ Sample Viability

16

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Connect*

Macro Environment

Deconvolution

Acquire and correlate images from different

Customize and automate ZEN using powerful

Enhance your 3D image stacks with deconvolution

instruments like light or electron microscopes to

Python scripts:

algorithms:

enable a sample-centric workflow:• Integrated script editor with debugging, record-• Efficient multi-CPU based processing• Interactive control of stage movement from theZEN Connect workspace

ing and code completion• Additional speed gain via GPU acceleration with

• Integration of APEER modules and external• Import of images into projects

software packages like Python, MATLAB or Fiji

• Import of third-party microscopy images pow-

in an automated workflow

ered by Bio-Formats• Export of merged project view as image or fly-(depending on imaging system)• Uses IronPython in order to integrate• Compatible with conventional widefield,• .NET-based functions­Apotome, Lightsheet 7, Lattice Lightsheet 7,

through video

confocal, or multi-photon microscopes.

• Export to SerialEM• Four primary methods, plus more than 15 published methods (e.g., Richardson-Lucy)* Add-ons to extend functionality of ZEN Connect available.
For more information, please see separate product info.

Included in: Connect Toolkit

multiple CUDA-compatible graphics cards• Improvements in resolution down to 120 nm

Included in: Developer Toolkit

Included in: Deconvolution Toolkit

ImageJ

FIJI

MATLAB

PythonCourtesy of G. Eichele, Department of Genes and Behavior, Max
Planck Institute for Biophysical Chemistry, Göttingen, Germany

17

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

FRAP Efficiency Analysis

FRET

Automated Photomanipulation*

Analyze FRAP / FLIP or similar time series acquisitions:

Analyze FRET datasets:

Automate photoactivation or photobleaching at mul-

• Analysis of time series acquisitions with bleach• Support of Sensitized Emission and Acceptor

tiple positions based on image analysis. The system

events to determine the half time of recovery /decrease of fluorescent signals• Support of mono or bi-exponential fit

Photobleaching• Special FRET view with calculation of control parameters, a color-coded display of the­algorithms including options for backgroundresulting images, and the intensity changes ofcorrection and correction of imaging-induced

selected image regions

photo-bleaching• Supported methods: Gordon, Xia, Youvan

executes the following steps without user interaction:• Acquisition of a multi-position image defined inTiles & Positions tools• Identification of photomanipulation ROIs basedon a customized, pre-defined image analysis• Photomanipulation experiment as defined forbleaching and time series tools• Evaluation of grouped ROIs

• For LSM 900, LSM 980 and Celldiscoverer 7
with LSM 900
Included in: Molecular Quantification Toolkit

Included in: Molecular Quantification Toolkit

Included in: Molecular Quantification Toolkit* requires Image Analysis

18

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

ServicePhysiology

Cell Counting

Confluency

Measure fast ion fluctuations such as intracellular

From our Bio Apps portfolio delivering out-

From our Bio Apps portfolio delivering out-­­

calcium in living specimens interactively:of-the-box image analysis, tailored result pre-of-the-box image analysis, tailored result pre-• Imaging with single wavelength (e.g., Fluo-4)

sentation with interactive measurement tables,

sentation with interactive measurement tables,

heatmaps and plots:

heatmaps and plots:• Automatically detect fluorescently labelled cell

• Automatically quantify cell confluency directly

and dual wavelength dyes (e.g., Fura-2)• Online ratio calculation and ratio image display• Flexible charting and image display• Off-line data table display with data exportfunctionality• Definable switches for online annotations andchange of acquisition speed• Pausing and refocusing via a live camera view

nuclei in biological samples• Suitable for measuring proliferation or survival• Measure cell counts, nuclear intensities, mean
intensities and mean areas• Optimized for measurements in screening­applications with multi-well setups• Freely configurable TTL triggers

Included in: Molecular Quantification Toolkit

from transmitted light or fluorescent images• Applicable for quality control in cell-based­assays and read-out in wound healing assays• Measure the area covered by cells or the area
percentage• Optimized for measurements in screening­applications with multi-well setups

Included in: Bio Apps

Included in: Bio Apps

19

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Automated Spot Detection

Gene and Protein Expression

The Bio Apps portfolio delivers out-of-the-box

The Bio Apps portfolio delivers out-of- the-box­image analysis and tailored result presentation:

image analysis and tailored result presentation:• Automatic quantification of spots in the cell

• Automatic quantification of the transfection

nuclei• Applicable for FISH applications, telomere / centromere analysis or focus counting• Measurement of the total number of spots, theaverage number of spots per cell or the mean
intensity of spots• Optimized for measurements in screening­applications with multi-well setups

efficiency in 2D cell culture• Applicable for transfection protocols or picking
positive clones• Measurement of the distribution of labelledmolecules in a cell population• Quantification of viral or bacterial infections• Total number and percentage of positive cells
and the mean signal intensity• Optimized for measurements in screening­applications with multi-well setups

Included in: Bio Apps

Included in: Bio Apps

20

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

ServiceSpecial Feature:

Special Feature:

For more information about the following special

Correlative Array Tomography (CAT)EM Processing Toolbox

features, please refer to the respective product

Image ultrathin serial sections automatically in

Improve your EM datasets:

information brochures:

widefield and scanning electron microscopes:• Easy import of EM images acquired with

• Regions of interest manually defined in one

SmartSEM• Peripheral Device Control

section will be automatically propagated to all• Removal of artifacts such as noise and stripes• LSM Plus

following sections.

• Reconstruction of 3D datasets out of subse-• Airyscan• Imaging of selected regions of interest withlight and electron microscopes• 2D image sequences are aligned into a 3D
Z stack, resulting in a correlative dataset, combining information from the light and electron
microscopes into one image volume

quent 2D images: automatic dataset equaliza-• Airyscan jDCVtion and alignment with z-alignment tool

• Photon Counting & FCS• Replacement of individual slices of poor quality
within the 3D Z stack• Cut out free-form 3D regions of interest to• Sample Navigator• Lightsheet Processing• Lattice Lightsheet Processing

remove unwanted areas from the EM dataset
for a customized 3D visualization

Click here to view this video

21

General Features of ZEN›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

General Features of ZEN
Graphical user interface can be switched between bright and dark design to adapt to ambient brightness
Step-less scaling and zooming of the user interface for optimal adjustment to the screen size
Essential functions are always displayed, while advanced options are auto-hidden under “Show All”
Full integration with ZEISS microscopes, Axiocam cameras, and 3rd party accessories using intuitive MicroToolbox (MTB) software
Interactive and automatic control of the individual motorized microscope components
Transfer of information from encoded components into the software
Complex acquisition experiments can be configured, saved and reused easily
Many powerful microscopy tools freely available, e.g., Axiocam control, movie recorder, manual panorama, 3D rendering, and more
Sequence of acquisition dimensions can be selected (depending on active dimensions)Hardware settings can be created with the help of a graphical light path
Sequences of commands can be easily combined to create hardware settings:• Contains the Smart Setup function for the fully automatic creation of experiments to acquire multichannel fluorescence and transmitted light images using motorized systems• Image acquisition with b/w, color, high-resolution and high-sensitivity cameras, b/w images with up to 16 bits, color images with up to 3 × 16 bits
Display parameters can be adjusted without changing the pixel values
Assignment of scaling is fully automatic when acquiring an image (depending on the microscope configuration)
Acquisition history is recorded and saved as metadata in CZI image format. This format has been developed in consideration of the standards of the OME-TIFF and OME-XML format of the Open Microscopy­Environment. This allows far-reaching compatibility with the Bio-Formats Reader of the Open Microscopy Environment
Acquired images are automatically saved in CZI or other image formats (including metadata). Saving in CZI format is also possible with advanced compression algorithm
Full integration into the Windows multi-user functionality (separation of user data and program installation, user-specific configurations, etc.)
Configuration options for the graphical user interface enable creation of menu bars, saving of workplace configurations, and definition of properties of standard graphic elements
Export into OME-TIFF (image format specification of the Open Microscopy Environment which enables the exchange of microscopic image data)
Export into ZVI, BMP, GIF, JPG, PNG, TIFF, HDP image formats; export into AVI and Windows Media video formats; batch export of images and videos
Image import (LSM, ZVI, BMP, TIFF, JPG, GIF, PNG) and function to convert images (TIFF, JPG, BMP) into CZI format
Navigator window available for easy navigation of large tile images
Interactive measurement: length, contour-based measurement data (area, box, perimeter, gray values), angle
ZEN Connect workspace with project-based file architecture: Zoom in from the full macroscopic view of a sample down to nanoscale details. Combination of data from any image source and view ofmultiple layers with adjustable transparency. Manual alignment of images allows correction of xy-shift, rotation, re-scaling, shearing and mirroring.

22

ZEN Package Details›

In Brief›

The Advantages›

What's New

Data Storage Client›

Packages and Features

APEER On-site Basic›

Application Examples›

Service

Base Software

Name

Content

Description

ZEN lite

Panorama

For basic offline data processing and control of manual microscopes / Axiocams
Optional packages limited to Base Acquisition only

Manual Extended Focus

Measurements

3D viewing Basic
Connect BasicZEN

All ZEN lite Contents
Base Acquisition Package

For control of motorized microscopes, Axiocams, lasers, and 3rd party components, as well as offline data processing
Can be upgraded with all packages and special features

Motorized Microscope Control
Spectral Unmixing
APEER On-site Advanced
ZEN desk

All ZEN lite Contents
Spectral Unmixing

For offline data processing only (no device control). Can be upgraded with all non-acquisition packages andnon-device control special features

APEER On-site Advanced
3rd Party Import
Direct Processing
Extended Focus
Colocalization

23

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Acquisition Package

Name

Content

Description

Base

Multi-Channel

Included in ZEN and optional for ZEN lite Base Software

Time Lapse
Motorized

Acquisition Base Package

Optional for ZEN Base Software

Z Stack
Extended Focus
Software Autofocus
Tiles & Positions
Direct Processing
Advanced

ServiceAcquisition Motorized Package

Optional for ZEN Base Software, includes content of Motorized Acquisition Package

Colocalization
HDR-Confocal
Smart

Guided Acquisition

Optional for ZEN Base Sofware, requires Motorized/Advanced Acquisition Package and 2D Toolkit Package

Experiment DesignerExperiment Feedback
Toolkit Package

Name

Content

Description

2D

Image Analysis

Optional for ZEN and ZEN desk Base Software. AI ready (pre-trained models can be executed)

Advanced Processing
3D

3D Visualization

Optional for ZEN and ZEN desk Base Software. AI ready (pre-trained models can be executed)

Advanced 3D Visualization
3D Analysis
Advanced Processing
Vision4D

Vision4D

Stand-alone software for demanding big data, 4D visualization and analysis

AIIntellesis Segmentation

Optional for ZEN and ZEN desk Base Software
Machine Learning- and Deep Learning-based algorithms with user training interface

Intellesis Object Classification
Intellesis Denoising
Connect

Connect
Connect 2D Add-on

Optional for ZEN and ZEN desk Base Software
For light-light and light-electron correlative microscopy with advanced calibration, acquisition and visualization tools

Connect 3D Add-on
3rd Party Import
Developer

Macro Environment

Optional for ZEN and ZEN desk Base Software, for Python based scripting functions

Molecular
Quantification

FRAP Efficiency Analysis

Optional for ZEN and ZEN desk Base Software, for advanced fluorescence-based molecular quantification functions

FRET
Physiology
Automated Photomanipulation

Deconvolution

Deconvolution

Optional for ZEN and ZEN desk Base Software

24

ZEN Package Details›

In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Application Package

Name

Content

Description

Bio Apps

Cell Counting

Optional for ZEN and ZEN desk Base Software, AI ready (pre-trained models can be executed)

Confluency
Automated Spot Detection
Gene and Protein Expression

Special Features

Content

Description

Peripheral Device Drivers

Optional for ZEN Base Software, for control of ASI, Ludl, PIFOC, Sutter and Uniblitz devices

LSM Plus

Optional for LSM 900 and LSM 980 systems

Airyscan & jDCV

Optional for LSM 900 and LSM 980 with Airyscan systems

Photon Counting, FCS and RICS

Optional for LSM 980 system

Sample Navigator

Optional for LSM 900 and LSM 980 systems

Lightsheet Processing

Optional for Lightsheet 7 system

Lattice Lightsheet Processing

Optional for Lattice Lightsheet 7 system

EM Processing

Optional for ZEN and ZEN desk Base Software

25

ZEN at Work›In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

ServiceTime Lapse Imaging

20 µm

Click here to view this video

Click here to view this video

Living cell with mitochondria in green and microtubule tips in red (EB3). ZEN allows to gain insights

Lateral line primordium migration and deposition of immature neuromasts in a Zebrafish embryo

into fast dynamic cellular processes while providing you with tools to process your data in the same

(Danio rerio). Maximum intensity projection of 155 z-planes, acquired with Airyscan 2. Mebranes infamiliar user interface.

green, actin in violet.
ZEN allows you to observe your specimen longer and under more natural conditions than everbefore, as it precisely controls acquisition in widefield or LSM modes. No photons are wasted andimages are processed and restored to yield the highest signal to noise ratio.
Sample courtesy of J. Hartmann and D. Gilmour, EMBL, Heidelberg, Germany

26

ZEN at Work›In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Large Area Imaging

1000 µm

Tiled image of a mouse kidney section with four labels. ZEN provides you with the best strategy
to optimize sample focus across large areas at high resolution. You get better images in shorter time.

Brightfield images of a tissue section acquired using Live Panorama. ZEN automatically takes images
and stitches them, while you manually navigate the area of interest on your sample.

27

ZEN at Work›In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

3D Imaging

Ortho view of mouse brain slice, acquired with LSM 900.

3D rendering of a Zebrafish embryo. Deconvolved Apotome Z stack.

Z stack of the hippocampus area of a brain slide with neurons (green) and nuclei (red)With its powerful viewing and processing options ZEN gives you the insights into your specimen that

ZEN assists you in finding the perfect spot in your sample and effortlessly handles large files so thatyou need to draw conclusions and to plan further experiments.

you can always concentrate on examining your data.

28

ZEN at Work›In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

Image Analysis

A 129 slice Z stack of cell nuclei, fully segmented and quantified, using APEER on-site in ZEN.

Counting of DAB-positive (brown with green outline) cells in tissue sections and calculation of­percentage of total cells (blue and brown): 36 %.

29

ZEN at Work›In Brief›

The Advantages›

What's New›

Packages and Features›

Application Examples›

Service

AI Toolkit

Deep Learning semantic segmentation in APEER

Model application in ZENIntellesis Segmentation Training

Intellesis Object Classification Training

3D Image Analysis & Visualization

Segmentation and Classification results

C.elegans embryo, acquired with Lattice Lightsheet 7. Sample courtesy of William Okafornta, Core

Drosophila embryo images recorded with ZEISS Celldiscoverer 7 and Airyscan 2. Images Courtesy ofFacility Cellular Imaging (CFCI), TU Dresden

University of Gothenburg

Segmentation of cell bodies (green), nuclei (blue) and microtubule-organizing centers (red). Cell bod-

Segmentation of embryos with Intellesis Segmentation is shown in upper left panel. Selection of em-

ies and nuclei were segmented by Deep Learning semantic segmentation employing annotation andbryos suitable for further analysis with Intellesis Object Classification is shown in upper right panel.

model training in APEER, and then applying the model directly in ZEN; 3D object segmentation in

Correct segmentation and classification results are shown in lower panel.

ZEN with 3D image analysis and visualization via 3Dxl.

30

ZEISS Service – Your Partner at All Times

Your microscope system from ZEISS is one of your most important tools. For over 170 years, the ZEISS brand andour experience have stood for reliable equipment with a long life in the field of microscopy. You can count on
superior service and support - before and after installation. Our skilled ZEISS service team makes sure that your›

In Brief

microscope is always ready for use.

›

The Advantages›

What's New

Procurement›

Packages and Features›

Application Examples›

Service

Operation• Lab Planning & Construction Site Management• Predictive Service Remote Monitoring• Site Inspection & Environmental Analysis• Inspection & Preventive Maintenance• GMP-Qualification IQ/OQ• Software Maintenance Agreements• Installation & Handover• Operation & Application Training• IT Integration Support• Expert Phone & Remote Support• Startup Training• Protect Service Agreements• Metrological Calibration• Instrument Relocation• Consumables• Repairs

New Investment

Retrofit• Decommissioning• Customized Engineering• Trade In• Upgrades & Modernization• Customized Workflows via APEER

Please note: Availability of services depends on product line and location>> www.zeiss.com/microservice

31Not for therapeutic use, treatment or medical diagnostic evidence. Not all products are available in every country. Contact your local ZEISS representative for more information.
EN_41_011_038 | Version 3.6 | CZ 01-2023 | Design, scope of delivery, and technical progress subject to change without notice. | © Carl Zeiss Microscopy GmbH

Carl Zeiss Microscopy GmbH07745 Jena, Germany
microscopy@zeiss.com
www.zeiss.com/zen