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Release Notes
ZEN 3.14
New Features & Improvements
ZEN 3.13
New Features & Improvements
ZEN 3.12
New Features & Improvements
Breaking Changes for Developer Toolkit and Smart Acquisition Toolkit
Converting OAD Macros in *.py Format
Converting OAD Macros in *.czmac Format
Special Notes
Compatibility of Windows Versions to Machine Learning and AI Features
Compatible Cameras
ZEN 3.11
New Features & Improvements
Breaking Changes
Repairing Scripts if a Specific .NET Function Cannot be Found
Changes for COM
Optional Parameters Replaced by Two Methods without Optional Parameters
New Methods Corresponding to Existing Methods
Renamed COM Methods
Additional Breaking Changes
Installation & Setup
System Requirements
ZEISS Microscopy Software
LSM 900
LSM 910
LSM 990
Requirements for Docker Desktop
Defining the Docker Image Location
Adapting the Resource Allocation for Docker Desktop Manually
Deactivating Experimental Docker Features
Compatible Cameras
Changes to the Operating System
Separation of Operating System and User Data
Setting Up Storage Locations
Moving Default Directories
Configuration of Security Software
Before Installation
After Installation
Default Folders
Temporary Files
System Specific Folders
Summary
Installing ZEN
Installing Docker Desktop with ZEISS Microscopy Installer
Installing Remote API Client (for SEM systems)
Installing MATLAB for Correlative Array Tomography
Backing Up and Restoring Settings
Creating a Desktop Shortcut to Start a Specific ZEN Profile
Troubleshooting
Fixing a failing ZeissPy installation (Ordinal242/MKL-load-failed error)
Removing files from the System32 folder
Setting a new environment variable
Fixing runtime or compatibility issues for externally trained neural networks
Getting started & First Steps
Starting Software
Welcome Screen
Overview Area
Start Buttons
User Interface
Title Bar
Workspace Configuration
Menu Bar
Tool Bar
Left Tool Area
Center Screen Area
Right Tool Area
Document Bar
Status Bar
System Messages
Setting User Language
Activating Show All Mode
Configuring Microscope Components
Acquiring Camera Image
Adding Annotations
Adjusting Live Image Settings
Creating Manual Scaling
Closing Software
Basic Concepts
Image Acquisition
Image Processing
Image Analysis
File Format
Extensions
Customizing the Application
Selecting Screen Design
Customizing Toolbar
Adjusting Workspace Zoom
Showing/Hiding Workspace Areas
Undocking/Docking Tool Windows
Displaying and Adapting a Grid in the Image Area
User Management
Creating a New User
Creating a new group
Adding Users to a Group
Managing Access Rights for User Groups
Managing Group Privileges
Setting Up the Login with Windows Credentials (Active Directory)
Options
Looking Up Active Directory Groups
Image Acquisition
Setting Up a New Experiment
Acquiring Multi-Channel Images with Cameras
Variant 1: Smart Setup
Variant 2: Channels Tool
Using the Dye Editor
Dye Editor Dialog
Dye Editor Menus
Creating a Custom Dye
Type in Data Manually
Copy Data from an Other Source
Copy Data from a Preset Dye
Adding a New Dye to the Data Set
Setting an Experiment as Startup Default
Creating Default Experiments as Templates Automatically
Applying an Experiment Template
Adding Annotations to Images or Movies
Editing Annotations in Images or Movies
Using Denoising During Continuous Acquisition
Working with Focus Strategies
Introduction
Using Software Autofocus
Using Definite Focus in Time Series Experiments
Using Local or Global Focus Surfaces
Import/Export
Workflow Export/Import
Exporting Images
Exporting Movies
Exporting Multichannel Images
Exporting Multiscene Images
Naming Convention for Image Export
Naming of xml Files for Exported Images
Importing Z-Stack Images
Docker Desktop and ZEN
Machine Learning and AI Functionalities in ZEN
Creating and Entering an Access Token
Downloading AI Models
Importing AI Models
Image Processing
Image Processing Workflow
Extracting Individual Fluorescence Images of a Multichannel Image
Applying Batch Processing
Example: Applying Image Export in Batch Processing
Cropping a ROI
Creating an EDF Image
Creating Image Subset and Split Dimensions
Using Analyze to Label Image
Image Processing Functions
General Settings
Adjust
Background Subtraction
Brightness/Contrast/Gamma
Color Balance
Color Temperature
Histogram Equalization
Hue/Saturation/Lightness
Rolling Ball
Shading Correction
Shading Reference for Acquisition
Shading Reference for Processing
Stack Correction
White Balance
Batch Processing Functions
Attach PSF (Point Spread Function)
Change Scaling
Draw Scale Bar Annotation
Split Multiblock Image (for Images until ZEN 2.1)
Undo Stitching
Deconvolution
Airyscan Joint Deconvolution
Deblurring
Deconvolution (adjustable)
Deconvolution Tab
Advanced Settings
PSF Settings Tab Deconvolution (adjustable)
Microscope Parameters Section
Advanced Section
Aberration Correction Section
Channel Specific Section
Microscope Info Section
PSF View Section
Deconvolution (defaults)
LSM DCV Processing
PSF Wizard
EM Processing
Change Pixel Type
Coarse Z-Stack Alignment
Coarse Z-Stack Alignment Setup
Alignment Controls Section
Create Image Subset
Cut Out Regions
Define Regions Setup
Region Edit Section
Support Regions Tab
Denoise
Enhance Local Contrast
Gauss
Highpass
Import SmartFIB TIFFs
Median
Not
Remove Stripes
Shading Correction
Slices Replacement
Sort SmartFIB Tiffs
Z-Stack Alignment with ROI
Z-Stack Equalization
Export/Import
Convert TXM Files to CZI
Image Export
File Type Section
Image Data Section
Dimensions Section
Export To Section
Image Import
Import SmartFIB TIFFs
Import TXM
Movie Export
File Type Section
Image Data Section
Fitting Section
Sequence Section
Mapping Section
Dimensions Section
Export to Section
OME TIFF Export
Image Format Section
Image Data Section
Dimensions Section
Export to Section
ZVI Export
Export to Section
Geometric
Apply Channel Alignment Transformation
Change Orientation
Channel Alignment
Channel Alignment (Extended)
Color-coded Projection
Create Channel Alignment Transformation
Image Overlay
Mirror
Orthogonal Projection
Resample
Rotate
Rotate 2D
Sample Down
Shift
Shift Z
Stage Alignment
Stitching
Tiles Blending
Z-Stack Alignment
Z-Stack Alignment with ROI
Image Analysis
Analyze
Analyze to File
Analyze Batch
Analyze Batch to File
Analyze to Label Image
Analyze to Label Image Batch
Analyze Interactive Batch
Lightsheet
Dual Side Fusion
Lightsheet Convert Dimensions
Lightsheet Processing
Landmark Based Alignment
Intensity Based Alignment
Use Registration from File
Interactive Registration
Maximum Intensity Projection
Segmentation
Canny
Marr
Threshold
Threshold (Auto)
Threshold (Dynamic)
Valleys
Sharpen
Delineate
Enhance Contour
Extended Depth of Focus
Unsharp Mask
Smooth
Binomial Filter
Denoise
Gauss
Lowpass
Median
Sigma
Single Pixel Filter
Whitening
Time Series
Gliding Average
Kymograph
Time Alignment
Time Concatenation
Time Differential
Time Stitching
Utilities
Add Channels
Airyscan Processing
Airyscan Sheppard Sum
ApoTome Deconvolution
ApoTome RAW Convert
Calculate Histogram
Change Pixel Type
Combine RGB
Convert To Lambda
Copy Annotations
Copy Image
Correct Stage Jitter
Correlation
Create Gray Scale Image
Create Image Subset
Create Image Subset and Split
Create Image Subset and Split (Write files)
Create PSF
Fuse Image Subset
Generate Image Pyramid
Image Calculator
Image Generator
Linear Unmixing
LSM Plus Processing
Split into RGB
Split Multiblock Image
Split Scenes
Split Scenes (Write files)
Basic Functionality
Colocalization
Colocalization View
X/Y Scatter Plot
Coloc. Tools Tab
Colocalization Table
Region
Quadrant
Pixel Number
Area (µm²)
Relative Area (%)
Pearson's Correlation Coefficient
Manders' Correlation Coefficient
Coloc. Coefficient 1
Coloc. Coefficient 2
CC (Weighted) 1
CC (Weighted) 2
Average Intensity 1
Average Intensity 2
Standard Deviation 1
Standard Deviation 2
Z Index
T Index
Relative Time
Relative Focus
Direct Processing
System Requirements
Hardware Requirements
Software Requirements
Overview Direct Processing
Connecting Acquisition Computer and Processing Computer
Connecting Computers Without Discovery Proxy
Connecting Computers With Discovery Proxy
Setting Up Your PC as Discovery Proxy
Defining Settings in the Auto Save Tool
Using Direct Processing
Using Direct Processing with Airyscan Processing
Direct Processing Tool on Acquisition Tab
Airyscan Processing Parameters
Deconvolution Parameters
Direct Processing PCs Dialog
Direct Processing Tool on Applications Tab
Sharing a Folder for Direct Processing
Creating a Shared Folder on the Processing Computer
Accessing the Shared Folder from the Acquisition Computer
Looking Up the IP Address of Your Computer
Connecting Computers via Cable
Extended Focus Processing
Manual Extended Focus
Preparing a Manual EDF Acquisition
Acquiring EDF Images with Timer
Acquiring EDF Images with F12 Key
Comparing Images Using Split Display
Manual Extended Depth of Focus Tool
Measurement
Using Interactive Measurements
Interactive Measurement Tool
Feature Selection Dialog
Feature Subset Definition Dialog
Interactive Measurement Sequence Definition Dialog
Interactive Measurement Sequence Execution Dialog
Panorama
Prerequisites
Acquiring a Reference Image
Settings for a Panorama Experiment
Acquiring a Panorama Image
Acquiring a Panorama Image Automatically
Processing a Panorama Image
Stitching (Defaults)
Stitching with Shading Correction
Stitching with Fuse Tiles
Stitching with Fuse Tiles and Shading Correction
Image Comparison via Split Display
Panorama Tool
Panorama View
Stage View
Tools Window
Live Panorama Tool
Third Party Import
ZEN Data Storage Client
Setting up ZEN Data Storage Server
Validating the ZEN Data Storage Settings
Saving an Image to ZEN Data Storage
Saving a ZEN Connect Project to ZEN Data Storage
Exporting a ZEN Connect Project from ZEN Data Storage
Uploading Images Automatically After Acquisition
Opening or Deleting an Image from ZEN Data Storage
Opening or Deleting a ZEN Connect Project from ZEN Data Storage
Configuring the Stored Documents Table
Filtering Connect Projects and Images in ZEN Data Storage
Adding and Deleting Tags for ZEN Data Storage Images
Creating a Collection for Data
Editing or Deleting a Data Collection
Adding Data to a Collection
Sharing Data Directly With Users and Groups
Adding an Active Directory User
Stored Documents Dialog
Stored Data Section
Stored Documents Right Click Menu
Image Control Section
Add to Collection Dialog
Share and Manage Access Dialog
ImageJ
Preparations
Activate ImageJ Extension
Sending and Retrieving Images
Use ImageJ Methods
Image Type Send/Retrieve Conventions
ZEN Application Programming Interface (ZEN API)
Additional ZEN API Information and Reference
Toolkits & Modules
Acquisition Toolkits
Experiment Designer
Experiment Designer Tool
Loops and Repetitions Section
Execute Block Options
Import Experiment Blocks Dialog
Experiment Feedback
Workflow Experiment Feedback
Editing the Feedback Script
Selecting Script Runtime Conditions
Experiment Feedback Tool
Script Editor for Experiment Feedback Dialog
Input Windows
Commands Tab
Script Commands - Observables
Observables - Analysis
Observables - Experiment
Observables - Environment
Observables - Hardware
Script Commands - Available Actions
Actions - Experiment
Actions - Experiment - LSM
Actions - Hardware
Actions - Extra
Debugging Tab
Guided Acquisition
Preliminary Work to Guided Acquisition
Performing a Guided Acquisition
Using Guided Acquisition Settings
Guided Acquisition Tool
HDR Confocal Basic
Multi-Channel
Software Autofocus
Terminology & Abbreviations
When is focus the "right" focus?
Software Autofocus in ZEN
Software Autofocus Tool
Software Autofocus Using LSM Tracks
Tiles & Positions
Licensing and Functionalities of Tiles & Positions
General Preparations
Setting Up a Simple Tiles Experiment Without the Tiles & Positions Module
Setting Up a Simple Positions Experiment without the Tiles & Positions Module
Adjusting Z-Values
Adjusting Z-Values of Tile Regions
Adjusting Z-Values of Positions
Exporting Tile Images
Calibrating the Stage and Selecting the Channel
Tiles & Positions with Advanced Setup
Generating a Preview Scan
Creating Tile Regions by Contour
Creating Tile Regions by Predefined
Creating Tile Regions by Carrier
Creating Positions by Location
Creating Positions by Array
Creating Positions by Carrier
Importing Images into the Advanced Setup
Copying a Tile Region or Position
Local and Global Focus Surfaces
Introduction
Creating a Local Focus Surface
Distributing Support Points
Verifying Z-Values of Support Points
Selecting Interpolation Degree
Creating a Global Focus Surface
Distributing Support Points
Verifying Z-Values of Support Points
Selecting Interpolation Degree
Assigning Categories to Tile Regions and Positions
Using Sample Carriers
Selecting a Sample Carrier Template
Customizing a Sample Carrier Template
Re-positioning Sample Carrier after Incubation
Tiles Tool
Tile Regions Section
Positions Section
Options for Editing Single Positions
Options for Editing Position Arrays
Sample Carrier Section
Focus Surface and Support Points Section
Options Section
Verify Tile Regions or Verify Positions Dialog
Tiles Advanced Setup
Stage View
Specific Tiles & Positions Context Menu Options
Tiles Toolbars
Left Toolbar
Top Toolbar
Preview Scan Toolbar
Contour Toolbar
Predefined Toolbar
Stake Toolbar
Tiles Carrier Toolbar
Positions Location Toolbar
Position Array Toolbar
Positions Carrier Toolbar
Tiles View Options
Tiles Tab
Carrier Tab
Tiles Options
Select Template Dialog
Edit Sample Carrier Template dialog
Basic Template Settings
Global Support Points Settings
Time Series
Acquiring Time Series Images
Time Series Tool
Experiment Conditions Section
Interactive Switches Section
Z-Stack
Acquiring Z-Stack Images
Configuring a Z-Stack Automatically
Configuring a Z-Stack Manually (First/Last Mode)
Configuring a Z-Stack Manually (Center Mode)
Z-Stack Tool
Auto Z Brightness Correction with LSM
Visualization and Analysis Toolkits
Image Analysis
Creating a New Image Analysis Setting
Measuring Fluorescence Intensity in a Multichannel Image
Step 1: Classes
Step 2: (Measurement frame)
Step 3: Automatic Segmentation
Step 4: Region Filter
Step 5: Interactive Segmentation
Step 6: Features
Step 7: Results Preview
Executing the Analysis Setting
Counting Number of Fluorescence Signals per Nuclei
Step 1: Classes
Step 2: Measurement Frame
Step 3: Automatic Segmentation
Step 4: Region Filter
Step 5: Interactive Segmentation
Step 6: Features
Step 7: Results Preview
Executing the Analysis Setting
Measuring Mean Fluorescence Intensity on a Ring around the Primary Object
Step 1: Classes
Step 2: Frame
Step 3: Automatic Segmentation
Step 4: Region Filter
Step 5: Features
Step 6: Result Preview
Executing the Analysis Setting
Counting the Number of Objects in a Ring around the Nucleus
Step 1: Classes
Step 2: Frame
Step 3: Automatic Segmentation
Step 4: Region Filter
Step 5: Features
Step 6: Preview Result
Creating a Measurement Data Table
Creating an Image Analysis Setting from an Analyzed Image
Performing an Interactive Analysis
Creating Custom Features
Creating Custom Statistical Features
Creating an Image Analysis Setting From an AI Model
Analysis View
Analysis Tab
Chart Export Tab
Sample Carrier Tab
Table Export Tab
Custom Chart Tab
Copy Operations for Features
Charts and Tables of the Analysis View
Selecting Data for the Multiple Scenes Chart
Heatmap Calculation
Examples for Custom Features
Example 1: Number of Spots per Cell
Example 2: Average Area per Spot
Examples for Custom Statistical Features
Example 1: Percentage of Positive Cells
Example 2: Nuclear Cytoplasmic Transport
Image Analysis Tool
Segmentation Method Dialog
Image Analysis Wizard
Classes
Frame
Automatic Segmentation
Smoothing Section
Sharpen Section
Threshold & Histogram Section
Color Model
Variance Section
Model Section
Select Model Dialog
Subtract BG Section
Object Size & Hole Section
Binary Section
Separate Section
Suppress Section
3D Preview Section
Segmentation Method Selection Dialog
Region Filter
Region Filter Editor
Features
Select Features of Individual Regions Dialog
Select Features of All Regions Dialog
Annotations Dialog
Custom Feature Editor
Statistics
Custom Statistic Feature Editor
Results Preview
Measurement Features
ACP X Unscaled
ACP X Unscaled WCS
ACP Y Unscaled
ACP Y Unscaled WCS
Area
Area Convex (arivis)
Area Cut
Area Cut Unscaled
Area Filled
Area Filled Unscaled
Area Frame
Area Frame Unscaled
Area Percentage of Holes
Area Unscaled
Bound Back
Bound Back Unscaled
Bound Back Unscaled WCS
Bound Back WCS
Bound Bottom
Bound Bottom Unscaled
Bound Bottom Unscaled WCS
Bound Bottom WCS
Bound Center
Bound Center Unscaled
Bound Center Unscaled WCS
Bound Center WCS
Bound Depth
Bound Depth Unscaled
Bound Front
Bound Front Unscaled
Bound Front Unscaled WCS
Bound Front WCS
Bound Height
Bound Height Unscaled
Bound Left
Bound Left Unscaled
Bound Left Unscaled WCS
Bound Left WCS
Bound Right
Bound Right Unscaled
Bound Right Unscaled WCS
Bound Right WCS
Bound Top
Bound Top Unscaled
Bound Top Unscaled WCS
Bound Top WCS
Bound Width
Bound Width Unscaled
Center X
Center X Unscaled
Center X Unscaled WCS
Center X WCS
Center Y
Center Y Unscaled
Center Y Unscaled WCS
Center Y WCS
Center Z
Center Z Unscaled
Center Z Unscaled WCS
Center Z WCS
Circularity (arivis)
Compactness (arivis)
Convexity (arivis)
Count
Count Objects Direct Subclasses
Count per mm2
Diameter
Diameter Maximum Inscribed Circle
Diameter Maximum Inscribed Circle Unscaled
Diameter Unscaled
Ellipse Angle
Ellipse Angle Unscaled
Ellipse Semi-Major
Ellipse Semi-Major Unscaled
Ellipse Semi-Minor
Ellipse Semi-Minor Unscaled
Ellipsoid Semi-Major
Ellipsoid Semi-Major Unscaled
Ellipsoid Semi-Mean
Ellipsoid Semi-Mean Unscaled
Ellipsoid Semi-Minor
Ellipsoid Semi-Minor Unscaled
Feret Maximum
Feret Maximum Angle (arivis)
Feret Maximum Unscaled (arivis)
Feret Minimum
Feret Minimum Angle (arivis)
Feret Minimum Unscaled (arivis)
Feret Ratio (arivis)
Feret Vertical to Maximum (arivis)
Fiber Length
Fiber Length Unscaled
Form Circle
Frame Area Percentage
Frame Area Percentage Cut
Frame Data Area
Frame Data Area Percentage
Frame Data Area Unscaled
ID
ID Object Storage
Advanced Processing
Edges
Gradient Max
Gradient Sum
Highpass
Laplace
Local Variance
Roberts
Sobel
Arithmetics
Add
Add Constant
Average
Combine
Divide
Exponential
Invert
Logarithm
Maximum
Minimum
Multiply
Multiply Constant
Reciprocal
Square
Square Root
Subtract
Binary
And
Apply Mask
Distance
Exoskeleton
Fill Holes
Label Image
Mark Regions
Not
Or
Scrap
Separation
Thinning
Ultimate Erode
Xor
Morphology
Structure Elements
Smooth
Rank
Utilities
3Dxl
Animating the 3D Volume
3D View
Tool Bars
Tool Bar (Left)
Tool Bar (Right)
Tool Bar (Bottom)
3D Tab
Appearance Tab
Transparency Tab
Surface Tab
Channels Tab
Background Tab
Light Tab
Projection Tab
Clipping Tab
Series Tab
Measurements Tab
3D Graphics Tab
3Dxl Plus
Tomo3D View
Left Toolbar (Tomo3D)
Bottom Toolbar (Tomo3D)
Ortho Display Tab (Tomo3D)
Appearance Tab (Tomo3D)
Transparency Tab (Tomo3D)
Background Tab
Light Tab (Tomo3D)
3D Tab (Tomo3D)
Create Image Tab (Tomo3D)
3D Image Analysis
Creating a 3D Image Analysis Setting
Performing and Saving a 3D Analysis
Viewing and Exporting the Results of a 3D Analysis
Analysis Tab
Analysis Objects Table
Intellesis Segmentation
Licensing and Functionalities of Intellesis Segmentation
Fact Sheet
FAQ/Terminology
Operating Concept Intellesis Segmentation
Workflow Overview for Intellesis Segmentation
Training User Interface Intellesis Segmentation
Intellesis Training Options
Postprocessing Options
Labeling Options
Image Gallery
Select Channel Dialog
Intellesis Segmentation Models
Creating and Training an Intellesis Segmentation Model
Importing an Intellesis Segmentation Model
Exporting an Intellesis Segmentation Model
Exporting an Intellesis Segmentation Model with Images
Renaming an Intellesis Segmentation Model
Cloning an Intellesis Segmentation Model
Creating an Image Analysis Setting from an Intellesis Segmentation Model
Deleting an Intellesis Segmentation Model
Editing Classes
Importing Labels from Binary Mask
Converting Segmentations to Labels
Using Pretrained Deep Learning Networks for Image Segmentation
Segmenting an Image Using the Intellesis Segmentation Image Processing Function
Performing an Image Analysis Using an Intellesis Segmentation Model
Changing the Tile Border Size for Deep Learning Networks
Using Intellesis Segmentation Models in OAD
Remarks and Additional Information
Feature Extractors
Intellesis Basic Features
Basic Features 25
Basic Features 33
Intellesis Deep Features
Image Processing Functions
Minimum Confidence
Intellesis Segmentation
Utilities
Intellesis Segmentation Tool
Change Border Size Dialog
Tile Border Size Example
Intellesis Denoising
Licensing and Functionalities of Intellesis Denoising
Training User Interface Intellesis Denoising
Creating and Training an Intellesis Denoising Model
Importing an Intellesis Denoising Model
Exporting an Intellesis Denoising Model
Using an Intellesis Denoising Model for Image Processing
Intellesis Denoising Tool
IP Function
Intellesis Denoising
Intellesis Object Classification
Licensing and Functionalities of Intellesis Object Classification
Workflow Overview for Intellesis Object Classification
Training User Interface Intellesis Object Classification
Classification Settings
Image Gallery (Object Classification)
Labeling Options Tab
Object Classification Table
Creating and Training an Intellesis Object Classification Model
Importing an Intellesis Object Classification Model
Exporting an Intellesis Object Classification Model
Exporting an Intellesis Object Classification Model with Images
Using an Intellesis Object Classification Model for Image Processing
Intellesis Object Classification Tool
IP Function
Intellesis Object Classification
Deconvolution
Licensing and Functionalities of Deconvolution
Basics of Deconvolution
Deconvolution Methods in ZEN
Performing Deconvolution Using Default Values
Performing Configurable Deconvolution
Step 1: Loading an Input Image for Deconvolution
Step 2: Set Parameters for Deconvolution
Step 3: Performing Deconvolution
Step 4: Info View and Re-Using Deconvolution Parameters from a Processed Image
Creating Deconvolution Settings
Creating a PSF - With Wizard and Without
Measuring the PSF Using Subresolution Beads
Using Deconvolution in Direct Processing
Image Types Suitable for Deconvolution
Table of Default Parameter for Deconvolution
Dynamics Profiler
Overview Supported Laser Lines
Setting Up and Performing a Dynamics Profiler Acquisition
Exporting Data From Tables
Exporting Data From Charts
Opening the Reference Image as Separate Image
Cutting Out a Data Region
Saving Dynamics Profiler Documents as Compressed CZI
Creating a Custom ωr Calibration
Using Custom ωr Calibration
Dynamics Profiler Acquisition Wizard
Correlation View
Diffusion View
Flow View
Parameter Table Context Menu
Dynamics Profiler Calculations
Physiology (Dynamics)
Licensing and Functionalities of Physiology
Opening the MeanROI View
Workflow MeanROI View (Offline)
Drawing in ROIs
Adjusting ROIs for Time Points
Adjusting the Display
Using Background Correction
Exporting a Data Table
Calculating a Ratio for One Wavelength
Calculating a Ratio for Two Wavelengths
Basics of Calculation of Intensity and Ratio Values
Interaction with a Table in MeanROI View
Workflow Physiology (Dynamics) Experiments
Setting up the Online Ratio Calculation
Calculating the Online Ratio for Single Wavelength
Calculation of the Ratio Value R
Setting up an Experiment in MeanROI Setup
Drawing in ROIs
Adjusting the Display
Using Background Correction
Starting and Influencing an Experiment
Adjusting ROIs during Experiments
Sample Experiment Fura-2 with DG4/5
Step 1: Creating Channels
Step 2: Setting Up a Time Series and Creating Switches
Step 3: Setting Up an Online Ratio
Step 4: MeanROI Setup
Step 5: Starting, Analyzing and Influencing an Experiment
Mean ROI View
Time Line View Panel
Mean ROI Tab
Layout Tab
Charts Tab
Export Tab
Ratio Tab
Online Ratio Tab
ROI Tracing Tab
FRAP Efficiency Analysis
FRAP View
FRAP Tab
Fit Model
Automated Photomanipulation
Using Automated Photomanipulation Settings
Performing an Automated Photomanipulation Experiment
Automated Photomanipulation Tool
FRET
Acquisiton Prerequisites
Analysis Method for Acceptor Bleaching
Analysis Methods for Sensitized Emission
FC or Youvan Method
FRETN or Gordon Method
N-FRET or Xia Method
Crosstalk Correction for Gordon and Xia Methods
Determining Donor Coefficient Values
Determining Acceptor Coefficient Values
FRET View
Data Table Sensitized Emission
Data Table Acceptor Bleaching
FRET Tab
Parameters Tab
Threshold Tab
Settings Tab
General Tab
Acceptor Photobleach Tab
Sensitized Emission Tab
ZEN Connect
Licensing and Functionalities of ZEN Connect
User Interface
ZEN Connect 3D View
Alignment Tab ZEN Connect 3D
Connect 3D Tab
Opening the Correlative Workspace
Opening Images in the ZEN Connect 3D View
Non Image Data
Raman Images
Project and Image Management
Creating a ZEN Connect Project
Loading a ZEN Connect Project
Adding an Image to the ZEN Connect Project
Adding an Open Image to the ZEN Connect Project
Adding Datasets when Adding Images
Zooming Images
Removing Images from the ZEN Connect Project
Renaming Images in a ZEN Connect Project
Opening Images in ZEN
Showing an Image in the Explorer
Moving or Hiding Images
Starting a New Session
Toggling View Modes
Closing a ZEN Connect Project
Import and Export
Importing Data
Importing Third-party Images
Importing a SmartFIB Stack into ZEN Connect
Importing Non Image Data
Exporting Single Image Data
Exporting a ZEN Connect Project as a Video
Exporting Data for SerialEM
Alignment
Activating the Alignment Process
Aligning Image Data
Aligning Images in Z Direction
Example for Z Alignment
Rotating a Z-Stack
Aligning Images in the ZEN Connect 3D View
Aligning Non Image Data
Aligning Images in the Manual Alignment Wizard
Aligning Images in the Point Alignment Wizard
Aligning Images in the 3D Point Alignment Wizard
Handling of Images and Data
Zooming to Extent
Panning & Zooming
Selecting Region
Toggling the Display of Region Caption and Frame
Selecting and Clearing Carrier/Holder
Grabbing an Image
Using Regions of Interest in Zen Connect
Drawing a Region of Interest in ZEN Connect
Deleting a Region of Interest in ZEN Connect
Renaming a Region of Interest in ZEN Connect
Zooming to a Region of Interest in ZEN Connect
Moving the Stage to a Region of Interest in ZEN Connect
Adding Measurements to a ZEN Connect Project
Editing Measurements in a ZEN Connect Project
ZEN Connect Tool
ZEN Connect Project view
ZEN Connect Project Layer view
Button Bar
Select Template Dialog
Alignment Tab
Measurement Tab
Button Bar below Image View
ZEN Connect Single Image Export Wizard
Field of View Width Dialog
Pixel Size Dialog
Video Export Wizard
Regions Tool
ZEN Connect Manual Alignment Wizard
Alignment Parameter Section
ZEN Connect Point Alignment Wizard
Step 1: Setup Points
Point Alignment Options
Step 2: Preview
ZEN Connect 3D Point Alignment Wizard
Step 1: Setup Points
3D Point Alignment Options
Step 2: Preview
Shuttle & Find
Settings and Image Acquisition with the Light Microscope
Mounting the Sample Holder to the LM
Starting the LM Software
Selecting the Sample Holder
Defining a New Sample Holder Template
Calibrating the Sample Holder
Preparing Calibration
Setting Calibration Options
Performing Calibration
Acquiring the LM Image
Shuttle & Find Sample Positions at the Electron Microscope
Mounting the Sample Holder to the SEM
Starting the ZEN SEM Software
Selecting the Sample Holder
Calibrating the Sample Holder
Acquiring an EM Image
Fine Calibration of the Sample Holder
Correlating Two Loaded Images
Correlation of Live Image and Loaded Image
Shuttle & Find with an EVO 10
User Interface
Shuttle & Find Tool
Shuttle & Find View
S&F Tab
Options
Regions, Find and Dimensions
S&F Correlation Tab
Sample Holder Calibration Wizard
Step 1: Options
Step 2-4: Calibration
Correlative Sample Holders
Application and Workflow Toolkits
Bio Applications
Available Bio Applications
General Workflow
Creating a General Bio Application Setting
Running Bio Applications
Creating a Setting for Cell Counting
Creating a Setting for Confluency
Creating a Setting for Gene- and Protein Expression
Creating a Setting for Automated Spot Detection
Creating a Setting for Translocation
Running Bio Applications in Batch Mode
Exporting Results of the Bio Applications Analysis
Bio Applications View
Export Tab
Objects Tab
Chart Tab
Bio Applications Tool
Bio Applications Wizard
Cell Counting Specific Settings
Confluency Specific Settings
Gene- and Protein Expression Specific Settings
Automated Spot Detection Specific Settings
Translocation Specific Settings
Macro Environment
Running an Existing Macro
Recording a Macro
EM Processing Toolbox
Workflow Overview
Aligning Z-Planes Manually
Aligning Z-Planes Automatically (Based on a ROI)
Replacing Z-Slices in a Z-Stack
Cutting Out a Volume from a Z-Stack
Importing SmartFIB Tiffs
Microscopy Copilot
Using the Microscopy Copilot
Microscopy Copilot Dialog
AI Tissue Detection
Input Data for AI Tissue Detection
Sample Requirements for AI Tissue Detection
FINE (Fluorescence Intensity Normalization and Evaluation)
Tissue Image Alignment
Tissue Image Alignment
Combining Multi-Channel Images of Different Staining and Imaging Cycles
Axioscan User Mode
Customizing a Reference Scan Profile
Customize Reference Scan Profile Wizard
Step 1: Set Up Batch
Step 2: Review Channels
Step 3: Set Exposure Time
Axioscan Advanced Spectral Unmixing
Overview for Creating New Reference Spectra
Sample Preparation for Creating New Reference Spectra
Information for Acquisition and Preparation of Reference Scans
Starting the Calibrated Unmixing Wizard
Selecting Autofluorescence Spectra
Selecting Dye Spectra
Checking the Calculated Dye Spectra
Applying Unmixing in the Scan Profile
Calibrated Unmixing Wizard
Step 1: Selection of Autofluorescence Spectra
Step 2: Selection of Dye Spectra
Dye Selection Table
Step 3: Calculated Dye Spectra
ZEN Workflows
User Interface for Workflows in ZEN
Creating a Workflow
Opening a Workflow
Adding a Loop to a Workflow
Adding a Group to a Workflow
Duplicating and Replacing a Workflow Step
Moving or Deleting a Workflow Step
Customizing Steps and Tools
Exporting and Importing Workflows
Running a Workflow Stepwise
Running a Workflow Automatically
Running Parts of a Workflow or Individual Steps
Example Workflow Acquisition and Processing
Example Workflow Image Analysis
Special/Hardware Related Modules
32ch Quasar detector
Airyscan RAW Data
Saving Images in 32ch Airyscan Format
Exporting Data in 1ch Sheppard Sum Format
Apotome Plus
Apotome Plus (defaults)
Apotome Plus (adjustable)
Apotome Plus Tab
Advanced Settings
PSF Settings Tab Apotome Plus (adjustable)
Microscope Parameters Section
Advanced Section
Aberration Correction Section
Channel Specific Section
Using Apotome Plus in Direct Processing
Creating Apotome Plus Settings
Coded Microscope
Confocal Topography
Acquiring Topography Images
Measuring Layer Thickness
Topography Tool
Topography Measurement Wizard
Step 1: Setup
Step 2: Z-Stack Acquisition
Layer Thickness Measurement Tool
Layer Thickness Measurement Wizard
Step 1: Setup
Step 2: Sectioning
Step 3: Measurement
Acquisition Mode Tool in Topography Measurement Wizard
Channel Tool in Topography Measurement Wizard
Tiles Tool in Topography Measurement Wizard
Z-Stack Tool in Topography Measurement Wizard
Correlative Array Tomography (CAT)
Basics of Array Tomography
Sample Preparation
Pre-Settings (Light Microscope)
Experiment Settings
CAT Workflow
Creating a New Sample
Selecting the Sample Holder
Defining a New Sample Holder Template
Calibrating the Sample Holder
Preparing Calibration
Setting Calibration Options
Performing Calibration
Acquiring the LM image
Acquiring the Overview Image
Defining the Ribbons
Imaging the Ribbons
Specifying the Sections
Specifying the ROIs
Imaging the ROIs
Re-Shooting ROIs
Aligning the Z-Stack Image
Correlating the LM and SEM images
CAT Tool
Select Sample Dialog
Sample Holder Calibration Wizard
Step 1: Options
Step 2-4: Calibration
Acquisition Wizard
Overview Imaging
Ribbon Definition
Ribbon Imaging
Section Specification
ROI Specification
ROI Imaging
Re-Shoot
Z-Stack Alignment Wizard
Image Import
Pre-Processing
Image Review
Alignment
Manual Correction
Final Image Creation
Correlation Wizard
Import Z-Stacks
Correlation
Manual Correction
Create Final Correlation Image
Correlative Sample Holders
Lightfield 4D
Lightfield 4D Volume Color Coding
Setting Up a Lightfield 4D Track without Smart Setup
Setting Up a Lightfield 4D Track with Smart Setup
Focus Strategies in Lightfield 4D Experiments
Starting a Live Acquisition for Lightfield 4D
Setting Up and Starting a Lightfield 4D Experiment
Defining a Lightfield 4D Multi-Position Experiment with the Tiles Advanced Setup
Defining a Lightfield 4D Multi-Position Experiment without the Tiles Advanced Setup
Processing a Lightfield 4D Image with the Processing Function
Processing a Lightfield 4D Image with the View Options Tab
Using Lightfield 4D in Direct Processing
Lightfield 4D Processing
Lightfield 4D Tab
Image Analysis
Segmentation methods in ZEN
Automatic image segmentation
What is segmentation?
How does segmentation work?
Instance vs. Semantic Segmentation
Segmentation methods
Classical segmentation methods
Global Thresholding
Background Subtraction
Variance-based Thresholding
Dynamic Thresholding
AI-based methods
AI Semantic Segmentation
AI Instance Segmentation
Intellesis Trainable Segmentation
Machine Learning vs. Deep Learning
Choosing the right segmentation method
Release Notes
ZEN 3.14
New Features & Improvements
ZEN 3.13
New Features & Improvements
ZEN 3.12
New Features & Improvements
Breaking Changes for Developer Toolkit and Smart Acquisition Toolkit
Converting OAD Macros in *.py Format
Converting OAD Macros in *.czmac Format
Special Notes
Compatibility of Windows Versions to Machine Learning and AI Features
Compatible Cameras
ZEN 3.11
New Features & Improvements
Breaking Changes
Repairing Scripts if a Specific .NET Function Cannot be Found
Changes for COM
Optional Parameters Replaced by Two Methods without Optional Parameters
New Methods Corresponding to Existing Methods
Renamed COM Methods
Additional Breaking Changes
Installation & Setup
System Requirements
ZEISS Microscopy Software
LSM 900
LSM 910
LSM 990
Requirements for Docker Desktop
Defining the Docker Image Location
Adapting the Resource Allocation for Docker Desktop Manually
Deactivating Experimental Docker Features
Compatible Cameras
Changes to the Operating System
Separation of Operating System and User Data
Setting Up Storage Locations
Moving Default Directories
Configuration of Security Software
Before Installation
After Installation
Default Folders
Temporary Files
System Specific Folders
Summary
Installing ZEN
Installing Docker Desktop with ZEISS Microscopy Installer
Installing Remote API Client (for SEM systems)
Installing MATLAB for Correlative Array Tomography
Backing Up and Restoring Settings
Creating a Desktop Shortcut to Start a Specific ZEN Profile
Troubleshooting
Fixing a failing ZeissPy installation (Ordinal242/MKL-load-failed error)
Removing files from the System32 folder
Setting a new environment variable
Fixing runtime or compatibility issues for externally trained neural networks
Getting started & First Steps
Starting Software
Welcome Screen
Overview Area
Start Buttons
User Interface
Title Bar
Workspace Configuration
Menu Bar
Tool Bar
Left Tool Area
Center Screen Area
Right Tool Area
Document Bar
Status Bar
System Messages
Setting User Language
Activating Show All Mode
Configuring Microscope Components
Acquiring Camera Image
Adding Annotations
Adjusting Live Image Settings
Creating Manual Scaling
Closing Software
Basic Concepts
Image Acquisition
Image Processing
Image Analysis
File Format
Extensions
Customizing the Application
Selecting Screen Design
Customizing Toolbar
Adjusting Workspace Zoom
Showing/Hiding Workspace Areas
Undocking/Docking Tool Windows
Displaying and Adapting a Grid in the Image Area
User Management
Creating a New User
Creating a new group
Adding Users to a Group
Managing Access Rights for User Groups
Managing Group Privileges
Setting Up the Login with Windows Credentials (Active Directory)
Options
Looking Up Active Directory Groups
Image Acquisition
Setting Up a New Experiment
Acquiring Multi-Channel Images with Cameras
Variant 1: Smart Setup
Variant 2: Channels Tool
Using the Dye Editor
Dye Editor Dialog
Dye Editor Menus
Creating a Custom Dye
Type in Data Manually
Copy Data from an Other Source
Copy Data from a Preset Dye
Adding a New Dye to the Data Set
Setting an Experiment as Startup Default
Creating Default Experiments as Templates Automatically
Applying an Experiment Template
Adding Annotations to Images or Movies
Editing Annotations in Images or Movies
Using Denoising During Continuous Acquisition
Working with Focus Strategies
Introduction
Using Software Autofocus
Using Definite Focus in Time Series Experiments
Using Local or Global Focus Surfaces
Import/Export
Workflow Export/Import
Exporting Images
Exporting Movies
Exporting Multichannel Images
Exporting Multiscene Images
Naming Convention for Image Export
Naming of xml Files for Exported Images
Importing Z-Stack Images
Docker Desktop and ZEN
Machine Learning and AI Functionalities in ZEN
Creating and Entering an Access Token
Downloading AI Models
Importing AI Models
Image Processing
Image Processing Workflow
Extracting Individual Fluorescence Images of a Multichannel Image
Applying Batch Processing
Example: Applying Image Export in Batch Processing
Cropping a ROI
Creating an EDF Image
Creating Image Subset and Split Dimensions
Using Analyze to Label Image
Image Processing Functions
General Settings
Adjust
Background Subtraction
Brightness/Contrast/Gamma
Color Balance
Color Temperature
Histogram Equalization
Hue/Saturation/Lightness
Rolling Ball
Shading Correction
Shading Reference for Acquisition
Shading Reference for Processing
Stack Correction
White Balance
Batch Processing Functions
Attach PSF (Point Spread Function)
Change Scaling
Draw Scale Bar Annotation
Split Multiblock Image (for Images until ZEN 2.1)
Undo Stitching
Deconvolution
Airyscan Joint Deconvolution
Deblurring
Deconvolution (adjustable)
Deconvolution Tab
Advanced Settings
PSF Settings Tab Deconvolution (adjustable)
Microscope Parameters Section
Advanced Section
Aberration Correction Section
Channel Specific Section
Microscope Info Section
PSF View Section
Deconvolution (defaults)
LSM DCV Processing
PSF Wizard
EM Processing
Change Pixel Type
Coarse Z-Stack Alignment
Coarse Z-Stack Alignment Setup
Alignment Controls Section
Create Image Subset
Cut Out Regions
Define Regions Setup
Region Edit Section
Support Regions Tab
Denoise
Enhance Local Contrast
Gauss
Highpass
Import SmartFIB TIFFs
Median
Not
Remove Stripes
Shading Correction
Slices Replacement
Sort SmartFIB Tiffs
Z-Stack Alignment with ROI
Z-Stack Equalization
Export/Import
Convert TXM Files to CZI
Image Export
File Type Section
Image Data Section
Dimensions Section
Export To Section
Image Import
Import SmartFIB TIFFs
Import TXM
Movie Export
File Type Section
Image Data Section
Fitting Section
Sequence Section
Mapping Section
Dimensions Section
Export to Section
OME TIFF Export
Image Format Section
Image Data Section
Dimensions Section
Export to Section
ZVI Export
Export to Section
Geometric
Apply Channel Alignment Transformation
Change Orientation
Channel Alignment
Channel Alignment (Extended)
Color-coded Projection
Create Channel Alignment Transformation
Image Overlay
Mirror
Orthogonal Projection
Resample
Rotate
Rotate 2D
Sample Down
Shift
Shift Z
Stage Alignment
Stitching
Tiles Blending
Z-Stack Alignment
Z-Stack Alignment with ROI
Image Analysis
Analyze
Analyze to File
Analyze Batch
Analyze Batch to File
Analyze to Label Image
Analyze to Label Image Batch
Analyze Interactive Batch
Lightsheet
Dual Side Fusion
Lightsheet Convert Dimensions
Lightsheet Processing
Landmark Based Alignment
Intensity Based Alignment
Use Registration from File
Interactive Registration
Maximum Intensity Projection
Segmentation
Canny
Marr
Threshold
Threshold (Auto)
Threshold (Dynamic)
Valleys
Sharpen
Delineate
Enhance Contour
Extended Depth of Focus
Unsharp Mask
Smooth
Binomial Filter
Denoise
Gauss
Lowpass
Median
Sigma
Single Pixel Filter
Whitening
Time Series
Gliding Average
Kymograph
Time Alignment
Time Concatenation
Time Differential
Time Stitching
Utilities
Add Channels
Airyscan Processing
Airyscan Sheppard Sum
ApoTome Deconvolution
ApoTome RAW Convert
Calculate Histogram
Change Pixel Type
Combine RGB
Convert To Lambda
Copy Annotations
Copy Image
Correct Stage Jitter
Correlation
Create Gray Scale Image
Create Image Subset
Create Image Subset and Split
Create Image Subset and Split (Write files)
Create PSF
Fuse Image Subset
Generate Image Pyramid
Image Calculator
Image Generator
Linear Unmixing
LSM Plus Processing
Split into RGB
Split Multiblock Image
Split Scenes
Split Scenes (Write files)
Basic Functionality
Colocalization
Colocalization View
X/Y Scatter Plot
Coloc. Tools Tab
Colocalization Table
Region
Quadrant
Pixel Number
Area (µm²)
Relative Area (%)
Pearson's Correlation Coefficient
Manders' Correlation Coefficient
Coloc. Coefficient 1
Coloc. Coefficient 2
CC (Weighted) 1
CC (Weighted) 2
Average Intensity 1
Average Intensity 2
Standard Deviation 1
Standard Deviation 2
Z Index
T Index
Relative Time
Relative Focus
Direct Processing
System Requirements
Hardware Requirements
Software Requirements
Overview Direct Processing
Connecting Acquisition Computer and Processing Computer
Connecting Computers Without Discovery Proxy
Connecting Computers With Discovery Proxy
Setting Up Your PC as Discovery Proxy
Defining Settings in the Auto Save Tool
Using Direct Processing
Using Direct Processing with Airyscan Processing
Direct Processing Tool on Acquisition Tab
Airyscan Processing Parameters
Deconvolution Parameters
Direct Processing PCs Dialog
Direct Processing Tool on Applications Tab
Sharing a Folder for Direct Processing
Creating a Shared Folder on the Processing Computer
Accessing the Shared Folder from the Acquisition Computer
Looking Up the IP Address of Your Computer
Connecting Computers via Cable
Extended Focus Processing
Manual Extended Focus
Preparing a Manual EDF Acquisition
Acquiring EDF Images with Timer
Acquiring EDF Images with F12 Key
Comparing Images Using Split Display
Manual Extended Depth of Focus Tool
Measurement
Using Interactive Measurements
Interactive Measurement Tool
Feature Selection Dialog
Feature Subset Definition Dialog
Interactive Measurement Sequence Definition Dialog
Interactive Measurement Sequence Execution Dialog
Panorama
Prerequisites
Acquiring a Reference Image
Settings for a Panorama Experiment
Acquiring a Panorama Image
Acquiring a Panorama Image Automatically
Processing a Panorama Image
Stitching (Defaults)
Stitching with Shading Correction
Stitching with Fuse Tiles
Stitching with Fuse Tiles and Shading Correction
Image Comparison via Split Display
Panorama Tool
Panorama View
Stage View
Tools Window
Live Panorama Tool
Third Party Import
ZEN Data Storage Client
Setting up ZEN Data Storage Server
Validating the ZEN Data Storage Settings
Saving an Image to ZEN Data Storage
Saving a ZEN Connect Project to ZEN Data Storage
Exporting a ZEN Connect Project from ZEN Data Storage
Uploading Images Automatically After Acquisition
Opening or Deleting an Image from ZEN Data Storage
Opening or Deleting a ZEN Connect Project from ZEN Data Storage
Configuring the Stored Documents Table
Filtering Connect Projects and Images in ZEN Data Storage
Adding and Deleting Tags for ZEN Data Storage Images
Creating a Collection for Data
Editing or Deleting a Data Collection
Adding Data to a Collection
Sharing Data Directly With Users and Groups
Adding an Active Directory User
Stored Documents Dialog
Stored Data Section
Stored Documents Right Click Menu
Image Control Section
Add to Collection Dialog
Share and Manage Access Dialog
ImageJ
Preparations
Activate ImageJ Extension
Sending and Retrieving Images
Use ImageJ Methods
Image Type Send/Retrieve Conventions
ZEN Application Programming Interface (ZEN API)
Additional ZEN API Information and Reference
Toolkits & Modules
Acquisition Toolkits
Experiment Designer
Experiment Designer Tool
Loops and Repetitions Section
Execute Block Options
Import Experiment Blocks Dialog
Experiment Feedback
Workflow Experiment Feedback
Editing the Feedback Script
Selecting Script Runtime Conditions
Experiment Feedback Tool
Script Editor for Experiment Feedback Dialog
Input Windows
Commands Tab
Script Commands - Observables
Observables - Analysis
Observables - Experiment
Observables - Environment
Observables - Hardware
Script Commands - Available Actions
Actions - Experiment
Actions - Experiment - LSM
Actions - Hardware
Actions - Extra
Debugging Tab
Guided Acquisition
Preliminary Work to Guided Acquisition
Performing a Guided Acquisition
Using Guided Acquisition Settings
Guided Acquisition Tool
HDR Confocal Basic
Multi-Channel
Software Autofocus
Terminology & Abbreviations
When is focus the "right" focus?
Software Autofocus in ZEN
Software Autofocus Tool
Software Autofocus Using LSM Tracks
Tiles & Positions
Licensing and Functionalities of Tiles & Positions
General Preparations
Setting Up a Simple Tiles Experiment Without the Tiles & Positions Module
Setting Up a Simple Positions Experiment without the Tiles & Positions Module
Adjusting Z-Values
Adjusting Z-Values of Tile Regions
Adjusting Z-Values of Positions
Exporting Tile Images
Calibrating the Stage and Selecting the Channel
Tiles & Positions with Advanced Setup
Generating a Preview Scan
Creating Tile Regions by Contour
Creating Tile Regions by Predefined
Creating Tile Regions by Carrier
Creating Positions by Location
Creating Positions by Array
Creating Positions by Carrier
Importing Images into the Advanced Setup
Copying a Tile Region or Position
Local and Global Focus Surfaces
Introduction
Creating a Local Focus Surface
Distributing Support Points
Verifying Z-Values of Support Points
Selecting Interpolation Degree
Creating a Global Focus Surface
Distributing Support Points
Verifying Z-Values of Support Points
Selecting Interpolation Degree
Assigning Categories to Tile Regions and Positions
Using Sample Carriers
Selecting a Sample Carrier Template
Customizing a Sample Carrier Template
Re-positioning Sample Carrier after Incubation
Tiles Tool
Tile Regions Section
Positions Section
Options for Editing Single Positions
Options for Editing Position Arrays
Sample Carrier Section
Focus Surface and Support Points Section
Options Section
Verify Tile Regions or Verify Positions Dialog
Tiles Advanced Setup
Stage View
Specific Tiles & Positions Context Menu Options
Tiles Toolbars
Left Toolbar
Top Toolbar
Preview Scan Toolbar
Contour Toolbar
Predefined Toolbar
Stake Toolbar
Tiles Carrier Toolbar
Positions Location Toolbar
Position Array Toolbar
Positions Carrier Toolbar
Tiles View Options
Tiles Tab
Carrier Tab
Tiles Options
Select Template Dialog
Edit Sample Carrier Template dialog
Basic Template Settings
Global Support Points Settings
Time Series
Acquiring Time Series Images
Time Series Tool
Experiment Conditions Section
Interactive Switches Section
Z-Stack
Acquiring Z-Stack Images
Configuring a Z-Stack Automatically
Configuring a Z-Stack Manually (First/Last Mode)
Configuring a Z-Stack Manually (Center Mode)
Z-Stack Tool
Auto Z Brightness Correction with LSM
Visualization and Analysis Toolkits
Image Analysis
Creating a New Image Analysis Setting
Measuring Fluorescence Intensity in a Multichannel Image
Step 1: Classes
Step 2: (Measurement frame)
Step 3: Automatic Segmentation
Step 4: Region Filter
Step 5: Interactive Segmentation
Step 6: Features
Step 7: Results Preview
Executing the Analysis Setting
Counting Number of Fluorescence Signals per Nuclei
Step 1: Classes
Step 2: Measurement Frame
Step 3: Automatic Segmentation
Step 4: Region Filter
Step 5: Interactive Segmentation
Step 6: Features
Step 7: Results Preview
Executing the Analysis Setting
Measuring Mean Fluorescence Intensity on a Ring around the Primary Object
Step 1: Classes
Step 2: Frame
Step 3: Automatic Segmentation
Step 4: Region Filter
Step 5: Features
Step 6: Result Preview
Executing the Analysis Setting
Counting the Number of Objects in a Ring around the Nucleus
Step 1: Classes
Step 2: Frame
Step 3: Automatic Segmentation
Step 4: Region Filter
Step 5: Features
Step 6: Preview Result
Creating a Measurement Data Table
Creating an Image Analysis Setting from an Analyzed Image
Performing an Interactive Analysis
Creating Custom Features
Creating Custom Statistical Features
Creating an Image Analysis Setting From an AI Model
Analysis View
Analysis Tab
Chart Export Tab
Sample Carrier Tab
Table Export Tab
Custom Chart Tab
Copy Operations for Features
Charts and Tables of the Analysis View
Selecting Data for the Multiple Scenes Chart
Heatmap Calculation
Examples for Custom Features
Example 1: Number of Spots per Cell
Example 2: Average Area per Spot
Examples for Custom Statistical Features
Example 1: Percentage of Positive Cells
Example 2: Nuclear Cytoplasmic Transport
Image Analysis Tool
Segmentation Method Dialog
Image Analysis Wizard
Classes
Frame
Automatic Segmentation
Smoothing Section
Sharpen Section
Threshold & Histogram Section
Color Model
Variance Section
Model Section
Select Model Dialog
Subtract BG Section
Object Size & Hole Section
Binary Section
Separate Section
Suppress Section
3D Preview Section
Segmentation Method Selection Dialog
Region Filter
Region Filter Editor
Features
Select Features of Individual Regions Dialog
Select Features of All Regions Dialog
Annotations Dialog
Custom Feature Editor
Statistics
Custom Statistic Feature Editor
Results Preview
Measurement Features
ACP X Unscaled
ACP X Unscaled WCS
ACP Y Unscaled
ACP Y Unscaled WCS
Area
Area Convex (arivis)
Area Cut
Area Cut Unscaled
Area Filled
Area Filled Unscaled
Area Frame
Area Frame Unscaled
Area Percentage of Holes
Area Unscaled
Bound Back
Bound Back Unscaled
Bound Back Unscaled WCS
Bound Back WCS
Bound Bottom
Bound Bottom Unscaled
Bound Bottom Unscaled WCS
Bound Bottom WCS
Bound Center
Bound Center Unscaled
Bound Center Unscaled WCS
Bound Center WCS
Bound Depth
Bound Depth Unscaled
Bound Front
Bound Front Unscaled
Bound Front Unscaled WCS
Bound Front WCS
Bound Height
Bound Height Unscaled
Bound Left
Bound Left Unscaled
Bound Left Unscaled WCS
Bound Left WCS
Bound Right
Bound Right Unscaled
Bound Right Unscaled WCS
Bound Right WCS
Bound Top
Bound Top Unscaled
Bound Top Unscaled WCS
Bound Top WCS
Bound Width
Bound Width Unscaled
Center X
Center X Unscaled
Center X Unscaled WCS
Center X WCS
Center Y
Center Y Unscaled
Center Y Unscaled WCS
Center Y WCS
Center Z
Center Z Unscaled
Center Z Unscaled WCS
Center Z WCS
Circularity (arivis)
Compactness (arivis)
Convexity (arivis)
Count
Count Objects Direct Subclasses
Count per mm2
Diameter
Diameter Maximum Inscribed Circle
Diameter Maximum Inscribed Circle Unscaled
Diameter Unscaled
Ellipse Angle
Ellipse Angle Unscaled
Ellipse Semi-Major
Ellipse Semi-Major Unscaled
Ellipse Semi-Minor
Ellipse Semi-Minor Unscaled
Ellipsoid Semi-Major
Ellipsoid Semi-Major Unscaled
Ellipsoid Semi-Mean
Ellipsoid Semi-Mean Unscaled
Ellipsoid Semi-Minor
Ellipsoid Semi-Minor Unscaled
Feret Maximum
Feret Maximum Angle (arivis)
Feret Maximum Unscaled (arivis)
Feret Minimum
Feret Minimum Angle (arivis)
Feret Minimum Unscaled (arivis)
Feret Ratio (arivis)
Feret Vertical to Maximum (arivis)
Fiber Length
Fiber Length Unscaled
Form Circle
Frame Area Percentage
Frame Area Percentage Cut
Frame Data Area
Frame Data Area Percentage
Frame Data Area Unscaled
ID
ID Object Storage
Advanced Processing
Edges
Gradient Max
Gradient Sum
Highpass
Laplace
Local Variance
Roberts
Sobel
Arithmetics
Add
Add Constant
Average
Combine
Divide
Exponential
Invert
Logarithm
Maximum
Minimum
Multiply
Multiply Constant
Reciprocal
Square
Square Root
Subtract
Binary
And
Apply Mask
Distance
Exoskeleton
Fill Holes
Label Image
Mark Regions
Not
Or
Scrap
Separation
Thinning
Ultimate Erode
Xor
Morphology
Structure Elements
Smooth
Rank
Utilities
3Dxl
Animating the 3D Volume
3D View
Tool Bars
Tool Bar (Left)
Tool Bar (Right)
Tool Bar (Bottom)
3D Tab
Appearance Tab
Transparency Tab
Surface Tab
Channels Tab
Background Tab
Light Tab
Projection Tab
Clipping Tab
Series Tab
Measurements Tab
3D Graphics Tab
3Dxl Plus
Tomo3D View
Left Toolbar (Tomo3D)
Bottom Toolbar (Tomo3D)
Ortho Display Tab (Tomo3D)
Appearance Tab (Tomo3D)
Transparency Tab (Tomo3D)
Background Tab
Light Tab (Tomo3D)
3D Tab (Tomo3D)
Create Image Tab (Tomo3D)
3D Image Analysis
Creating a 3D Image Analysis Setting
Performing and Saving a 3D Analysis
Viewing and Exporting the Results of a 3D Analysis
Analysis Tab
Analysis Objects Table
Intellesis Segmentation
Licensing and Functionalities of Intellesis Segmentation
Fact Sheet
FAQ/Terminology
Operating Concept Intellesis Segmentation
Workflow Overview for Intellesis Segmentation
Training User Interface Intellesis Segmentation
Intellesis Training Options
Postprocessing Options
Labeling Options
Image Gallery
Select Channel Dialog
Intellesis Segmentation Models
Creating and Training an Intellesis Segmentation Model
Importing an Intellesis Segmentation Model
Exporting an Intellesis Segmentation Model
Exporting an Intellesis Segmentation Model with Images
Renaming an Intellesis Segmentation Model
Cloning an Intellesis Segmentation Model
Creating an Image Analysis Setting from an Intellesis Segmentation Model
Deleting an Intellesis Segmentation Model
Editing Classes
Importing Labels from Binary Mask
Converting Segmentations to Labels
Using Pretrained Deep Learning Networks for Image Segmentation
Segmenting an Image Using the Intellesis Segmentation Image Processing Function
Performing an Image Analysis Using an Intellesis Segmentation Model
Changing the Tile Border Size for Deep Learning Networks
Using Intellesis Segmentation Models in OAD
Remarks and Additional Information
Feature Extractors
Intellesis Basic Features
Basic Features 25
Basic Features 33
Intellesis Deep Features
Image Processing Functions
Minimum Confidence
Intellesis Segmentation
Utilities
Intellesis Segmentation Tool
Change Border Size Dialog
Tile Border Size Example
Intellesis Denoising
Licensing and Functionalities of Intellesis Denoising
Training User Interface Intellesis Denoising
Creating and Training an Intellesis Denoising Model
Importing an Intellesis Denoising Model
Exporting an Intellesis Denoising Model
Using an Intellesis Denoising Model for Image Processing
Intellesis Denoising Tool
IP Function
Intellesis Denoising
Intellesis Object Classification
Licensing and Functionalities of Intellesis Object Classification
Workflow Overview for Intellesis Object Classification
Training User Interface Intellesis Object Classification
Classification Settings
Image Gallery (Object Classification)
Labeling Options Tab
Object Classification Table
Creating and Training an Intellesis Object Classification Model
Importing an Intellesis Object Classification Model
Exporting an Intellesis Object Classification Model
Exporting an Intellesis Object Classification Model with Images
Using an Intellesis Object Classification Model for Image Processing
Intellesis Object Classification Tool
IP Function
Intellesis Object Classification
Deconvolution
Licensing and Functionalities of Deconvolution
Basics of Deconvolution
Deconvolution Methods in ZEN
Performing Deconvolution Using Default Values
Performing Configurable Deconvolution
Step 1: Loading an Input Image for Deconvolution
Step 2: Set Parameters for Deconvolution
Step 3: Performing Deconvolution
Step 4: Info View and Re-Using Deconvolution Parameters from a Processed Image
Creating Deconvolution Settings
Creating a PSF - With Wizard and Without
Measuring the PSF Using Subresolution Beads
Using Deconvolution in Direct Processing
Image Types Suitable for Deconvolution
Table of Default Parameter for Deconvolution
Dynamics Profiler
Overview Supported Laser Lines
Setting Up and Performing a Dynamics Profiler Acquisition
Exporting Data From Tables
Exporting Data From Charts
Opening the Reference Image as Separate Image
Cutting Out a Data Region
Saving Dynamics Profiler Documents as Compressed CZI
Creating a Custom ωr Calibration
Using Custom ωr Calibration
Dynamics Profiler Acquisition Wizard
Correlation View
Diffusion View
Flow View
Parameter Table Context Menu
Dynamics Profiler Calculations
Physiology (Dynamics)
Licensing and Functionalities of Physiology
Opening the MeanROI View
Workflow MeanROI View (Offline)
Drawing in ROIs
Adjusting ROIs for Time Points
Adjusting the Display
Using Background Correction
Exporting a Data Table
Calculating a Ratio for One Wavelength
Calculating a Ratio for Two Wavelengths
Basics of Calculation of Intensity and Ratio Values
Interaction with a Table in MeanROI View
Workflow Physiology (Dynamics) Experiments
Setting up the Online Ratio Calculation
Calculating the Online Ratio for Single Wavelength
Calculation of the Ratio Value R
Setting up an Experiment in MeanROI Setup
Drawing in ROIs
Adjusting the Display
Using Background Correction
Starting and Influencing an Experiment
Adjusting ROIs during Experiments
Sample Experiment Fura-2 with DG4/5
Step 1: Creating Channels
Step 2: Setting Up a Time Series and Creating Switches
Step 3: Setting Up an Online Ratio
Step 4: MeanROI Setup
Step 5: Starting, Analyzing and Influencing an Experiment
Mean ROI View
Time Line View Panel
Mean ROI Tab
Layout Tab
Charts Tab
Export Tab
Ratio Tab
Online Ratio Tab
ROI Tracing Tab
FRAP Efficiency Analysis
FRAP View
FRAP Tab
Fit Model
Automated Photomanipulation
Using Automated Photomanipulation Settings
Performing an Automated Photomanipulation Experiment
Automated Photomanipulation Tool
FRET
Acquisiton Prerequisites
Analysis Method for Acceptor Bleaching
Analysis Methods for Sensitized Emission
FC or Youvan Method
FRETN or Gordon Method
N-FRET or Xia Method
Crosstalk Correction for Gordon and Xia Methods
Determining Donor Coefficient Values
Determining Acceptor Coefficient Values
FRET View
Data Table Sensitized Emission
Data Table Acceptor Bleaching
FRET Tab
Parameters Tab
Threshold Tab
Settings Tab
General Tab
Acceptor Photobleach Tab
Sensitized Emission Tab
ZEN Connect
Licensing and Functionalities of ZEN Connect
User Interface
ZEN Connect 3D View
Alignment Tab ZEN Connect 3D
Connect 3D Tab
Opening the Correlative Workspace
Opening Images in the ZEN Connect 3D View
Non Image Data
Raman Images
Project and Image Management
Creating a ZEN Connect Project
Loading a ZEN Connect Project
Adding an Image to the ZEN Connect Project
Adding an Open Image to the ZEN Connect Project
Adding Datasets when Adding Images
Zooming Images
Removing Images from the ZEN Connect Project
Renaming Images in a ZEN Connect Project
Opening Images in ZEN
Showing an Image in the Explorer
Moving or Hiding Images
Starting a New Session
Toggling View Modes
Closing a ZEN Connect Project
Import and Export
Importing Data
Importing Third-party Images
Importing a SmartFIB Stack into ZEN Connect
Importing Non Image Data
Exporting Single Image Data
Exporting a ZEN Connect Project as a Video
Exporting Data for SerialEM
Alignment
Activating the Alignment Process
Aligning Image Data
Aligning Images in Z Direction
Example for Z Alignment
Rotating a Z-Stack
Aligning Images in the ZEN Connect 3D View
Aligning Non Image Data
Aligning Images in the Manual Alignment Wizard
Aligning Images in the Point Alignment Wizard
Aligning Images in the 3D Point Alignment Wizard
Handling of Images and Data
Zooming to Extent
Panning & Zooming
Selecting Region
Toggling the Display of Region Caption and Frame
Selecting and Clearing Carrier/Holder
Grabbing an Image
Using Regions of Interest in Zen Connect
Drawing a Region of Interest in ZEN Connect
Deleting a Region of Interest in ZEN Connect
Renaming a Region of Interest in ZEN Connect
Zooming to a Region of Interest in ZEN Connect
Moving the Stage to a Region of Interest in ZEN Connect
Adding Measurements to a ZEN Connect Project
Editing Measurements in a ZEN Connect Project
ZEN Connect Tool
ZEN Connect Project view
ZEN Connect Project Layer view
Button Bar
Select Template Dialog
Alignment Tab
Measurement Tab
Button Bar below Image View
ZEN Connect Single Image Export Wizard
Field of View Width Dialog
Pixel Size Dialog
Video Export Wizard
Regions Tool
ZEN Connect Manual Alignment Wizard
Alignment Parameter Section
ZEN Connect Point Alignment Wizard
Step 1: Setup Points
Point Alignment Options
Step 2: Preview
ZEN Connect 3D Point Alignment Wizard
Step 1: Setup Points
3D Point Alignment Options
Step 2: Preview
Shuttle & Find
Settings and Image Acquisition with the Light Microscope
Mounting the Sample Holder to the LM
Starting the LM Software
Selecting the Sample Holder
Defining a New Sample Holder Template
Calibrating the Sample Holder
Preparing Calibration
Setting Calibration Options
Performing Calibration
Acquiring the LM Image
Shuttle & Find Sample Positions at the Electron Microscope
Mounting the Sample Holder to the SEM
Starting the ZEN SEM Software
Selecting the Sample Holder
Calibrating the Sample Holder
Acquiring an EM Image
Fine Calibration of the Sample Holder
Correlating Two Loaded Images
Correlation of Live Image and Loaded Image
Shuttle & Find with an EVO 10
User Interface
Shuttle & Find Tool
Shuttle & Find View
S&F Tab
Options
Regions, Find and Dimensions
S&F Correlation Tab
Sample Holder Calibration Wizard
Step 1: Options
Step 2-4: Calibration
Correlative Sample Holders
Application and Workflow Toolkits
Bio Applications
Available Bio Applications
General Workflow
Creating a General Bio Application Setting
Running Bio Applications
Creating a Setting for Cell Counting
Creating a Setting for Confluency
Creating a Setting for Gene- and Protein Expression
Creating a Setting for Automated Spot Detection
Creating a Setting for Translocation
Running Bio Applications in Batch Mode
Exporting Results of the Bio Applications Analysis
Bio Applications View
Export Tab
Objects Tab
Chart Tab
Bio Applications Tool
Bio Applications Wizard
Cell Counting Specific Settings
Confluency Specific Settings
Gene- and Protein Expression Specific Settings
Automated Spot Detection Specific Settings
Translocation Specific Settings
Macro Environment
Running an Existing Macro
Recording a Macro
EM Processing Toolbox
Workflow Overview
Aligning Z-Planes Manually
Aligning Z-Planes Automatically (Based on a ROI)
Replacing Z-Slices in a Z-Stack
Cutting Out a Volume from a Z-Stack
Importing SmartFIB Tiffs
Microscopy Copilot
Using the Microscopy Copilot
Microscopy Copilot Dialog
AI Tissue Detection
Input Data for AI Tissue Detection
Sample Requirements for AI Tissue Detection
FINE (Fluorescence Intensity Normalization and Evaluation)
Tissue Image Alignment
Tissue Image Alignment
Combining Multi-Channel Images of Different Staining and Imaging Cycles
Axioscan User Mode
Customizing a Reference Scan Profile
Customize Reference Scan Profile Wizard
Step 1: Set Up Batch
Step 2: Review Channels
Step 3: Set Exposure Time
Axioscan Advanced Spectral Unmixing
Overview for Creating New Reference Spectra
Sample Preparation for Creating New Reference Spectra
Information for Acquisition and Preparation of Reference Scans
Starting the Calibrated Unmixing Wizard
Selecting Autofluorescence Spectra
Selecting Dye Spectra
Checking the Calculated Dye Spectra
Applying Unmixing in the Scan Profile
Calibrated Unmixing Wizard
Step 1: Selection of Autofluorescence Spectra
Step 2: Selection of Dye Spectra
Dye Selection Table
Step 3: Calculated Dye Spectra
ZEN Workflows
User Interface for Workflows in ZEN
Creating a Workflow
Opening a Workflow
Adding a Loop to a Workflow
Adding a Group to a Workflow
Duplicating and Replacing a Workflow Step
Moving or Deleting a Workflow Step
Customizing Steps and Tools
Exporting and Importing Workflows
Running a Workflow Stepwise
Running a Workflow Automatically
Running Parts of a Workflow or Individual Steps
Example Workflow Acquisition and Processing
Example Workflow Image Analysis
Special/Hardware Related Modules
32ch Quasar detector
Airyscan RAW Data
Saving Images in 32ch Airyscan Format
Exporting Data in 1ch Sheppard Sum Format
Apotome Plus
Apotome Plus (defaults)
Apotome Plus (adjustable)
Apotome Plus Tab
Advanced Settings
PSF Settings Tab Apotome Plus (adjustable)
Microscope Parameters Section
Advanced Section
Aberration Correction Section
Channel Specific Section
Using Apotome Plus in Direct Processing
Creating Apotome Plus Settings
Coded Microscope
Confocal Topography
Acquiring Topography Images
Measuring Layer Thickness
Topography Tool
Topography Measurement Wizard
Step 1: Setup
Step 2: Z-Stack Acquisition
Layer Thickness Measurement Tool
Layer Thickness Measurement Wizard
Step 1: Setup
Step 2: Sectioning
Step 3: Measurement
Acquisition Mode Tool in Topography Measurement Wizard
Channel Tool in Topography Measurement Wizard
Tiles Tool in Topography Measurement Wizard
Z-Stack Tool in Topography Measurement Wizard
Correlative Array Tomography (CAT)
Basics of Array Tomography
Sample Preparation
Pre-Settings (Light Microscope)
Experiment Settings
CAT Workflow
Creating a New Sample
Selecting the Sample Holder
Defining a New Sample Holder Template
Calibrating the Sample Holder
Preparing Calibration
Setting Calibration Options
Performing Calibration
Acquiring the LM image
Acquiring the Overview Image
Defining the Ribbons
Imaging the Ribbons
Specifying the Sections
Specifying the ROIs
Imaging the ROIs
Re-Shooting ROIs
Aligning the Z-Stack Image
Correlating the LM and SEM images
CAT Tool
Select Sample Dialog
Sample Holder Calibration Wizard
Step 1: Options
Step 2-4: Calibration
Acquisition Wizard
Overview Imaging
Ribbon Definition
Ribbon Imaging
Section Specification
ROI Specification
ROI Imaging
Re-Shoot
Z-Stack Alignment Wizard
Image Import
Pre-Processing
Image Review
Alignment
Manual Correction
Final Image Creation
Correlation Wizard
Import Z-Stacks
Correlation
Manual Correction
Create Final Correlation Image
Correlative Sample Holders
Lightfield 4D
Lightfield 4D Volume Color Coding
Setting Up a Lightfield 4D Track without Smart Setup
Setting Up a Lightfield 4D Track with Smart Setup
Focus Strategies in Lightfield 4D Experiments
Starting a Live Acquisition for Lightfield 4D
Setting Up and Starting a Lightfield 4D Experiment
Defining a Lightfield 4D Multi-Position Experiment with the Tiles Advanced Setup
Defining a Lightfield 4D Multi-Position Experiment without the Tiles Advanced Setup
Processing a Lightfield 4D Image with the Processing Function
Processing a Lightfield 4D Image with the View Options Tab
Using Lightfield 4D in Direct Processing
Lightfield 4D Processing
Lightfield 4D Tab
Image Analysis
Segmentation methods in ZEN
Automatic image segmentation
What is segmentation?
How does segmentation work?
Instance vs. Semantic Segmentation
Segmentation methods
Classical segmentation methods
Global Thresholding
Background Subtraction
Variance-based Thresholding
Dynamic Thresholding
AI-based methods
AI Semantic Segmentation
AI Instance Segmentation
Intellesis Trainable Segmentation
Machine Learning vs. Deep Learning
Choosing the right segmentation method
Homepage
ZEN
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Basic Concepts
Customizing the Application
Showing/Hiding Workspace Areas
Showing/Hiding Workspace Areas
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