ZEISS Microscopy Knowledge Base
Help
ZEISS Microscopy Knowledge Base
Search
Major brand refresh for arivis image analysis software solutions
Release Notes
arivis Pro 4.6
arivis Pro 4.5
arivis Pro 4.4
arivis Pro 4.3.1
arivis Pro 4.3
arivis Pro 4.2
arivis Vision4D 4.1.2
arivis Vision4D 4.1.1
New & Noteworthy
Analysis
4D Viewer
General
arivis Vision4D 4.1
New & Noteworthy
arivis AI Toolkit
Tools
Analysis
Visualization
Data Handling
General
Archive
arivis Vision4D 4.0
arivis Vision4D 3.6.2
arivis Vision4D 3.6.1
arivis Vision4D 3.6
arivis Vision4D 3.5.1
arivis Vision4D 3.5
arivis Vision4D 3.4
arivis Vision4D 3.3
arivis Vision4D 3.2
arivis Vision4D 3.1.4
arivis Vision4D 3.1.3
arivis Vision4D 3.1.2
arivis Vision4D 3.0.1
arivis Vision4D 2.12.6
arivis Vision4D 2.12.5
arivis Vision4D 2.12.4
arivis Vision4D 2.12.3
arivis Vision4D 2.12.2
arivis Vision4D 2.12.1
arivis Vision4D 2.12
arivis Vision4D 2.11.2
arivis Vision4D 2.11
System requirements
Basic requirements
Additional requirements by feature
Setting up arivis Pro
Installation and configuration
Installing arivis Pro
Activating the license
Configuring the application after installation
Directories for new and temporary documents
GPU configuration
Graphics acceleration
ML & DL acceleration
Activating, updating and transferring licenses
Introduction
License activation
Online license activation
Offline license activation
Installing the license tool
Opening the license tool
Updating a license
Transferring a license
Conclusion
Using the GPU package installation
Overview
Introduction
Using the GPU for ML Operations
Compatible GPUs
Using arivis Pro on laptops with a GPU
Overview
Introduction
Setting default GPU
On systems running Windows version earlier than windows 10
For system running Windows 10 and higher
GPU selection on launch
Using arivis software and virtual machines
Introduction
Licensing
Graphics cards
Data access
Conclusions
Running arivis Pro on Amazon AWS
Setup a suitable system
Setup 3D graphics
Setup arivisPro
Optional: using NICE DCV
Using arivis Pro over remote desktop
Introduction
GPUs and RDP
Licensing
Conclusions
Installing arivis Pro on Apple hardware
arivis Vision4D is not available as a native macOS application, it requires Microsoft Window 10 (64Bit) or better.
Why does arivis Pro not use all the computer resources?
Introduction
RAM availability
Visualising images
Visualising 3D datasets
Conclusions
Creating a system report
Licensing setup
arivis Network License setup
Introduction
Selecting a License server
Installing Floating Licenses on Windows Computers
Installing Floating License on Linux Computers
Network Configurations for Floating Licenses
Additional License Management Tools
Limiting access from remote clients
Aggressive search for licenses
Conclusion
HASP License Troubleshooting
Introduction
Installing HASP drivers
Port configuration
Troubleshooting issues
License Count Exceeded
No License Found
License is Out of Date
Hardware changes detected
Unable to contact a network license server
Licensing FAQ
Arivis License Tool - FAQ
Choosing the right license type
Introduction
Soft vs Hard Licenses
Local vs Floating Licenses
Typical Configurations
Single user, one workstation
Single user, multiple workstations
Multiple users, distributed workstation
Multiple users, shared workstation
Imaging basics
What is an image?
What is resolution
Introduction
The different types of resolution
Optical resolution
Sampling resolution
Noise
Bit depth
Conclusions
What is segmentation
What is segmentation?
Instance vs. Semantic Segmentation
How does arivis handle large datasets
How do computers process image data?
So what can we do to optimize the processing of such potentially large datasets?
Visualizing larger datasets
Analyzing and processing lager datasets
The arivis file format
So how does Vision4D work with my microscopy images?
How does arivis render datasets that are larger than the video memory in 3D?
Introduction
Rendering 3D stacks as volumes
How can we improve the rendering in the 4D viewer?
Upgrading the GPU
Clipping the dataset to a manageable volume
Changing application preferences
Conclusions
Why does processing a 3D animation movie export take so long?
Overview
Introduction
How is producing a high-resolution snapshot different?
So what about movies?
Conclusions
What is metadata, and why is it important?
What is metadata?
Using arivis Pro
Getting started with arivis Pro
Introduction
Importing Images
Checking and updating calibrations
Navigating through Image Sets
Calibrating datasets
Overview
Introduction
Spatial calibrations
Temporal calibrations
Using intensity range and visualization settings
Basic concepts
Dynamic Range
Grey Scale
Intensity Range
Full Dynamic Range
Partial Dynamic Range
Color scalebar
Color settings
Gamma correction
Measuring distances in images
Using local deep learning with arivis AI toolkit
Summary
Introduction
Creating a new DL model
Accessing the DL Trainer and creating classes
Annotating objects
Training the network
Using a DL training in a pipeline
Setting opacity in 3D renderings
Basic concepts
Setting the opacity
Coloring volumes by depth in 3D view
Introduction
Changing channel colors
Changing 4D mapping to axis
Exporting CSV files out of arivis Pro
Introduction
Changing exports to CSV
Using CSV export with batch analysis
CSV export in arivis VisionHub
Backround substraction vs. Shading correction
Shading correction
Background subtraction
Background subtraction operator anatomy
Backround source
Background comparison
Morphological Background subtraction operator anatomy
Morphological Background subtraction options
Objects segmentation after morphological Background subtraction
Drawing objects interactively
Overview
Drawing objects in 4D
Placing new objects in 3D
Adding a spherical object with a variable radius
Adding a spherical object with a predefined radius
Adding a marker (point)
Selecting an object with the Magic Wand tool in 3D
Drawing objects in 2D
Placing new objects in 2D
Adding a spherical object with a variable radius
Adding a marker (single point) on the active Z Plane
Selecting a region on the active Z Plane
Drawing a 3D Polyline
Using the Draw Objects tool
Using the Move Objects tool
Using the Magic Wand tool
Measuring a structure of interest
What is a TAG
Configuring the result storage operator
Introduction
Adding Result Storage to a pipeline
Default Result Storage targets
Changing the Result Storage options
Voxels Storage
Segments Storage
Advanced Result Storage options
Enabling extended channel selection
Using extended channel selection
Which option should I use, and when?
Conclusion
Performing SIS file optimization
Opening the working dataset
Checking the file status
Applying the defragment task
Creating Maximum Intensity Projections in arivis Pro
Overview
Introduction
Generating MIPs in arivis Pro
Additional remarks
Image analysis in arivis Pro
Overview
Workflow Description
Opening the Analysis panel
Adding pipeline operations
Input ROI
Blob Finder (Segmentation)
Tracking (Using segmented objects)
Export Object Features
Store Objects
Saving changes
Conclusions
Detecting spines with neurite/neuron tracer
Overview
Introduction
Adding Spine Detection to a Pipeline
AI Assisted Spine Detection
Assigning previously segmented objects as spines
Using a probability map
Reviewing spine detection results
Tutorials
Lunch-time Academy
Getting Started with ZEISS arivis Pro
Basic 3D Segmentation & Analysis Tasks
Advanced 3D Image Analysis Operations
AI Approaches for Advanced 3D Image Analysis
A Focus on Tracking
A Focus on Neuron Tracing
4D Viewer Basics
Analysis Operations
Pipeline Basics
Segmentation
Inter object relationships
Adjusting channel colors
Contextualising segmentation to Atlas regions
Background
Analysis Pipeline
Analysis Results
Creating movies
Overview
Introduction
Exporting time/plane progressions
Using the Storyboard panel to create animations in the 4D Viewer
Getting started with the Storyboard
Exporting Movies
Movie saving options
Video Resolution and Framerate
Data Resolution
Creating movies for video tutorials or to show arivis processes
Creating random sub-population of objects
Deep Learning and Machine Learning
Tracking & Tracing
Image transformations and stitching
Importing and moving objects in a 3D volume
Background
Importing objects
Moving objects
Video
Image Courtesy
Measuring the ratio of objects inside other objects?
Performing compartmentalization analysis
Overview
The compartments operator
Compartment hierarchy settings
Structures relationship settings
Compartment output settings
Performing segmentation
Overview
The analysis panel
What next?
Using compartments operation
What does the Compartments operation do?
Example uses of the Compartments operation
Configuring the Compartments operation in a pipeline
Compartment operation inputs
Configuring relationship parameters
Compartments operation results
Custom features related to children
Object table layout
Exporting compartmentalization results
Conclusions
Sample Pipeline How To`s
Aggregating well plate data
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Normalization
Normalization parameters
Blob Finder
Blob Finder parameters
Intensity Threshold Segmenter
Intensity Threshold Segmenter parameters
Object Feature Filter
Object Feature Filter parameters
Aggregate Features
Configure Data Aggregation dialog
Store Objects
Executing the pipeline
Single-field execution
Multi-run execution
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Compartmentalizing cells or particles
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Intensity Threshold Segmenter
Intensity Threshold Segmenter parameters
Blob Finder
Blob Finder parameters
Object Feature Filter
Object Feature Filter parameters
Object Feature Filter
Object Feature Filter parameters
Compartmentalization
Compartmentalization parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting big structures automatically
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Denoising
Denoising parameters
Intensity Threshold Segmenter
Intensity Threshold Segmenter parameters
Object Feature Filter
Object Feature Filter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting big structures manually
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Denoising
Denoising parameters
Intensity Threshold Segmenter
Intensity Threshold Segmenter parameters
Object Feature Filter
Object Feature Filter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells (Cellpose-based Segmenter)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Cellpose-based Segmenter
Cellpose-based Segmenter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Results in the Viewer
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells (Region Growing)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Denoising
Denoising parameters
Blob Finder
Blob Finder parameters
Blob Finder results
Region Growing
Region Growing parameters
Region Growing results
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells (Seeded Region Growing)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Denoising
Denoising parameters
Seeded Region Growing
Seeded Region Growing parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Results in the Viewer
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells based on membranes
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Membrane-based Segmenter
Membrane-based Segmenter parameters
Membrane-based Segmenter results
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells based on menbranes with enhancement
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Membrane Detection
Membrane Detection parameters
Membrane Detection results
Membrane-based Segmenter
Membrane-based Segmenter parameters
Membrane-based Segmenter results
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells or particles
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Blob Finder
Blob Finder parameters
Blob Finder results
Object Feature Filter
Object Feature Filter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting dendritic spines (AI-assisted)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Neurite Tracer
Neurite Tracer parameters
Spine Tracer
Spine Tracer parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting dendritic spines (Probability Map)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Deep Learning Reconstruction
Deep Learning Reconstruction parameters
Neurite Tracer
Neurite Tracer parameters
Spine Tracer
Spine Tracer parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting dendritic spines (Segments)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Neurite Tracer
Neurite Tracer parameters
Deep Learning Segmenter
Deep Learning Segmenter parameters
Spine Tracer
Spine Tracer parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting neurites
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Neurite Tracer
Neurite Tracer parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Visualization examples
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Editing the traces
Detecting neurons
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Blob Finder
Blob Finder parameters
Neuron Tracer
Neuron Trace parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Visualization Examples
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Editing the traces
Detecting nuclei and cells (Machine Learning)
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Machine Learning Segmenter
Machine Learning Segmenter parameters
Object Feature Filter
Object Feature Filter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the Results
Results in the Viewer
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Machine Learning Trainer
Opening the ML Trainer panel
Setting up the ML Trainer
Detecting small structures (Watershed)
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Normalization
Normalization parameters
Watershed
Watershed parameters
Watershed results
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Tracking cells or particles
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Watershed
Watershed parameters
Tracking
Tracking parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Tracking cells or particles with lineage
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Blob Finder
Blob Finder parameters
Blob Finder results
Tracking
Tracking parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Using manually drawn regions in pipelines
Overview
Introduction
Document vs Analysis object
Potential use cases for manually drawn objects
Using an existing objects in the pipeline
Masking
Importing the document objects
Image pre-processing, stitching and volume fusion
Introduction to volume fusion
Overview
Introduction
Prerequisites
Volumes to be fused need to start as different image sets in the same SIS file
The volumes must be of the same bit depth
Calibrations need to be correct for the sample
Fusing Volumes
Landmark registration - Creating landmarks
Landmark Registration - Fusing the volumes
Surface registration - extracting and transferring the surface
Surface registration - Transforming the surface in Vision4D
Surface registration - Transforming the surface in VisionVR
Surface registration - Applying the surface transformation for fusion
Additional considerations
Multimodal imaging
Merging more than two sets
Time lapse analysis
Tracking in arivis Pro
Introduction
Image quality
Sampling resolution
Segmentation
Intensity tracks
Segmenting objects for tracking
Tracking segmented objects
Motion type
Fusions and Divisions
Weighing
Reviewing Tracking results
Editing tracks
Summary
Performing manual tracking on existing segments»
Opening the working dataset
Detecting the objects
Selecting objects manually
Tracking pipeline execution
Viewing the results
Editing tracks
Quantifying contacts over time
Segmenting Objects
Tagging contact events
Tracking objects
Interpreting the data
Object Colouring
Custom Features
Scripting and interaction with other programs
Color Deconvolution
Introduction
Importing and editing the script
RGB Color Mapping
Dye Selection
Inverting the Output
Applying the script to an image
Interpreting the results
Conclusions
Download the script
Creating concentric sub volume - matryoshka dolls
Opening the working dataset
Selecting the Python Operator and loading the Python code
Set the Operator parameters
Running the pipeline
Creating freely XY oriented sub volumes
Opening the working dataset
Drawing the reference ROI
Loading the Python script
Setting the script features
Running the Python script
Creating Heat-Map – density distribution
Opening the working dataset
Loading the Python script
Set the Script features
Running the Python script
Analysis options overview
The Compartments operator
Simple Compartments (2 levels)
Multiple Compartments (multiple levels)
Single Compartments (multiple subjects)
Compartments example
Heat-Map Compartments application
Building the analysis pipeline
Running the analysis Pipeline
Viewing the results
Creating spiral oriented sub volume»
Opening the working dataset
Drawing the reference 3D polyline
Loading the Python script
Setting the script features
Running the Python script
Building the analysis pipeline
Running the analysis Pipeline
Viewing the results
Creating XYZ matrix of sub-volumes
Opening the working dataset
Loading the Python script
Setting the script features
Running the Python script
Image Registration for Multiplexing Experiments in arivis Pro
Overview
Introduction
Image registration in a nutshell
Application Workflow
Preliminary Remarks
Installing the prerequisites
Installing Anaconda
Setting up the image registration environment
Running image registration for multiplexing data in arivis Pro
Install Anaconda Python for Vision4D
Introduction
Installing Anaconda
Configuring Vision4D
Objects contacts analysis
Introduction
Contacts analysis theory
Set the stand alone Script options
Set and run the Script operator
Performing contrast limited adaptive histogram equalization (CLAHE)»
Opening the working dataset
Loading the Python script
Setting the script features
Installing the Anaconda3 package and the OpenCV module
Performing objects density (heat-map) and object distribution gradient plotting (profile)
Opening the working dataset
Drawing the reference ROI
Loading the Python script
Setting the script features
Running the Python script
Building the analysis Pipeline
Running the analysis Pipeline
Viewing the results
Segmenting objects into equal parts in arivis Pro
Import the image set(s) in arivis Pro
Download the Anaconda package
Install the Anaconda package
Install the Anaconda environment
Test python Registration environment in arivis Pro
Run the python script in arivis Pro
Visualization of the results
Using cellpose models in arivis Pro
About the Cellpose to ONNX Converter tool
Setting up and using the converter tool
Using the models in arivis Pro
Option 1: Adding models to the Cellpose model directory
Option 2: Loading a model directly in the operation
arivis AI: Machine Learning and Deep Learning
Using StarDist
Introduction
Preliminary Remarks
How does it work?
Objects annotation
Creating and training a neural network
Image analysis
Why use StarDist within Vision4D?
Application examples
Nuclei Tracking
Distribution Analysis
Measuring Cell Volumes
How to get StarDist working with Vision4D
Setting up Vision4D preferences
Loading the script
Applying cellpose models (arivis Vision4D 3.4.0 to 4.1.0)
Overview
Introduction
Preliminary Remarks
Installing the prerequisites
Installing Anaconda
Setting up the cellpose environment
Using cellpose in Vision4D
Setting up cellpose parameters
Using cellpose in pipelines
Docker support for instance segmentation
What is Docker?
Using Docker in arivis Pro
What is difference between Docker Desktop and Docker Engine?
Docker virtualization requirements
Docker GPU Support
Installing Docker for AI Instance Segmentation
Overview
Introduction
Docker Licenses
Installing Docker Desktop
Configuring Docker Desktop
Troubleshooting
Windows 10
Windows 11
Installing Docker Engine on AWS
Overview
Introduction
Selecting size and image
Installing Docker Engine
Enabling Docker Remote access
Configuring arivis Pro to use Remote Docker Engine
Installing Docker Engine on Azure
Overview
Introduction
Selecting size and image
Configuring Disk
Installing the nVidia GPU Extension
Installing Docker Engine
Enabling Docker Remote access
Installing nVidia Container Toolkit
Configuring arivis Pro to use Remote Docker Engine
Deep Learning segmentation pipelines
Overview
Introduction
Linking arivis Pro to your arivis Cloud account
Creating access tokens
Configuring arivis Pro using access tokens
Creating Pipelines with DL Segmentation
Exporting Pipelines with DL Instance Segmentation
Exporting the pipeline
Sharing an arivis Cloud model
Importing the pipeline and model
Importing the analysis pipeline
SIS Converter
Using SIS Converter
Opening the arivis SIS Converter
Setting the preferences
Importing channel colors
Disable blending
Using GZIP compression
Creating Restore Point
More options
Importing files
Importing complex or multiple input files
Modifying the list of files
Complex Import
Manual import mapper
Apply dimension order
Arranging the order of the template elements
Pattern matching
Detecting channel names
Saving import scenario definitions
Supported image formats
Amira-Mesh Media Handler
Aperio Media Handler
Metamorph Media Handler
The DeltaVision media handler
Dicom Media Handler
Hamamatsu Media Handler
FreeImage Media Handler
ICS Media Handler
Imaris Media Handler
JPEG Media Handler
Leica Media Handler
LSM Media Handler
Mirax Media Handler
NIfTI Media Handler
Nikon Media Handler
Olympus Media Handler
RAWInfo Media Handler
Slide Book Media Handler
Tiff Media Handler
VOL Media Handler
Zeiss ZVI Media Handler
Release Notes
SIS Converter 4.5
SIS Converter 4.3
SIS Converter 4.1
SIS Converter 4.0
SIS Converter 3.5.1
Archive
SIS Converter 3.4
SIS Converter 3.3
SIS Converter 3.2
SIS Converter 3.1.4
Supported File Formats
Supported Image File Formats
Major brand refresh for arivis image analysis software solutions
Release Notes
arivis Pro 4.6
arivis Pro 4.5
arivis Pro 4.4
arivis Pro 4.3.1
arivis Pro 4.3
arivis Pro 4.2
arivis Vision4D 4.1.2
arivis Vision4D 4.1.1
New & Noteworthy
Analysis
4D Viewer
General
arivis Vision4D 4.1
New & Noteworthy
arivis AI Toolkit
Tools
Analysis
Visualization
Data Handling
General
Archive
arivis Vision4D 4.0
arivis Vision4D 3.6.2
arivis Vision4D 3.6.1
arivis Vision4D 3.6
arivis Vision4D 3.5.1
arivis Vision4D 3.5
arivis Vision4D 3.4
arivis Vision4D 3.3
arivis Vision4D 3.2
arivis Vision4D 3.1.4
arivis Vision4D 3.1.3
arivis Vision4D 3.1.2
arivis Vision4D 3.0.1
arivis Vision4D 2.12.6
arivis Vision4D 2.12.5
arivis Vision4D 2.12.4
arivis Vision4D 2.12.3
arivis Vision4D 2.12.2
arivis Vision4D 2.12.1
arivis Vision4D 2.12
arivis Vision4D 2.11.2
arivis Vision4D 2.11
System requirements
Basic requirements
Additional requirements by feature
Setting up arivis Pro
Installation and configuration
Installing arivis Pro
Activating the license
Configuring the application after installation
Directories for new and temporary documents
GPU configuration
Graphics acceleration
ML & DL acceleration
Activating, updating and transferring licenses
Introduction
License activation
Online license activation
Offline license activation
Installing the license tool
Opening the license tool
Updating a license
Transferring a license
Conclusion
Using the GPU package installation
Overview
Introduction
Using the GPU for ML Operations
Compatible GPUs
Using arivis Pro on laptops with a GPU
Overview
Introduction
Setting default GPU
On systems running Windows version earlier than windows 10
For system running Windows 10 and higher
GPU selection on launch
Using arivis software and virtual machines
Introduction
Licensing
Graphics cards
Data access
Conclusions
Running arivis Pro on Amazon AWS
Setup a suitable system
Setup 3D graphics
Setup arivisPro
Optional: using NICE DCV
Using arivis Pro over remote desktop
Introduction
GPUs and RDP
Licensing
Conclusions
Installing arivis Pro on Apple hardware
arivis Vision4D is not available as a native macOS application, it requires Microsoft Window 10 (64Bit) or better.
Why does arivis Pro not use all the computer resources?
Introduction
RAM availability
Visualising images
Visualising 3D datasets
Conclusions
Creating a system report
Licensing setup
arivis Network License setup
Introduction
Selecting a License server
Installing Floating Licenses on Windows Computers
Installing Floating License on Linux Computers
Network Configurations for Floating Licenses
Additional License Management Tools
Limiting access from remote clients
Aggressive search for licenses
Conclusion
HASP License Troubleshooting
Introduction
Installing HASP drivers
Port configuration
Troubleshooting issues
License Count Exceeded
No License Found
License is Out of Date
Hardware changes detected
Unable to contact a network license server
Licensing FAQ
Arivis License Tool - FAQ
Choosing the right license type
Introduction
Soft vs Hard Licenses
Local vs Floating Licenses
Typical Configurations
Single user, one workstation
Single user, multiple workstations
Multiple users, distributed workstation
Multiple users, shared workstation
Imaging basics
What is an image?
What is resolution
Introduction
The different types of resolution
Optical resolution
Sampling resolution
Noise
Bit depth
Conclusions
What is segmentation
What is segmentation?
Instance vs. Semantic Segmentation
How does arivis handle large datasets
How do computers process image data?
So what can we do to optimize the processing of such potentially large datasets?
Visualizing larger datasets
Analyzing and processing lager datasets
The arivis file format
So how does Vision4D work with my microscopy images?
How does arivis render datasets that are larger than the video memory in 3D?
Introduction
Rendering 3D stacks as volumes
How can we improve the rendering in the 4D viewer?
Upgrading the GPU
Clipping the dataset to a manageable volume
Changing application preferences
Conclusions
Why does processing a 3D animation movie export take so long?
Overview
Introduction
How is producing a high-resolution snapshot different?
So what about movies?
Conclusions
What is metadata, and why is it important?
What is metadata?
Using arivis Pro
Getting started with arivis Pro
Introduction
Importing Images
Checking and updating calibrations
Navigating through Image Sets
Calibrating datasets
Overview
Introduction
Spatial calibrations
Temporal calibrations
Using intensity range and visualization settings
Basic concepts
Dynamic Range
Grey Scale
Intensity Range
Full Dynamic Range
Partial Dynamic Range
Color scalebar
Color settings
Gamma correction
Measuring distances in images
Using local deep learning with arivis AI toolkit
Summary
Introduction
Creating a new DL model
Accessing the DL Trainer and creating classes
Annotating objects
Training the network
Using a DL training in a pipeline
Setting opacity in 3D renderings
Basic concepts
Setting the opacity
Coloring volumes by depth in 3D view
Introduction
Changing channel colors
Changing 4D mapping to axis
Exporting CSV files out of arivis Pro
Introduction
Changing exports to CSV
Using CSV export with batch analysis
CSV export in arivis VisionHub
Backround substraction vs. Shading correction
Shading correction
Background subtraction
Background subtraction operator anatomy
Backround source
Background comparison
Morphological Background subtraction operator anatomy
Morphological Background subtraction options
Objects segmentation after morphological Background subtraction
Drawing objects interactively
Overview
Drawing objects in 4D
Placing new objects in 3D
Adding a spherical object with a variable radius
Adding a spherical object with a predefined radius
Adding a marker (point)
Selecting an object with the Magic Wand tool in 3D
Drawing objects in 2D
Placing new objects in 2D
Adding a spherical object with a variable radius
Adding a marker (single point) on the active Z Plane
Selecting a region on the active Z Plane
Drawing a 3D Polyline
Using the Draw Objects tool
Using the Move Objects tool
Using the Magic Wand tool
Measuring a structure of interest
What is a TAG
Configuring the result storage operator
Introduction
Adding Result Storage to a pipeline
Default Result Storage targets
Changing the Result Storage options
Voxels Storage
Segments Storage
Advanced Result Storage options
Enabling extended channel selection
Using extended channel selection
Which option should I use, and when?
Conclusion
Performing SIS file optimization
Opening the working dataset
Checking the file status
Applying the defragment task
Creating Maximum Intensity Projections in arivis Pro
Overview
Introduction
Generating MIPs in arivis Pro
Additional remarks
Image analysis in arivis Pro
Overview
Workflow Description
Opening the Analysis panel
Adding pipeline operations
Input ROI
Blob Finder (Segmentation)
Tracking (Using segmented objects)
Export Object Features
Store Objects
Saving changes
Conclusions
Detecting spines with neurite/neuron tracer
Overview
Introduction
Adding Spine Detection to a Pipeline
AI Assisted Spine Detection
Assigning previously segmented objects as spines
Using a probability map
Reviewing spine detection results
Tutorials
Lunch-time Academy
Getting Started with ZEISS arivis Pro
Basic 3D Segmentation & Analysis Tasks
Advanced 3D Image Analysis Operations
AI Approaches for Advanced 3D Image Analysis
A Focus on Tracking
A Focus on Neuron Tracing
4D Viewer Basics
Analysis Operations
Pipeline Basics
Segmentation
Inter object relationships
Adjusting channel colors
Contextualising segmentation to Atlas regions
Background
Analysis Pipeline
Analysis Results
Creating movies
Overview
Introduction
Exporting time/plane progressions
Using the Storyboard panel to create animations in the 4D Viewer
Getting started with the Storyboard
Exporting Movies
Movie saving options
Video Resolution and Framerate
Data Resolution
Creating movies for video tutorials or to show arivis processes
Creating random sub-population of objects
Deep Learning and Machine Learning
Tracking & Tracing
Image transformations and stitching
Importing and moving objects in a 3D volume
Background
Importing objects
Moving objects
Video
Image Courtesy
Measuring the ratio of objects inside other objects?
Performing compartmentalization analysis
Overview
The compartments operator
Compartment hierarchy settings
Structures relationship settings
Compartment output settings
Performing segmentation
Overview
The analysis panel
What next?
Using compartments operation
What does the Compartments operation do?
Example uses of the Compartments operation
Configuring the Compartments operation in a pipeline
Compartment operation inputs
Configuring relationship parameters
Compartments operation results
Custom features related to children
Object table layout
Exporting compartmentalization results
Conclusions
Sample Pipeline How To`s
Aggregating well plate data
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Normalization
Normalization parameters
Blob Finder
Blob Finder parameters
Intensity Threshold Segmenter
Intensity Threshold Segmenter parameters
Object Feature Filter
Object Feature Filter parameters
Aggregate Features
Configure Data Aggregation dialog
Store Objects
Executing the pipeline
Single-field execution
Multi-run execution
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Compartmentalizing cells or particles
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Intensity Threshold Segmenter
Intensity Threshold Segmenter parameters
Blob Finder
Blob Finder parameters
Object Feature Filter
Object Feature Filter parameters
Object Feature Filter
Object Feature Filter parameters
Compartmentalization
Compartmentalization parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting big structures automatically
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Denoising
Denoising parameters
Intensity Threshold Segmenter
Intensity Threshold Segmenter parameters
Object Feature Filter
Object Feature Filter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting big structures manually
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Denoising
Denoising parameters
Intensity Threshold Segmenter
Intensity Threshold Segmenter parameters
Object Feature Filter
Object Feature Filter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells (Cellpose-based Segmenter)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Cellpose-based Segmenter
Cellpose-based Segmenter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Results in the Viewer
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells (Region Growing)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Denoising
Denoising parameters
Blob Finder
Blob Finder parameters
Blob Finder results
Region Growing
Region Growing parameters
Region Growing results
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells (Seeded Region Growing)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Denoising
Denoising parameters
Seeded Region Growing
Seeded Region Growing parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Results in the Viewer
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells based on membranes
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Membrane-based Segmenter
Membrane-based Segmenter parameters
Membrane-based Segmenter results
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells based on menbranes with enhancement
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Membrane Detection
Membrane Detection parameters
Membrane Detection results
Membrane-based Segmenter
Membrane-based Segmenter parameters
Membrane-based Segmenter results
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting cells or particles
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Blob Finder
Blob Finder parameters
Blob Finder results
Object Feature Filter
Object Feature Filter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting dendritic spines (AI-assisted)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Neurite Tracer
Neurite Tracer parameters
Spine Tracer
Spine Tracer parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting dendritic spines (Probability Map)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Deep Learning Reconstruction
Deep Learning Reconstruction parameters
Neurite Tracer
Neurite Tracer parameters
Spine Tracer
Spine Tracer parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting dendritic spines (Segments)
Introduction
Workflow
Demo dataset
Downloading demo dataset
Opening demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Neurite Tracer
Neurite Tracer parameters
Deep Learning Segmenter
Deep Learning Segmenter parameters
Spine Tracer
Spine Tracer parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Detecting neurites
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Neurite Tracer
Neurite Tracer parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Visualization examples
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Editing the traces
Detecting neurons
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Blob Finder
Blob Finder parameters
Neuron Tracer
Neuron Trace parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Visualization Examples
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Editing the traces
Detecting nuclei and cells (Machine Learning)
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Machine Learning Segmenter
Machine Learning Segmenter parameters
Object Feature Filter
Object Feature Filter parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the Results
Results in the Viewer
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Machine Learning Trainer
Opening the ML Trainer panel
Setting up the ML Trainer
Detecting small structures (Watershed)
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Normalization
Normalization parameters
Watershed
Watershed parameters
Watershed results
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Tracking cells or particles
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Watershed
Watershed parameters
Tracking
Tracking parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Tracking cells or particles with lineage
Introduction
Workflow
Demo dataset
Downloading the demo dataset
Opening the demo dataset
Activating the Sample Pipeline
Pipeline operations layout
Input ROI
Input ROI parameters
Blob Finder
Blob Finder parameters
Blob Finder results
Tracking
Tracking parameters
Store Objects
Executing the pipeline
Executing step by step
Executing in a single run
Operation status
Viewing the results
Modifying the current pipeline
Previewing the results
Adjusting the operations
Adding or removing operations
Using manually drawn regions in pipelines
Overview
Introduction
Document vs Analysis object
Potential use cases for manually drawn objects
Using an existing objects in the pipeline
Masking
Importing the document objects
Image pre-processing, stitching and volume fusion
Introduction to volume fusion
Overview
Introduction
Prerequisites
Volumes to be fused need to start as different image sets in the same SIS file
The volumes must be of the same bit depth
Calibrations need to be correct for the sample
Fusing Volumes
Landmark registration - Creating landmarks
Landmark Registration - Fusing the volumes
Surface registration - extracting and transferring the surface
Surface registration - Transforming the surface in Vision4D
Surface registration - Transforming the surface in VisionVR
Surface registration - Applying the surface transformation for fusion
Additional considerations
Multimodal imaging
Merging more than two sets
Time lapse analysis
Tracking in arivis Pro
Introduction
Image quality
Sampling resolution
Segmentation
Intensity tracks
Segmenting objects for tracking
Tracking segmented objects
Motion type
Fusions and Divisions
Weighing
Reviewing Tracking results
Editing tracks
Summary
Performing manual tracking on existing segments»
Opening the working dataset
Detecting the objects
Selecting objects manually
Tracking pipeline execution
Viewing the results
Editing tracks
Quantifying contacts over time
Segmenting Objects
Tagging contact events
Tracking objects
Interpreting the data
Object Colouring
Custom Features
Scripting and interaction with other programs
Color Deconvolution
Introduction
Importing and editing the script
RGB Color Mapping
Dye Selection
Inverting the Output
Applying the script to an image
Interpreting the results
Conclusions
Download the script
Creating concentric sub volume - matryoshka dolls
Opening the working dataset
Selecting the Python Operator and loading the Python code
Set the Operator parameters
Running the pipeline
Creating freely XY oriented sub volumes
Opening the working dataset
Drawing the reference ROI
Loading the Python script
Setting the script features
Running the Python script
Creating Heat-Map – density distribution
Opening the working dataset
Loading the Python script
Set the Script features
Running the Python script
Analysis options overview
The Compartments operator
Simple Compartments (2 levels)
Multiple Compartments (multiple levels)
Single Compartments (multiple subjects)
Compartments example
Heat-Map Compartments application
Building the analysis pipeline
Running the analysis Pipeline
Viewing the results
Creating spiral oriented sub volume»
Opening the working dataset
Drawing the reference 3D polyline
Loading the Python script
Setting the script features
Running the Python script
Building the analysis pipeline
Running the analysis Pipeline
Viewing the results
Creating XYZ matrix of sub-volumes
Opening the working dataset
Loading the Python script
Setting the script features
Running the Python script
Image Registration for Multiplexing Experiments in arivis Pro
Overview
Introduction
Image registration in a nutshell
Application Workflow
Preliminary Remarks
Installing the prerequisites
Installing Anaconda
Setting up the image registration environment
Running image registration for multiplexing data in arivis Pro
Install Anaconda Python for Vision4D
Introduction
Installing Anaconda
Configuring Vision4D
Objects contacts analysis
Introduction
Contacts analysis theory
Set the stand alone Script options
Set and run the Script operator
Performing contrast limited adaptive histogram equalization (CLAHE)»
Opening the working dataset
Loading the Python script
Setting the script features
Installing the Anaconda3 package and the OpenCV module
Performing objects density (heat-map) and object distribution gradient plotting (profile)
Opening the working dataset
Drawing the reference ROI
Loading the Python script
Setting the script features
Running the Python script
Building the analysis Pipeline
Running the analysis Pipeline
Viewing the results
Segmenting objects into equal parts in arivis Pro
Import the image set(s) in arivis Pro
Download the Anaconda package
Install the Anaconda package
Install the Anaconda environment
Test python Registration environment in arivis Pro
Run the python script in arivis Pro
Visualization of the results
Using cellpose models in arivis Pro
About the Cellpose to ONNX Converter tool
Setting up and using the converter tool
Using the models in arivis Pro
Option 1: Adding models to the Cellpose model directory
Option 2: Loading a model directly in the operation
arivis AI: Machine Learning and Deep Learning
Using StarDist
Introduction
Preliminary Remarks
How does it work?
Objects annotation
Creating and training a neural network
Image analysis
Why use StarDist within Vision4D?
Application examples
Nuclei Tracking
Distribution Analysis
Measuring Cell Volumes
How to get StarDist working with Vision4D
Setting up Vision4D preferences
Loading the script
Applying cellpose models (arivis Vision4D 3.4.0 to 4.1.0)
Overview
Introduction
Preliminary Remarks
Installing the prerequisites
Installing Anaconda
Setting up the cellpose environment
Using cellpose in Vision4D
Setting up cellpose parameters
Using cellpose in pipelines
Docker support for instance segmentation
What is Docker?
Using Docker in arivis Pro
What is difference between Docker Desktop and Docker Engine?
Docker virtualization requirements
Docker GPU Support
Installing Docker for AI Instance Segmentation
Overview
Introduction
Docker Licenses
Installing Docker Desktop
Configuring Docker Desktop
Troubleshooting
Windows 10
Windows 11
Installing Docker Engine on AWS
Overview
Introduction
Selecting size and image
Installing Docker Engine
Enabling Docker Remote access
Configuring arivis Pro to use Remote Docker Engine
Installing Docker Engine on Azure
Overview
Introduction
Selecting size and image
Configuring Disk
Installing the nVidia GPU Extension
Installing Docker Engine
Enabling Docker Remote access
Installing nVidia Container Toolkit
Configuring arivis Pro to use Remote Docker Engine
Deep Learning segmentation pipelines
Overview
Introduction
Linking arivis Pro to your arivis Cloud account
Creating access tokens
Configuring arivis Pro using access tokens
Creating Pipelines with DL Segmentation
Exporting Pipelines with DL Instance Segmentation
Exporting the pipeline
Sharing an arivis Cloud model
Importing the pipeline and model
Importing the analysis pipeline
SIS Converter
Using SIS Converter
Opening the arivis SIS Converter
Setting the preferences
Importing channel colors
Disable blending
Using GZIP compression
Creating Restore Point
More options
Importing files
Importing complex or multiple input files
Modifying the list of files
Complex Import
Manual import mapper
Apply dimension order
Arranging the order of the template elements
Pattern matching
Detecting channel names
Saving import scenario definitions
Supported image formats
Amira-Mesh Media Handler
Aperio Media Handler
Metamorph Media Handler
The DeltaVision media handler
Dicom Media Handler
Hamamatsu Media Handler
FreeImage Media Handler
ICS Media Handler
Imaris Media Handler
JPEG Media Handler
Leica Media Handler
LSM Media Handler
Mirax Media Handler
NIfTI Media Handler
Nikon Media Handler
Olympus Media Handler
RAWInfo Media Handler
Slide Book Media Handler
Tiff Media Handler
VOL Media Handler
Zeiss ZVI Media Handler
Release Notes
SIS Converter 4.5
SIS Converter 4.3
SIS Converter 4.1
SIS Converter 4.0
SIS Converter 3.5.1
Archive
SIS Converter 3.4
SIS Converter 3.3
SIS Converter 3.2
SIS Converter 3.1.4
Supported File Formats
Supported Image File Formats
Homepage
arivis Pro
...
Time lapse analysis
Tracking in arivis Pro
Tracking in arivis Pro
Introduction
Image quality
Sampling resolution
Segmentation
Tracking segmented objects
Reviewing Tracking results
Editing tracks
Summary
Background and integration of tracking systems in arivis Vision4D.
See also
Measuring the ratio of objects inside other objects?
Quantifying contacts over time