ZEISS Microscopy Knowledge Base
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Major brand refresh for arivis image analysis software solutions
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
arivis Vision4D 4.1
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System requirements
Installation and configuration
Activating, updating and transferring licenses
Using the GPU package installation
Using arivis Pro on laptops with a GPU
Using arivis software and virtual machines
Running arivis Pro on Amazon AWS
Using arivis Pro over remote desktop
Installing arivis Pro on Apple hardware
Why does arivis Pro not use all the computer resources?
Creating a system report
arivis Network License setup
HASP License Troubleshooting
Licensing FAQ
Choosing the right license type
What is an image?
What is resolution
What is segmentation
How does arivis handle large datasets
How does arivis render datasets that are larger than the video memory in 3D?
Why does processing a 3D animation movie export take so long?
What is metadata, and why is it important?
Getting started with arivis Pro
Calibrating datasets
Using intensity range and visualization settings
Measuring distances in images
Using local deep learning with arivis AI toolkit
Setting opacity in 3D renderings
Coloring volumes by depth in 3D view
Exporting CSV files out of arivis Pro
Backround substraction vs. Shading correction
Drawing objects interactively
Configuring the result storage operator
Performing SIS file optimization
Creating Maximum Intensity Projections in arivis Pro
Image analysis in arivis Pro
Detecting spines with neurite/neuron tracer
Lunch-time Academy
4D Viewer Basics
Analysis Operations
Adjusting channel colors
Contextualising segmentation to Atlas regions
Creating movies
Creating random sub-population of objects
Deep Learning and Machine Learning
Image transformations and stitching
Importing and moving objects in a 3D volume
Measuring the ratio of objects inside other objects?
Performing compartmentalization analysis
Performing segmentation
Using compartments operation
Compartmentalizing cells or particles
Detecting big structures automatically
Detecting big structures manually
Detecting cells based on menbranes with enhancement
Detecting cells based on membranes
Detecting cells or particles
Detecting cells (Cellpose-based Segmenter)
Detecting cells (Region Growing)
Detecting cells (Seeded Region Growing)
Detecting neurites
Detecting neurons
Detecting nuclei and cells (Machine Learning)
Detecting small structures (Watershed)
Detecting dendritic spines (AI-assisted)
Detecting dendritic spines (Probability Map)
Detecting dendritic spines (Segments)
Tracking cells or particles
Tracking cells or particles with lineage
Using manually drawn regions in pipelines
Introduction to volume fusion
Tracking in Vision4D
Performing manual tracking on existing segments»
Quantifying contacts over time
Segmenting objects into equal parts in arivis Pro
Image Registration for Multiplexing Experiments in arivis Pro
Converting Cellpose models for use in arivis
Install Anaconda Python for Vision4D
Performing contrast limited adaptive histogram equalization (CLAHE)»
Objects contacts analysis
Color Deconvolution
Creating XYZ matrix of sub-volumes
Creating Heat-Map – density distribution
Creating freely XY oriented sub volumes
Performing objects density (heat-map) and object distribution gradient plotting (profile)
Creating concentric sub volume - matryoshka dolls
Creating spiral oriented sub volume»
Using StarDist
Applying cellpose models (arivis Vision4D 3.4.0 to 4.1.0)
Docker support for instance segmentation
Installing Docker for AI Instance Segmentation
Installing Docker Engine on AWS
Installing Docker Engine on Azure
Deep Learning segmentation pipelines
Using SIS Converter
Release Notes
Supported File Formats
  1. Homepage
  2. arivis Pro
  3. ...
  4. Tutorials
  5. Lunch-time Academy

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

ON THIS PAGE

  • 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
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