ZEISS Microscopy Knowledge Base
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Setting up arivis Pro
- 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
Using arivis Pro
- 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
Tutorials
- 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
Sample Pipeline How To`s
- 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
Scripting and interaction with other programs
- 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»