Episode 3: Advanced 3D Image Analysis Operations

The third video in a series of six tutorials to teach microscopists how to use a Cellpose-based model in combination with advanced 3D image analysis tools, using ZEISS arivis Pro: Defining relationships and diverse quantifying calculations.
In this training video tutorial, Dr. Delisa Garcia demonstrates the use of a deep learning Cellpose model for cell segmentation, followed by advanced 3D image analysis operations such as object filtering, compartments (or per cell analysis), distance calculations, and applying a Python script for the so called “Matryoshka” analysis.

Key Learnings:

• Using a Cellpose (open source) model within ZEISS arivis Pro
• Filtering objects
• Defining relationships using the Compartments operation
• Calculating distances
• Applying a pre-defined python script for image analysis
  

Dr. Delisa Garcia explains the main functions of the ZEISS arivis Pro software, so you can start your own automated, end-to-end image analysis pipelines with ease. In just six sessions, you will learn enough about Advanced and 3D image analysis - basic principles, tools and best practices - to take your image analysis skills to the next level.

Topics such as data import and result export, 3D rendering, and segmentation types will get you on the right track. Explore various processing tools, measurements, relationship quantification, neuron tracing and object tracking. By learning how to implement AI models and other advanced operations into your pipeline, you will become an expert in image analysis with ZEISS arivis Pro in no time.