Scientific Visualization 210: Avizo and Ilastik for Image Segmentation and 3D Analysis

Overview

This workshop will give participants an introduction and hands-on experience with AI-assisted image segmentation and 3D analysis using Ilastik and Avizo. Ilastik is a powerful open-source software that can be used for segmenting image stacks, while Avizo is a commercial software for general-purpose scientific data visualization and analysis. In this workshop, the instructor will demonstrate how to perform the whole image segmentation and 3D analysis pipeline using Avizo. This will include pre-processing/filtering of the input image stack, semi-automatic segmentation using AI tools, and finally 3D analysis. This will be followed by an introduction on how to use Ilastik's AI tools for segmenting image stacks and exporting the results back to Avizo to continue with post-processing and analysis.

Participants are expected to know the basics of using Avizo, i.e., opening data and creating modules for visualization (e.g., Ortho Slice). Attending the introductory workshop on Avizo is highly recommended.

Who Should Attend?

The target audience for this workshop are KAUST users who want to leverage new AI segmentation tools to perform image segmentation and analysis on their image data, e.g., CT, microscopy.

Agenda