Data Visualization and Analysis using Avizo

Overview

The KAUST Visualization Core Lab (KVL), in collaboration with ThermoFisher Scientific, is offering three half-day workshops on how to use Avizo (also known as Amira) for data visualization, quantitative analysis, image processing, segmentation, and 3D reconstruction. Avizo/Amira is a powerful multi-platform data analysis and scientific visualization tool. Attendees will participate in tutorials, hands-on sessions, and discussions with Avizo/Amira engineers on how to leverage Avizo in their scientific domains. This training is provided FREE of charge to KAUST participants with the estimated training cost/value to be around 1,500 SAR per user.

Below are example KAUST projects that benefitted from using Avizo:

• In Situ Ptychographic X-ray CT of Fully Hydrated Polyamide Membranes
• Multimodal Analysis of Rocks and Sediments in Shallow Marine Environments
• Segmentation and 3D Reconstruction of Glycogen Granules and Mitochondria in Microwave-fixed Brain EM
• Micro-CT and Holographic Visualization of Late Cretaceous Benthic Foraminifera in Saudi Arabia
• 3D Modeling of Composite Membranes from TEM
• Ordered Macroporous ZIF-67 as a Filler in Mixed Matrix Membranes for Enhanced Propylene/Propane Separation
• A Novel Multi-scale uCT Characterization Method to Quantify Biogenic Carbonate Production

KAUST users can access Avizo/Amira software for free (sponsored by the KAUST Visualization Core Lab) at the AR/VR Hub and throughout the campus through IT provided workstations and laptops.

Who Should Attend?

If your research involves visualization and analysis of 2D and 3D datasets such as microscopy image stacks (e.g., CT, SEM, TEM, or Confocal, etc.), this workshop will help you process, visualize, analyze, and ultimately acquire new insight into your data. This event is open to all KAUST community and staff.

Agenda

This is a three-day event with topics ranging from beginner, intermediate, and advanced topics. The training will be facilitated by Dr. Sarawuth Wantha - a product application specialist from ThermoFisher.

Beginner to Intermediate Topics in Avizo: October 12 (Monday)

• Introduction to image/volume data and processing
• Software overview, general concepts and user interface
• Data visualization in 2D & 3D and annotations
• Basic Data Manipulation: cropping, re-sampling, pixel type and conversion
• Image processing: denoising, filters, background correction
• Automatic Segmentation: binarization and thresholding
• Separation, classification, analysis & measurement
• Screen capture and animation
• KVL services and collaboration opportunities
• KVL segmentation and analysis workstations in AR/VR Hub

AI-Assisted Segmentation in Avizo: October 13 (Tuesday)

• If you are new to Avizo, you should attend the first session on October 12.
• Introduction to image segmentation
• CellPose Xtra (pre-trained model)
• New Segmentation+ workroom (requires Avizo 2022.2 and later)
• AI-assisted segmentation tools
• Deep Learning Denoising Module
• Deep Learning Module (advanced)
• KVL services and collaboration opportunities
• KVL segmentation and analysis workstations in AR/VR Hub

Geoscience/Materials/Bio/Neuroscience Workflows in Avizo: October 14 (Wednesday)

• If you are new to Avizo, you should attend the first session on October 12.
• AI-assisted segmentation tools
• Quantitative Analysis
• Processing and visualization of optical microscopy (multichannel) data, e.g., skin cells
• Processing and visualization of electron microscopy (EM) data, e.g., mitochondria
• Processing and visualization of computed tomography (CT) data, e.g., core plug
  • Core Profile (features from PerGeos)
  • Porosity Analysis
  • Pore Network Modeling
• KVL services and collaboration opportunities
• KVL segmentation and analysis workstations in AR/VR Hub

One-on-one Sessions

If you would like to have a one-on-one session with the presenter to discuss your own dataset/question/project, sign up here. Time slots are spread across the week between October 11-19.