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training:scivis:2026:avizo [2026/02/03 13:15] – Ronell Sicattraining:scivis:2026:avizo [2026/02/04 06:55] (current) – Ronell Sicat
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   * April 20-22, 2026 \\ Monday-Wednesday   * April 20-22, 2026 \\ Monday-Wednesday
   * 1:30pm - 5:00pm    * 1:30pm - 5:00pm 
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 <WRAP quarter column> <WRAP center round box 110%> {{:icon:twbs:link:w-25:h-auto:map.svg?nolink&}} <tab1> <fs:26px>** Venue**</fs> <WRAP quarter column> <WRAP center round box 110%> {{:icon:twbs:link:w-25:h-auto:map.svg?nolink&}} <tab1> <fs:26px>** Venue**</fs>
  
-  * Building 1 (Desert Side) \\ Level 2, Room 2418 \\ Multipurpose Room (MPR) +  * Building 1 (Desert Side) \\ Level 2, Room 2418 \\ Multipurpose Room (MPR)  
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 {{:icon:twbs:link:w-25:h-auto:person.svg?nolink&}} Ronell Sicat\\ {{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} Visualization Core Lab \\ {{:icon:twbs:link:w-25:h-auto:envelope-at.svg?nolink&}} help@vis.kaust.edu.sa </WRAP> </WRAP> {{:icon:twbs:link:w-25:h-auto:person.svg?nolink&}} Ronell Sicat\\ {{:icon:twbs:link:w-25:h-auto:headset-vr.svg?nolink&}} Visualization Core Lab \\ {{:icon:twbs:link:w-25:h-auto:envelope-at.svg?nolink&}} help@vis.kaust.edu.sa </WRAP> </WRAP>
  
-<WRAP quarter column> <WRAP center round box 100%>{{:icon:twbs:link:w-25:h-auto:person-add.svg?nolink&}} <tab1> <fs:26px>** Register**</fs>+<WRAP quarter column> <WRAP center round box 110%>{{:icon:twbs:link:w-25:h-auto:person-add.svg?nolink&}} <tab1> <fs:26px>** Register**</fs> 
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 +You only need to register once and select which session/s you want to attend. \\
  
 <wrap em button> [[https://kaustforms.formstack.com/forms/avizo2026|Register Here]] </wrap> \\ <wrap em button> [[https://kaustforms.formstack.com/forms/avizo2026|Register Here]] </wrap> \\
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 ===== Overview ===== ===== Overview =====
  
-The KAUST Visualization Core Lab (KVL), in collaboration with ThermoFisher Scientific, is offering three half-day workshops on [[https://www.thermofisher.com/sa/en/home/electron-microscopy/products/software-em-3d-vis/avizo-software.html|Avizo]] (also known as Amira) - a multi-platform data analysis and scientific visualization tool. Attendees will participate in tutorials, hands-on sessions, and discussions with the engineers on how to leverage Avizo in their scientific domains. Topics will include data visualization, quantitative analysis, image processing, segmentation, and 3D reconstruction. +The KAUST Visualization Core Lab (KVL), in collaboration with ThermoFisher Scientific, is offering three half-day workshops on how to use [[https://www.thermofisher.com/sa/en/home/electron-microscopy/products/software-em-3d-vis/avizo-software.html|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.  
 + 
 +Below are example KAUST projects that benefitted from using Avizo: 
 +   * [[https://wiki.vis.kaust.edu.sa/highlights/2025/membranespxct| In Situ Ptychographic X-ray CT of Fully Hydrated Polyamide Membranes]] 
 +   * [[https://wiki.vis.kaust.edu.sa/highlights/2025/carbonates| Multimodal Analysis of Rocks and Sediments in Shallow Marine Environments]] 
 +   * [[https://wiki.vis.kaust.edu.sa/highlights/2025/brainemposter|Segmentation and 3D Reconstruction of Glycogen Granules and Mitochondria in Microwave-fixed Brain EM]] 
 +   * [[https://wiki.vis.kaust.edu.sa/highlights/2025/arforams|Micro-CT and Holographic Visualization of Late Cretaceous Benthic Foraminifera in Saudi Arabia]] 
 +   * [[https://wiki.vis.kaust.edu.sa/highlights/2025/membrane3d|3D Modeling of Composite Membranes from TEM]] 
 +   * [[https://wiki.vis.kaust.edu.sa/highlights/2024/kvlmembranes|Ordered Macroporous ZIF-67 as a Filler in Mixed Matrix Membranes for Enhanced Propylene/Propane Separation]] 
 +   * [[https://wiki.vis.kaust.edu.sa/highlights/2024/kvlcarbonates|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.  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. 
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   * Introduction to image/volume data and processing   * Introduction to image/volume data and processing
   * Software overview, general concepts and user interface   * Software overview, general concepts and user interface
-  * Data visualization in 2D&3D and annotations+  * Data visualization in 2D & 3D and annotations
   * Basic Data Manipulation: cropping, re-sampling, pixel type and conversion   * Basic Data Manipulation: cropping, re-sampling, pixel type and conversion
   * Image processing: denoising, filters, background correction   * Image processing: denoising, filters, background correction
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   * Separation, classification, analysis & measurement   * Separation, classification, analysis & measurement
   * Screen capture and animation   * Screen capture and animation
 +  * KVL services and collaboration opportunities
 +  * KVL segmentation and analysis workstations in AR/VR Hub
  
 ==== Geoscience Workflows in Avizo: April 21 (Tuesday) ==== ==== Geoscience Workflows in Avizo: April 21 (Tuesday) ====
-  * TBA+  * **<fc #ff0000>If you are new to Avizo, you should attend the first session on April 20.</fc>** 
 +  * Core Profile (features from PerGeos) 
 +  * Introduction to image segmentation 
 +  * New Segmentation+ workroom (requires Avizo 2022.2 and later) 
 +  * AI-assisted segmentation tools 
 +  * Deep Learning Denoising Module 
 +  * Porosity Analysis 
 +  * Pore Network Modeling 
 +  * KVL services and collaboration opportunities 
 +  * KVL segmentation and analysis workstations in AR/VR Hub
  
-==== Bio/Neuroscience Workflows in Avizo: April 22 (Wednesday) ==== +==== Materials/Bio/Neuroscience Workflows in Avizo: April 22 (Wednesday) ==== 
-  * TBA+  * **<fc #ff0000>If you are new to Avizo, you should attend the first session on April 20.</fc>** 
 +  * Introduction to image segmentation 
 +  * New Segmentation+ workroom (requires Avizo 2022.2 and later) 
 +  * AI-assisted segmentation tools 
 +  * Quantitative Analysis 
 +  * Deep Learning Denoising Module 
 +  * Processing and visualization of optical microscopy (multichannel) data 
 +  * KVL services and collaboration opportunities 
 +  * KVL segmentation and analysis workstations in AR/VR Hub
  
 ===== One-on-one Sessions ===== ===== One-on-one Sessions =====