Introduction to Image Segmentation and 3D Reconstruction (Spring 2021)
Channel: KAUST Visualization Core Lab
Date: 2021-04-15

Introduces the general-purpose Avizo and ilastik image processing tools to efficiently process raw microscopy image stacks into segmented data that can be further analyzed and visualized.

The video includes a conceptual introduction to image segmentation, step-by-step tutorials, a demo of advanced pixel-classification workflows on the Ibex cluster, and more.

Chapters:
0:00:00​ Introduction
0:04:11​ Segmentation Overview
0:59:05​ 3D Reconstruction Tutorial
1:02:02 Pre-processing (Avizo)​ 
1:40:25 Segmentation (ilastik)​ 
1:54:44 Post-processing (Avizo)​ 
2:05:21 pixclass Workflows Demo (ilastik)
2:51:02​ Concluding