Quantitative Big Imaging

Kevin Mader
10 March 2016

Basic Segmentation and Discrete Binary Structures

Course Outline

  • 25th February - Introduction and Workflows
  • 3rd March - Image Enhancement (A. Kaestner)
  • 10th March - Basic Segmentation, Discrete Binary Structures
  • 17th March - Advanced Segmentation
  • 24th March - Analyzing Single Objects
  • 7th April - Analyzing Complex Objects
  • 14th April - Spatial Distribution
  • 21st April - Statistics and Reproducibility
  • 28th April - Dynamic Experiments
  • 12th May - Scaling Up / Big Data
  • 19th May - Guest Lecture - High Content Screening
  • 26th May - Guest Lecture - Machine Learning / Deep Learning and More Advanced Approaches
  • 2nd June - Project Presentations

Lesson Outline

  • Motivation
  • Qualitative Approaches
  • Thresholding
    • Other types of images
    • Selecting a good threshold
  • Implementation
  • Morphology
  • Contouring / Mask Creation

Applications

  • Simple two-phase materials (bone, cells, etc)
    • Beyond 1 channel of depth
  • Multiple phase materials
  • Filling holes in materials
  • Segmenting Fossils
  • Attempting to segment the cortex in brain imaging