Quantitative Big Imaging

Kevin Mader
5 March 2015

Basic Segmentation and Discrete Binary Structures

Course Outline

  • 19th February - Introduction and Workflows
  • 26th February - Image Enhancement (A. Kaestner)
  • 5th March - Basic Segmentation, Discrete Binary Structures
  • 12th March - Advanced Segmentation
  • 19th March - Applying Graphical Models and Machine Learning (A. Lucchi)
  • 26th March - Analyzing Single Objects
  • 2nd April - Analyzing Complex Objects
  • 16th April - Spatial Distribution
  • 23rd April - Statistics and Reproducibility
  • 30th April - Dynamic Experiments (K. Mader and A. Patera)
  • 7th May - Scaling Up / Big Data
  • 21th May - Guest Lecture, Applications in Material Science
  • 28th May - 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