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Automatic and manual image registration workflows course

Part of the I2K 2020 conference. Apply here.

Sessions:

  • 2020-11-30 21:00 – 2020-12-01 01:00 UTC
  • 2020-12-01 13:00 – 2020-12-01 17:00 UTC

Summary

Students will learn:

  • The principals of image transformation and registration (detailed outline)
    • Types of transformations (similarity, affine, non-linear)
    • Displacement fields for non-linear transformations
    • Basics of imglib2 spatial transformations
  • How to use elastix for automatic image registration (detailed outline)
    • Parameter choices
    • Jacobian of a transformation to measure deformation
  • How to use BigWarp to perform manual registration or to fine-tune an automatic registration (detailed outline).
    • concatenating transformations
    • converting transformations to convenient formats for use in different tools.

Prerequisites

Students should be familiar with ImageJ/Fiji, and understand basic image analysis concepts such as resampling and interpolation.

  1. Download and install Fiji
  2. Download and install elastix
    1. Windows instructions
    2. Mac/Linux instructions
  3. Download the code in this repository with this link (or git clone).

Download sample data