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

• Drosophila template samples
• CT-MR registration samples
• CLEM samples