Introduction to Image Analysis with ImageJ/Fiji & Ilastik

→ Europe/Berlin
Zoom

Zoom
Description

Registration deadline: 16 April 2021

Course aim:

Introduces novice users to basic concepts and techniques in quantitative image analysis.  Major topics covered include the basics of filtering and segmenting images along with techniques to extract useful measures from bio image data. Participants will learn how to use Fiji and Ilastik software and perform realistic bio-image analysis through numerous exercises and interactive hands-on sessions.

The course will take place online via zoom.

Some of the independent exercises will be given as homework so make sure you have some preparation time available outside of the course hours.

Content:

The following concepts will be introduced with many ImageJ/Fiji & Ilastik hands-on-sessions and exercises along the way:

  • Basic concepts: image characteristics, visualization, regions of interest and measurements
  • Segmentation 1: preprocessing, thresholding, mask/region analysis and spot detection
  • Image filters and morphological operations
  • Segmentation 2: Machine learning for image segmentation
  • ImageJ Macro language
  • Visualization, exploration and segmentation in 3D images
  • Stitching of tiled images and image registration
  • Time sequence analysis and object tracking in time sequences
  • Good practices for performing repeatable analysis as well as tips and tricks for bioimage analysis

The number of participants is limited to 20.  The course is open for DIPP PhD students and CBG Postdocs.

We will inform you after 19 April 2021 whether a slot in the course could be assigned to you!

Questions?