22-29 April 2020
Europe/Berlin timezone

Registration deadline: 16 April 2020

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 the Fiji software package and perform realistic bio-image analysis through numerous exercises and interactive hands-on sessions


The following concepts will be introduced with many ImageJ/Fiji 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
  • Segmentation 2: image filters such as erosion/dilation, distance maps and the watershed algorithm
  • 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 17 April 2020 whether a slot in the programming course could be assigned to you!


LECTURERS: Noreen Walker & Gayathri Nadar, MPI-CBG Scientific Computing Facility

COURSE STRUCTURE: Each part of the course contains some theoretical presentations, short exercises to apply new knowledge and a long exercise to start combining the tools and tackle more real life analysis.

Day 1 (Wed 22nd), 9.30-12.30

Image basics, visualization, region of interests, measurements

Day 2 (Thu 23rd), 9.30-12.30

Segmentation: simple pipeline and more advanced filtering methods

Day 3 (Fri 24th), 9.30-12.30

Introduction to ImageJ Macro

Day 4 (Mon 27th), 9.30-12.30

Visualization and analysis of 3D data

Day 5 (Tue 28th), 9.30-12.30

Time sequence analysis and tracking

Day 6 (Wed 29th), 9.30-12.30

Stitching and image registration, Feedback round

Background Reading:

ImageJ: https://imagej.net/Welcome

Bioimage data analysis book: https://www.imaging-git.com/applications/bioimage-data-analysis-0/

Fiji training notes: https://cloudstor.aarnet.edu.au/plus/index.php/s/bxRU7kkoj2rIjCh#pdfviewer


Get your laptop ready for the course. You will need it to perform all the hands-on sessions and exercises.

Before the course:

  • Install a fresh version of Fiji on your laptop
  • You will receive materials from Noreen and Gayathri
  • Contact us if you have any issue with one of the above!

On the day of the course bring your laptop including mouse, and your power cable.

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