Where Ideas grow

Introduction to digital bioimage analysis, 2nd Edition

23-25 September 2020 | i3S

With the advent of the digital era, nowadays images are multidimensional numerical data that can be processed and analyzed quantitatively to extract more information. With this course, we intend to give a general introduction to ImageJ/Fiji (imagej.net/), show how to use it to extract quantitative data and how to write simple macros. Also, the design of typical workflows to automate image analysis will be addressed not only in Fiji but also with Cellprofiler (cellprofiler.org). This course will be focused on the analysis of light microscopy images but is targeted to all people engaged in research.
Participants are invited to submit in advance an analysis problem/data of their interest that might be addressed in the course as an individual mini-project (with the help of the tutors).

Course Coordination:
Mafalda Sousa, i3S/ IBMC | Paula Sampaio, i3S/ IBMC


Requirements: The participant should bring a laptop for the sessions.


  • Principles, techniques and ethics of digital bioimage processing.
  • Basic commands of ImageJ/Fiji software.
  • Working with multidimensional (2D, 3D, time-lapse, position) bioimages.
  • Enhancement and processing of images.
  • Extract quantitative numerical data.
  • Design of simple workflows for automation of image analysis with ImageJ macros.
  • Introduction to Cellprofiler.



Registration fee includes coffee breaks, lunches, and course material.

Early bird registration | Until 15th June 2020 | Payment deadline: 22nd June 2020
i3S members - 100 €
External participants - 150 €

Late registration | Until 1st September 2020 | Payment deadline: 7th September 2020
i3S members - 130 €
External participants - 195 €

Limited number of participants: 15



More Information:
Advanced Training Unit | E-mail: training@i3s.up.pt | Tel: +351 226 074 900