2nd Edition

Introduction to digital image analysis with ImageJ / Fiji

i3S, Porto | 26-28 September, 2018


With the advent of the digital era, nowadays images are multidimensional numerical data that can be processed and analyzed quantitatively to extract more information. ImageJ/Fiji open source software(imagej.net/) is a powerful tool available to process and analyze digital images. Moreover, it also allows the automation of image analysis with custom macros and plugins. With this course, we intend to give a general introduction to ImageJ/Fiji, show how to use it to extract quantitative data and how to write simple macros. This course is focused on the analysis of microscopy images but is targeted to all people engaged in research, that wants to start using ImageJ/Fiji for image analysis in general.


Course Coordination: Paula Sampaio | sampaio@ibmc.up.pt



Mafalda Sousa

Paula Sampaio


Requirements: The participant should bring a personal 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. Creation of figures for publication. 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).


Registration Fee:

i3S members and PPBI staff - €100

Other - €150


Limited number of participants: 20

Registration Deadline: 7th September 2018 // Payment deadline: September 14th


Registrations are now closed. If you wish to be placed in the waiting list, please send an e-mail to events@i3s.up.pt 




Events Management Unit | Rua Alfredo Allen 208 | 4200-135 Porto, Portugal

Email: events@i3s.up.pt | Tel: +351 220 408 811