Where Ideas Grow

Introduction to digital bioimage analysis | 3rd Edition
11th-15th October 2021 | Online edition


Due to the current SARS-CoV-2/COVID-19 pandemic instability, this course edition will be fully online. 


About the course:
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.


Course approximate duration: 20 hours (Time: 2pm – 6pm (Lisbon time))
Target audience: All the scientific community with interest in the analysis of light microscopy images.
Requirements: Laptop with Image/Fiji installed. No previous experience in the analysis of light microscopy images is required. 

Course organizers: Mafalda Sousa, Advanced Light Microscopy, i3S, and Paula Sampaio, Advanced Light Microscopy, i3S



-    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.
-    Advanced ImageJ plugins (stitching, registration, colocalization)


Mafalda Sousa, Advanced Light Microscopy, i3S
Paula Sampaio, Advanced Light Microscopy, i3S 
Others (to be confirmed)


Registration fee includes access to the course, course material and certificate.

Certificate: requires 80% of course attendance (4 hours out of 20)

Early bird registration | Until 3rd September 2021 (Payment deadline: 10th September 2021) 

i3S members - 90 €
External participants - 100 €

Late registration | Until 23rd September 2021 (Payment deadline: 30th September 2021)
i3S members - 115 €
External participants - 125 €

Your pre-registration will be confirmed and the fee payment will be requested once the minimum of participants is guaranteed. 
Limited number of participants




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