Where Ideas Grow

BioImage Analysis for High Content Screening

25-28 May 2021 | ONLINE COURSE


Due to the SARS-CoV-2/COVID-19 pandemic situation, the course will be held online.  

High Content Screening generates a massive amount of image-based data in the biosciences field. Images contain diverse and valuable quantifiable data, however, many researchers lack the knowledge to extract those data in a practical, fast and repetitive way. Fundamentally practical, in this modular course, participants will get acquainted with several open-source image analysis software (ImageJ/Fiji, ilastik, CellProfiler, CellProfiler Analyst, Cytoscape and IDEAS®) designed to deal with large amounts of images. Experimental data will be used as datasets for image segmentation and quantification.
This course is organized into modules. Therefore, participants are free to choose the image analysis tools more convenient to their own work.


Target Audience: PhD students and junior and senior researchers

- Participants will need a laptop preferably with the course software installed.
- Previous knowledge about optical imaging in biosciences (e.g. microscopy imaging)

Course Organizers: André Maia and María Gómez Lázaro
andre.maia@i3s.up.pt | maria.glazaro@ineb.up.pt


- High content image analysis
- Image segmentation and quantification
- Batch analysis
- Open-source image analysis software


André Maia, i3S, Porto
Anna Kreshuk, EMBL, Heidelberg 
Eduardo Conde-Sousa, i3S, Porto
Huw Summers, College of Engineering, Swansea 
María Gómez Lázaro, i3S, Porto
Mafalda Sousa, i3S, Porto
Paul Rees, College of Engineering, Swansea 


The course modules are independent of each other, therefore you are free to choose the module(s) of your preference.
Minimum number of participants per module: 10.
Limited number of participants per module: 25.



Module Software Speakers
1 ImageJ/Fiji Eduardo Conde Sousa
Mafalda Sousa
2 ilastik Anna Kreshuk
Dominik Kutra
3 Cell Profiler
Cell Profiler Analyst
André Maia
Paul Rees
4 Cytoscape
Huw Summers
Paul Rees
Maria Lázaro




  Early Registration until 31st March 2021 | Payment deadline: 9th April 2021 Late Registration from 1st April until 1st May 2021 | Payment deadline: 7th May 2021
  i3S members Others i3S members Others
Individual module(s) 40 € 50 € 50 € 60 €
Full course 140 € 180 € 180 € 220 €


Module 1 is full. If you wish to stay in the waiting list, please send an e-mail to events@i3s.up.pt.

Payment will be requested only after confirmation of acceptance.
The organizer reserves the right to cancel the course in case of an insufficient number of participants or other unforeseeable events that render the execution of the course.



Advanced Training Unit | Email: training@i3s.up.pt | Tel: +351 220 408 800