Where Ideas grow

BioImage Analysis for High Content Screening

25-28 May 2021
i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto


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 in 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 should bring a suitable 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


Due to the SARS-CoV-2/COVID-19 pandemic situation, it might happen that an on-site meeting cannot take place. In that case, an on-line version of the meeting in the same date with the same program will be organized. 
In case of an on-line version, the registration fee will be deducted of 10 EUR per course day. 

Registration fee includes coffee breaks, lunch and course materials.
Registration is conditional, course acceptance depends on motivation and date of registration, and will be informed by 1st March 2021.

  Early Registration until 1st March 2021 | Payment deadline: 1st April 2021 Late Registration from 2nd March until 1st April 2021 | Payment deadline: 1st May 2021
  i3S members Others i3S members Others
Individual module(s) 50 € 60 € 60 € 70 €
Full course 180 € 220 € 220 € 260 €





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