Where Ideas Grow

High Throughput Screening and Image Analysis for BioSciences, 6th edition 

23-27 May 2022 | 9:30 to 17:30 | i3S - Instituto de Investigação e Inovação em Saúde  
Fundamentally practical, this course aims to introduce the participants in experimental design, image acquisition, image and data analysis for high throughput (HT) experiments. These are essential skills when generating a massive amount of data, especially image-based data in the biosciences field. Lectures will be given by specialists in the field and participants will learn how to use state-of-the-art technology for HT experimentation and open-source software for image and data analysis. The course includes lectures and theoretical-practical classes plus Lab-Sessions (optional) where the attendants will get acquainted with the use of automated liquid handling equipment, plate readers and high content (HC) imagers. Interaction with HTS/HCS specialists will be fostered due to the restricted number of participants.

Target: This course is intended for all students/researchers working in the fields of regenerative medicine, biomedical engineering, biomaterials, bioengineering, Neurosciences, oncology, biology, cellular biology, and image analysis.
It is open to postgraduate students (MSc and PhD programs) and researchers from the above-mentioned areas, working on research laboratories, universities and companies.

Course language: English 

Course duration: 
-    Full course: 36 hours 
-    Course without Lab Sessions: 30 hours

Requirements: Laptop. Image analysis software will be provided to the participants through the moodle platform.  

Certificate: The attendees must attend a minimum of 80% of the course. Exception for participants requiring ECTS, in this case, 100% of attendance is mandatory.      

Accreditation: This course is credited with 2 ECTS. Participants requiring ECTS must enroll in the full course.
Participants interested in ECTS should submit a copy of their ID card and the certificate of the higher degree in the registration form. Attendance to all sessions (including Lab Sessions) and to the final exam is mandatory. 

Organization: André Maia and María Gómez Lázaro

Poster >> 


- High throughput/content screening
- High content imaging systems    
- High throughput equipment
- Lab automation
- Target and drug discovery
- High content image analysis
- Data visualization and analysis



Monday, 23 May
09:30 Registration and Reception
10:00 Welcome & introduction to the course
10:15 High Content Imaging and Screening | André Maia, i3S
11:00 Coffee-break
11:30 Imaging in Flow | María Lázaro, i3S
12:15 Target and Drug Discovery | António Pombinho, i3S
13:00 Lunch
14:00 Light microscopy overview | Paula Sampaio, i3S
14:45 Introduction to image analysis | Paula Sampaio, i3S
15:30 Coffee-break
16:00 3D Cell Models | Marta Silva, i3S
16:45 Assay development and Lab sessions overview | André Maia / María Lázaro, i3S
17:30 End of day 1

Tuesday, 24 May
09:30 High Throughput Systems | To be announced, Molecular Devices, LusoPalex
10:00 High Throughput Flow imagers | Sandra Cuni, Izasa Scientific
10:30 Lab automation and liquid handling | To be announced, Formulatrix
11:00 Coffee-break
11:30 Tools for Drug Discovery | To be announced
12:00 Cellular Imaging Reagents & 3D HTS Image acquisition | Véronique Berchet, Perkin Elmer, ILC
13:00 Lunch
15:30 Coffee-break
17:30 End of day 2

Wednesday, 25 May
11:00 Coffee-break
13:00 Lunch
14:00 Image Analysis I – Image segmentation using machine learning – ilastik | all groups together | Dominik Kutra, EMBL
15:30 Coffee-break
16:00 Image Analysis I (cont)
17:30 End of day 3

Thursday, 26 May
09:30 Image Analysis II – CellProfiler | all groups together | André Maia, i3S
11:00 Coffee-break
11:30 Image Analysis II (cont)
13:00 Lunch
14:00 Image Analysis III – CellProfiler Analyst | all groups together | Huw Summers / Paul Rees, Swansea University
15:30 Coffee-break
15:45 Image Analysis III (cont)
16:45 End of day 4
17:00 Walking tour Porto Downtown
20:00 Dinner downtown (éLeBê Entreparedes)

Friday, 27 May
09:30 Data Analysis I - Introduction to Cytosplore | all groups together | Huw Summers, Swansea University
11:00 Coffee-break
11:30 Data Analysis | Hugo Botelho, BioISI, FCU
12:15 Data Analysis II - shinyHTM Explorer: Inspection and statistical analysis of high throughput microscopy data | Hugo Botelho, BioISI, FCUL
13:00 Lunch
14:00 Data Analysis II (cont)
15:30 Coffee-break and Group photo
16:00 Experimental work discussion and Q/A | André Maia, María Lázaro, i3S
16:30 Certificates of attendance
16:45 Goodbye!
17:00 ECTS exam


Program download [PDF] >> 






André Maia, i3S - Institute for Research and Innovation in Health, Porto, PT

António Pombinho, i3S - Institute for Research and Innovation in Health, Porto, PT

Dominik Kutra, EMBL, Heidelberg, DE

Hugo Botelho, BioISI, FCUL, PT

Huw Summers, College of Engineering, Swansea, UK

Maria Gomez Lazaro, i3S - Institute for Research and Innovation in Health, Porto, PT

Marta Silva, i3S - Institute for Research and Innovation in Health, Porto, PT

Paul Rees, College of Engineering, Swansea, UK

Paula Sampaio, i3S - Institute for Research and Innovation in Health, Porto, PT

Sandra Cuni, Izasa Scientific

Tatiana Lourenço, LusoPalex

Véronique Berchet, PerkinElmer


Limited number of participants for the full course: 20
Limited number of participants for the course without Lab Sessions: 30

The registration fee includes coffee breaks, lunches, and course materials.



  Early bird registration | Until 23rd April 2022
Payment deadline: 29th April 
Regular registration | From 24th April until 10th May 2022
Payment deadline: 10th May 
  Course without Lab Sessions Full course* Course without Lab Sessions Full course*
i3S members and UP
225 € 275 € 250 € 300 €
External participants (Academic)
275 € 325 € 300 € 350 €
External participants (Industry) 350 € 425 € 425 € 500 €


* Participants requiring ECTS must enroll in the full course.

Pre-registration form >>

Payment will be requested only after confirmation of acceptance. Details for payment will be sent in the confirmation registration e-mail.

Criteria for selection: 
- Higher education in areas related to regenerative medicine, biomedical engineering, biomaterials, cellular biology, biology, and image analysis
- Candidates will be selected according to their motivation letter (included in their application). Preference will be given to candidates to whom the training in the usage of the equipment and image analysis is fundamental to their research work.   






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