Hands-on workshop on Image Analysis for Imaging flow Cytometry

This hands-on course is divided in two main parts covering from the use of the imaging flow cytometer (Imagestream) and basic image analysis (Part A) to advanced image analysis focusing on machine learning for Imagestream data using the Cell Profiler environment and batch analysis with ImageJ amongst others (Part B). Essentially practical, this course aims at introducing the students in the use of the imaging flow cytometer and image data analysis. 

Imaging flow cytometry is a state of the art technology that combines the statistical strength, sensitivity, and high speed of a conventional flow cytometer by rapidly acquiring large number of cells with the quantitative image analysis of the detailed cellular imagery with morphologic (and functional) information captured by a microscope. Similar to flow cytometry, fluorescence intensity and cell complexity can be analyzed, but furthermore and amongst others, morphological characterization, protein translocation and colocalization, can also be evaluated. The high versatility of the analysis software allows for the quantification of a diverse set of parameters granting the user complete autonomy in regard to the features to be included in the data analysis. The second part of this workshop will cover machine learning for Imagestream data using the Cell Profiler environment, and batch analysis and script writing as well as several plugins for the solution of common issues using ImageJ.


June 6-8, 2017 | i3S, Porto


María Gómez Lázaro, i3S – INEB
Marina Leite, i3S – Ipatimup
Justyna Piasecka, College of Engineering, Swansea University
Romain Guiet, PT-BIOP, Ecole Polytechnique Fédérale de Lausanne



DATES: June 6-8, 2017 (Tuesday to Thursday, 3 full days) | 09:00 to 18:00

PLACE: i3S - Instituto de Investigação e Inovação em Saúde (Rua Alfredo Allen, 208 | 4200-393 Porto, Portugal)




  Before 8th May After 8th May
Part A - Use of the imaging flow cytometer
(ImageStream) and basic image analysis
60€ 100€
Part B - Advanced image analysis on machine learning for
ImageStream data using the Cell Profiler environment and batch
analysis with ImageJ amongst others
60€   100€
Part A+B 100€ 175€

The fee includes coffee breaks and workshop materials.
Registrations accepted up to a maximum of 6 participants in part A and up to 20 participants in part B.


Registration >>

Registrations for the full course are closed. If you wish to be placed in the waiting list, please send an email to events@i3s.up.pt.




This course is accredited with 1 ECTS. In case you want to get the ECTS credit, you have to be registered for the full course (A+B). Attendance to all sessions and a final exam are mandatory. Besides the normal registration, if you are interested in getting the credits please submit the copy of your ID and the certificate of your degree in the registration form.





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