Dates: 17 and 18 November 2026
Bioimage analysis is an increasingly important field in life science research, enabling the efficient handling of digital images to extract quantitative measurements which report on relevant biological phenomena. This course is aimed at life science researchers who are initiating any research projects involving the acquisition or handling of any type of microscopy data, or to researchers who already work with images on their day-to-day but who wish to get a more formal understanding of the most common bioimage analysis methods, concepts and tools.
The course will use the resources available on the Fiji/ImageJ software to guide participants through the basics of image analysis and processing. The program combines interactive plenary lectures with representative exercises performed in small groups, giving each participant the opportunity to test hands-on the most relevant concepts in bioimage analysis and clarify any doubts in close interaction with the trainers.
Participants will be requested to bring their own laptops and mouse (optional but recommended) with Fiji installed.
Note: Although the course is open to all the institutes from Lisbon, priority is given to participants that come from the organizer institutes (ITQB NOVA, GIMM, NMS, Champalimaud Foundation, FCUL and CBR).
Programme
17 November
9.30-11.00 [Trainer: Carolina Feliciano]
Working with ImageJ: Fiji and ImageJ, ImageJ interface, Basic concepts and common tasks and Opening, visualizing and saving an image
11.00-11.15 Coffee break
11.15-12.30 [Trainer: Carolina Feliciano]
Multi-dimensional images: 4D images: x, y, z, channels, Basic operations
12.30-14.00 Lunch
14.00-15.30 [Trainer: Diogo Coutinho]
Multi-dimensional images: 5D images: x, y, z, channels and time
15.30-15.45 Coffee break
15.45-17.00 [Trainer: Diogo Coutinho]
Quantitative bioimage analysis: images as a source of data, regions of interest, line profile and ROI Manager
18 November
9.30-11.00 [Trainer: Hugo Botelho]
Spatial measurements in ImageJ: pixel spatial calibration, setting a scale bar, measurement types
11.00-11.15 Coffee break
11.15-12.30 [Trainer: Luis Marques]
Image pre-processing and segmentation: basics of linear filtering, thresholding, basics of Binary filtering, object counting
12.30-14.00 Lunch
14.00-15.30 [Trainer: James Lillis]
Advanced Segmentation: labkit and stardist
15.30-15.45 Coffee break
15.45-17.00 [Trainer: James Lillis]
Introduction to automation: using the macro recorder, introduction to batch processing and best practices in reporting bioimage quantification
Organizers:
Aida Lima .aida.santos@gimm.pt
Beatriz Barbosa barbosa@gimm.pt
Carolina Feliciano cfeliciano@itqb.unl.pt
Diogo Coutinho coutinho@gimm.pt
Hugo Botelho hmbotelho@ciencias.ulisboa.pt
James Lillis lillis@nms.unl.pt
Luis Marques lfmarques@ciencias.ulisboa.pt
Anna Pezarossa anna.pezzarossa@research.fchampalimaud.org
Patricia Rodrigues patricia.rodrigues@gimm.pt
