Introduction to Image Analysis Course

organized by COLife and FCUL

21 set 2021

Course Program:

This course aims at providing researchers who are initiating microscopy-based projects with fundamental skills on digital imaging and biological image analysis. The course incorporates theoretical lectures as well as hands-on exercises which demonstrate image analysis procedures on Fiji/ImageJ, the reference open source image bioimage analysis software. Finally, trainees will learn about recording and automating image processing workflows. Trainees will be exposed to images produced by transmission, epifluorescence and confocal microscopes. At the end of the course, trainees will be able to use Fiji/ImageJ to open, visualize and perform basic image processing and analysis procedures on their own biological images.


21 September – 9:00 -13:00

Basics of digital images and image processing in Fiji

Trainer: Davide Accardi – Champalimaud Research


  • Opening and saving images in Fiji
  • Biological image formats
  • Image visualization
  • Multidimensional images: xyz, time and channels


22 September  – 9:00 -13:00

Quantitative image analysis

Trainer: Hugo Botelho – BioISI / FCUL


  • Regions of interest
  • Measurement types
  • Thresholding
  • Introduction to linear and morphological filters
  • Object counting
  • Particle dynamics measurements


23 September  – 9:00 -13:00

Automation and action recording in Fiji


  • Anna Pezzarossa
  • Clara Barreto – iMM
  • Hugo Botelho – BioISI / FCUL
  • José Marques – IGC
  • José Rino – iMM
  • Luis Marques – BioISI / FCUL
  • Mariana Ferreira – ITQB-NOVA
  • Telmo Pereira – CEDOC-NMS


  • ImageJ macros
  • Macro recorder
  • Batch processing

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