Introduction to image analysis – COLife and FCUL course

This course aimed 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.


You can find the program and recordings of each section below: 


Basics of digital images and image processing in Fiji

Trainer: Davide Accardi – Champalimaud Research

Topics covered:

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


Quantitative image analysis

Trainers: Hugo Botelho – BioISI / FCUL

Topics covered:

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


Automation and action recording in Fiji (the practical exercises were not recorded as we had 8 parallel practical sessions) 


Anna Pezzarossa – Champalimaud Research

Clara Barreto – iMM

Hugo Botelho – BioISI | FCUL

Luís Marques – BioISI | FCUL

José Marques – IGC

José Rino – iMM

Mariana Ferreira – ITQB

Telmo Pereira – CEDOC | NMS

Topics covered:

  • ImageJ macros
  • Macro recorder
  • Batch processing


Updated on 11 december 2021

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