Basics in Light Microscopy 2021

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Online Course

Basics in Light Microscopy

25-28 October 2021


This course will provide a solid understanding of the fundamental principles of light microscopy for cellular and developmental biology researchers. Through a series of interactive tutorials, trainees will be exposed to the photophysical, spectroscopic and optical background to optical microscopy, as well as instrumental and biological sample preparation considerations. Emphasis will be placed on bioimaging technologies available at FCUL: transmission, epifluorescence and confocal fluorescence microscopies. At the end of the course a short overview of advanced light microscopy technologies will be presented. This course is targeted to young researchers who use or intend to use light microscopy as part of research projects, especially MsC, PhD students and post-docs who did not have formal introduction to microscopy as part of their academic training.



Target audience

MsC and PhD students. Post-docs and facility trainees. Researchers who are starting microscopy projects for the first time.




Online course, using the Zoom platform.
Limit: 20 attendees


Registration: 11 October
Non-FCUL members will be asked to provide a short motivation statement


Registration form


  • Hugo Botelho
  • Luís Marques
  • Rui Malhó
  • Federico Herrera


Subject to change

25 October – Basic concepts in spectroscopy and sample preparation
9:30 – 11:10 Trainer: Hugo Botelho

  • Presentation and course overview
  • The electromagnetic nature of light
  • Absorption, fluorescence and other photophysical processes
  • Optical aberrations
11h10 – 11h30 Coffee Break
11h30 – 12h15 Trainer: Hugo Botelho

  • Absorption dyes
  • Fluorescent dyes
  • Fluorescent proteins
  • Labeling of biological samples
12h15 – 13h00 Trainer: Rui Malhó

  • Live cell imaging
  • Keeping cells alive during an observation
  • Bringing live cells into the microscope stage
26 October – The compound optical microscope
9:30 – 11:10 Trainer: Hugo Botelho

  • Construction of the compound optical microscope
  • Conjugated planes
  • Transmission and fluorescence light paths
  • Light sources
  • Objectives
11h10 – 11h30 Coffee Break
11h30 – 13h00 Trainer:

  • Eyepieces
  • Filters
  • Array detectors (cameras)
  • Slide and coverslip selection
  • Convolution and resolution in optical imaging systems
27 October – Transmission, epifluorescence and confocal microscopy
9:30 – 11:10 Trainer:

  • Bright field microscopy and contrasting techniques
  • Epifluorescence microscopy
  • Specific components: light sources, filters and detectors
11h10 – 11h30 Coffee Break
11h30 – 13h00 Trainer: Luís Marques

  • Confocal microscopy
  • Specific components: lasers, point detectors, spectral analyzers.
  • Muli-photon confocal
28 October – Advanced microscopy
9:30 – 11:10 Trainer: Hugo Botelho

  • Light sheet microscopy
  • High-throughput microscopy
  • F-techniques
  • Super resolution techniques
11h10 – 11h30 Coffee Break
11h30 – 12h30 Trainer: Federico Herrera

  • Applications of advanced fluorescence microscopy in cell biology
12h30 – 13h00
  • Final remarks and course finish

Hugo Botelho

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