Basics in fluorescence microscopy

Title: Basics in fluorescence microscopylogo_LCAM
Date: 23-26 January 2024 (annual)
Location: LCAM-FNWI, Sciencepark
Contact: Mark Hink
Previous editions: 1996-2013, 2017-2020, 2022-2023


A basic course for graduate students, postdocs and lab technicians in biology, biophysics and (bio)medicine. It  provides detailed knowledge of the working principles of confocal imaging, with special emphasis on experiment related issues, such as optical aberrations, bleaching, specimen preparation, fluorescent probes, data analysis and representation. The course integrates theoretical lectures with hands-on experiments and practical experience, focused at cell biological studies. Experts in the field of microscopy will give an overview of “state-of-the-art” imaging techniques in biological research.

Basics in fluorescence microscopy

This 4 day course is a basic course for PhD students, postdocs and technicians in biology and biomedical science who need widefield and/or confocal microscopy for their experiments. It is our aim to teach how these light microscopy techniques can be used in celbiological research. After this course, participants will understand the basic optical principles of the widefield and confocal microscope and its limitations. In this course we will focus on basic technologies that can be used in biology such as multi-color (confocal) microscopy, ratio imaging, co-localization, phototoxicity and how to keep cells alive under the microscope. Furthermore, participants will be introduced to the latest developments in fluorescent probe & biosensor technology, sample preparation and an overview is presented discussing advanced technologies like FRET, FLIM, FRAP, FCS & super-resolution microscopy. The course consists of theoretical lectures (~50%) and hands-on experiments (~50%) via practical work at the microscope and image analysis sessions. The teaching staff consists of experts in the field of light microscopy from the van Leeuwenhoek Centre of Advanced Microscopy. Participants are encouraged to discuss their specific problems during the course.


– Light, optics, microscopy and contrast
– Confocal principle and the effect of the pinhole
– Aberrations, magnification and resolution
– Fluorescence, spectra and filters
– Microscopy hardware: Lasers, lamps and detectors
– Nyquist sampling theorem
– Image deconvolution and restoration
– Colocalization and image analysis
– Dyes, fluorescent proteins and biosensors
– Microscopy sample preparation and incubation
– Overview functional imaging techniques FRET, FLIM, FRAP, FCS & SRM
– Image processing using ImageJ
– Microscopy data representation

After the course the participants will have practical experience in the basic operation steps of the confocal scanning and widefield microscope and basic knowledge of advanced functional imaging techniques, the preparation of biological specimen and be able to perform simple image processing steps.


Tue 23 Jan 2024:
Microscopy principles
Lecture Confocal microscopy
Lecture Microscopy hardware & laser safety
Practical Confocal microscopy basics

Wed 24 Jan 2024:
Live cell microscopy & sample preparation
Lecture Fluorescent dyes & probes
Practical Confocal microscopy advanced
Practical Co-localization, Spinning disk & Wide-field ratio imaging & Time series <session1>

Thu 25 Jan 2024:
Lecture with overview of functional imaging techniques
Tutorial ImageJ basics -> laptop required
Practical Co-localization, Spinning disk & Wide-field ratio imaging & Time series <session2>
Practical Co-localization, Spinning disk & Wide-field ratio imaging & Time series <session3>

Fri 26 Jan 2024:
Lecture Microscopy data analysis
Tutorial Advanced image processing using ImageJ  -> laptop required
Practical Co-localization, Spinning disk & Wide-field ratio imaging & Time series <session4>
Lecture Microscopy data representation
Final discussion


Participants: Minimum 12, Maximum 20 PhD students, technicians and postdocs.
Location: Sciencepark, University of Amsterdam

Level: Starting microscopist with minor experience (next level: Functional Imaging course)
Application: Application has been closed for the ’24 edition.
Selection will be based at “first come, first serve” principle. At Dec 19th the applicants will be notified if they can join the ‘Jan ’24 edition of the course.
Costs (including coffee and lunches):  500 Euros (UvA-SILS participants can receive discount).
Organiser & info: LCAM, Mark Hink (