Basics in fluorescence microscopy

Title: Basics in fluorescence microscopylogo_LCAM
Date: 15-18 Feb 2022 (annual)
Location: LCAM-FNWI, Sciencepark
Contact: Mark Hink
Previous editions: 1996-2013, 2017-2020


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 Feb 15th 2022:
Microscopy principles
Lecture Confocal microscopy
Lecture Microscopy hardware & laser safety
Practical Confocal microscopy basics

Wed Feb 16th 2022:
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 Feb 17th 2022:
Lecture with overview of functional imaging techniques
Practical Co-localization, Spinning disk & Wide-field ratio imaging & Time series <session2>
Practical Co-localization, Spinning disk & Wide-field ratio imaging & Time series <session3>
Tutorial ImageJ basics -> laptop required

Fri Feb 18th 2022:
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.
Level: Starting microscopist  (next level: Functional Imaging course)
Application:  Application form can be filled here (Deadline: Jan 15th 2022)
Costs (including coffee and lunches): unknown yet
Organiser & info: LCAM, Mark Hink

Health safety note: As long as the Dutch government and UvA allows us to organise courses without any >1.5 meter distance restrictions this BFM course will be organised as planned. However at the moment that >1.5 meter distance regulations would become active, we are not able to organise the many practical sessions and we will have to postpone or cancel this course.