ADM Course 2022

Advanced Optical Fluorescence Microscopy & Image Analysis Course, May 3-17, 2022

ADM offers a 11 hours course on Advanced Optical and Fluorescence Microscopy and Image Analysis.

This course targets Phd students, Postdocs and research staff from IRB Barcelona and institutions at the PCB, and will be held in person.

Registration is based on first come first served.

Attendance is strongly recommended for 1st year Phd candidates at IRB, who have guaranteed seat in the course.

Participation to all 5 sessions is compulsory / strongly expected for all confirmed participants.

The course capacity is about 60 seats.

Attendance is expected for all days of the course for people who register.

Registration will be prioritized this way:

- IRB research staff: automatic confirmation, first-come first-served.

- research staff from public institutions at the PCB: upon availability of seats, first-come first-served, confirmation by April 22.

- research staff from other public institutions: upon availability, confirmation by April 25.

- research staff from private entities: upon availability, selection case-to-case, priority given to users of the IRB facility. Confirmation by April 25.

Access the Registration Form here (fully booked)


Lídia Bardia, Anna Lladó, Nikolaos Giakoumakis, Sébastien Tosi, Julien Colombelli

Where: Sala Serratosa, Parc Científic de Barcelona PCB (C. Baldiri Reixac, 10. 08028 Barcelona)

PRELIMINARY Program (Subject to changes)

May 3rd, 12h-14h

Day 1 Image Formation and 3D Imaging

  • Optical Microscopy: Contrasts

  • Fluorescence: Basics of photophysics

  • Laser Scanned Confocal Microscopy principles

  • Detectors

  • Resolution in Optical Microscopy

  • 3D Imaging contrasts: Speed or Resolution ?

    • Multiphoton Microscopy, Spinning Disk, Airyscan

  • More Optical Sectioning modalities: special techniques

    • Second Harmonic Generation, Spectral Detection, TIRF

    • Hyperspectral imaging

  • Laser Safety: basic concepts

May 5th, 15h-17h30

Day 2 Nano-scale & Molecular Imaging


    • Protein Interaction with FRET

    • Acceptor Photobleaching, Sensitized Emission and Ratio Imaging

    • Lifetime of a fluorophore

    • Lifetime-based FRET

  • sm: single molecule techniques:

    • Time Correlated Single Photon Counting (TCSPC)

    • sm dynamics for FRET.

  • Photomanipulation I: Fluorescence Recovery After Photobleaching (FRAP)

    • How to tackle molecular kinetics with FRAP ?

    • Data Analysis, EasyFRAP

  • Super resolution (SR) / Nanoscopy

    • Resolution concepts, revisited with SR

    • SIM: Structured Illumination Microscopy

    • ISM: Image Scanning Microscopy, including Airyscan

    • Expansion Microscopy

    • SMLM: Single Molecule Localization Microscopy

      • PALM, STORM, Paint etc...

      • SMLM Analysis

    • Correlative Light to Electron Microscopy (CLEM)

May 10th, 12h-14h

Day 3 Meso-scale and High-Content

  • SPIM/LSFM: Single Plane Illumination Microscopy or Lightsheet Fluorescence Microscopy

    • Lightsheet imaging principles

    • Live Imaging with LSFM and variants: SPIM/DSLM, Oblique Plane Microscopy (OPM)

    • Optical Clearing for large samples

    • Large Samples Imaging with cleared organs

  • High-Content and High-Throughput Microscopy

    • Multidimensional Acquisition

    • Preparation of a High-content experiment

    • High-content Confocal Imaging

    • Intelligent Imaging

May 12th, 15h-17h30

Day 4 Image Analysis in Life science - Part I

  • Introduction to BioImage Analysis (BIA): motivations and aims

  • Commonly used software tools and typical workflows

  • Selection of projects/examples including advanced bioimage analysis

  • Practical Introduction to ImageJ /Fiji

May 17th, 12h-14h

Day 5 Image Analysis in Life science - Part II

  • Fundamentals: digital images & filters, image segmentation, binary mask processing, ...

  • Advanced Bioimage Analysis Exercises (hands-on, demo)