ADM Course 2021

Advanced Optical Fluorescence Microscopy & Image Analysis Course, May 18- June 1, 2021

ADM offers a 13 hours course on Advanced Optical and Fluorescence Microscopy, including Image Analysis.

This course targets Phd students, Postdocs and researchers from IRB and institutions at the PCB, and will be held this year online via Zoom.

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.

Attendance to the 5 sessions is expected for all registrants.

The course capacity is 95 seats (our Meeting limit via Zoom).

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

Access the Registration Form here:


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

Where: Online via Zoom (links will be sent for each day to registered participants)

PRELIMINARY Program (Subject to changes)

May 18th, 9h30-12h

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

  • Laser Safety: basic concepts

May 20th, 9h30-12h30

Day 2 From Meso- to Nano-scale: Lightsheet and Super-resolution

  • 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

  • Super resolution (SR)

    • 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 25th, 9h30-12h

Day 3 Image Analysis in Life science


    • 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.

    • FCS and FCCS: ensemble and sm molecular diffusion.

    • Anisotropy, HomoFRET.

  • Photomanipulation I: Fluorescence Recovery After Photobleaching (FRAP)

    • How to tackle Molecular kinetics with FRAP ?

    • FRAP on various instruments at ADM

    • Data Analysis, EasyFRAP

  • Photomanipulation II: In vivo Laser Nanosurgery

  • High-Content and High-Throughput Microscopy

    • Multidimensional Acquisition

    • Preparation of a High-content experiment

    • Intelligent Imaging

May 27th, 9h30-12h

Day 4 Image Analysis in Life science - Part I

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

  • Commonly used software tools and typical workflows

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

  • Selection of projects including advanced bioimage analysis at ADMCF

June 1st, 9h30-12h

Day 5 Image Analysis in Life science - Part II

  • Introduction to ImageJ /Fiji

  • Image deconvolution

  • Image stitching & visualization of large images

  • Introduction to Machine Learning & Deep Learning