ADM Course 2024

Advanced Optical & Fluorescence Microscopy & BioImage Analysis Course, Dec 2 & 5, 2024

ADM offers a 7 hours course on Advanced Optical and Fluorescence Microscopy and BioImage Analysis.

Where: Sala Serratosa, PCB, December 2 (9h30-14h00) and 5th (9h30-14h00)

This course targets research staff who need Bioimaging: Phd students, Postdocs and research staff from IRB Barcelona and institutions at the PCB. The course is free 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.

The course capacity is about 50 seats. Attendance is expected for both 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 and priority to junior research staff who has not attended earlier editions.

- research staff from other public institutions and private entities: upon availability, confirmation by November 25th.

Access the Registration Form HERE

Speakers/Trainers: Lídia Bardia, Anna Lladó, Nikolaos Giakoumakis, Chong Zhang, Julien Colombelli

PRELIMINARY Program (Subject to changes)

   DEC 2nd, 9h30-11h00 Trainer: Julien Colombelli

Day 1 / SESSION 1    Image Formation and 3D Imaging

•  Optical Microscopy, Optical Contrasts

•  Fluorescence: Basics, photophysics of fluorescence emission

•  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

break 30min

     DEC 2nd, 11h30-14h00  Trainers: Nikolaos Giakoumakis, Lídia Bardía, Julien Colombelli

Day 1 / SESSION 2    Nano-scale & Mesoscopy/Lightsheet

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

  • STED nanoscopy

Correlative Light to Electron Microscopy (CLEM)

12h45 short break

 SESSION 3  

Meso-scale Imaging (Mesoscopy), Lightsheet Fluorescence Microscopy

• • LSFM/SPIM: Single Plane Illumination Microscopy 

  • Lightsheet imaging principles

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

  • Lightsheet imaging with Optical Clearing for large samples

  • Large Samples Imaging with cleared organs

  DEC 5th, 9h30-11h Trainers: Anna Lladó, Nikolaos Giakoumakis

Day 2 / SESSION 4     Molecular Imaging and High-Content/High-Throughput

Photomanipulation: Fluorescence Recovery After Photobleaching (FRAP)

• • How to tackle molecular kinetics with FRAP ?

  • Data Analysis, EasyFRAP

FRET / FLIM

• • • 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. 

High-Content and High-Throughput Microscopy

• • Multidimensional Acquisition

  • Preparation of a High-content experiment

  • High-content Confocal Imaging

  • Intelligent Imaging

break 30min

  DEC 5th, 11h30-14h00     Trainer: Chong Zhang

Day 2 / SESSION 5     BioImage Analysis in Life science

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

• Digital Images & (image) Data Quality

• Introduction to Open-source BIA Software, ImageJ /Fiji etc..

12h45 short break

• Image processing fundamentals: filters, image segmentation, binary mask processing, ...

• Machine Learning 

• Deep Learning