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2nd Annual Workshop on

Advanced Microscopy and Biophotonics

November 23-27 of 2020

Institut Pasteur of Montevideo

Montevideo – Uruguay



Organizer: Dr. Leonel Malacrida


International speakers:

  • Dr. Enrico Gratton (UCI-USA)
  • Dr. David Jameson (U. Hawaii-USA)
  • Dr. Susana Sanchez (U. Concepción-Chile)
  • Dr. Per Niklas Hedde (UCI-USA)
  • Dr. Fernando Stefani (UBA-Argentina)
  • Dr. Suman Ranjit (Georgetown U-USA)
  • Dr. Luca Lanzanó (U. Catania-Italy)
  • Dr. Luis Bagatolli (I. Ferreyra-Argentina)
  • Dr. Michelle Digman (UCI-USA)
  • Dr. Valeria Levi (UBA-Argentina)
  • Dr. Francesco Cardarelli (U. Pisa-Italy)
  • Dr. German Gunther (U. Chile-Chile)
  • Dr. Laura Estrada (UBA-Argentina)
  • Dr. Belén Torrado (UCI-USA)
  • Dr. Lorenzo Scipioni (UCI-USA)
  • Dr. Alexander Vallmitjana (UCI-USA)
  • Dr. Francesco Palomba (UCI-USA)


Local speakers:

  • Dr. Federico Lecumberry (FIng-UdelaR)
  • Dr. Florencia Irigoín (FMed-UdelaR)
  • Dr. Ariel Fernandez (FIng-UdelaR)

Course target and goals:

The workshop in Advanced Microscopy and Biophotonics is dedicated to disseminate cutting-edge technology and advanced methods in fluorescence microscopy and biophotonics.

The target audience includes postgraduate students, postdocs, and academics from all Americas with a background in the fundamentals of fluorescence microscopy, seeking to learn about recent advances in the combination of spectroscopy with fluorescence microscopy.

In the course, we will cover the fundamentals of advanced instrumentation and methods, such as FCS, FLIM, Hyperspectral imaging, Super-resolution, Non-linear microscopy, Deep tissue imaging, light-sheet microscopy, among others.

Due to the global COVID19 outbreak, this year the workshop will be held as a virtual course. The course is organized with lectures of fundamentals (40+5 min), application talks (20+5 min), and an optional advanced section for a virtual practical section (two section 2hs/each) and e-poster. This last section is restricted to 20 students and will be given on the last day. The lectures will be given in English.


For further information, please contact 


Workshop agenda:

(Click here to download the preliminary programme)


Monday, November 23

09:45-10:00 – Opening and course introduction. Leonel Malacrida

10:00-10:45 – Lecture 1. David Jameson. Introduction to fluorescence fundamentals and methods.

10:45-11:30 – Lecture 2. Leonel Malacrida: Advanced fluorescence instrumentation and microscopy.

11:30-12:15 – Lecture 3. Enrico Gratton: Introduction to fluorescence correlation spectroscopy (FCS) and the photon counting histogram (PCH)

Virtual lunch break and meet with the instructors (Using zoom rooms I would like to organize small groups with the speakers from the previous sections for more informal and detailed discussion).

13:30-14:15 – Lecture 4. Per Niklas Hedde: Raster image correlation spectroscopy (RICS) and in vivo applications.

14:15 – 15:00 – Lecture 5. Per Niklas Hedde: Number & Brightness (N&B) and its applications for protein oligomerization studies in vivo.

15:00-15:45 – Lecture 6. Enrico Gratton: The pair-correlation function and its applications for deciphering the occurrence of barriers and obstacles inside the cell.

Virtual coffee break and meet with the instructors

16:15 – 16:40 – Application talk #1. Susana Sánchez: Ribosomal proteins detection by the PCH analysis in yeast.

16:40 – 17:05 – Application talk #2. Laura Estrada: Deciphering the Denge virus shuttling in the cell by 2D-pCF.

17:05 – 17:30 – Application talk #3. Enrico Gratton: Line-Scan FCS combined with pCF to understand the molecular traffic to the nucleus.


Tuesday, November 24

10:00-10:45 – Lecture 7. David Jameson: Introduction to lifetime measurements and the phasor plots.

10:45-11:30 – Lecture 8. Enrico Gratton: The phasor plots for FLIM and FRET.

11:30-12:15 – Lecture 9. Leonel Malacrida: The spectral phasor plot and its applications to hyperspectral imaging.

Virtual lunch break and meet with the instructors

13:30-14:15 – Lecture 10. Alex Vallmitjana: Blind four components analysis on FLIM data by the phasor approach.

14:15-15:00 – Lecture 11. Leonel Malacrida: Cell metabolism phenotyping and absolute NADH concentration by FLIM-Phasors.

15:00-15:45 – Lecture 12. Per Niklas Hedde. Hypespectral imaging in light-sheet microscope without hyperspectral detection.

Virtual coffee break and meet with the instructors

16:15 – 16:40 – Application talk #4. Susana Sánchez: Applications of FLIM-Phasors for biological questions: the pH and Ca++ case.

16:40 – 17:05 – Application talk #5. Suman Ranjit: FLIM-Phasor for cell metabolism phenotyping.

17:05 – 17:30 – Application talk #6. Leonel Malacrida: FLIM and Hyperspectral imaging using phasors to study membrane dynamics by LAURDAN fluorescence.

Virtual coffee break and meet with the instructors


Wednesday, November 25

10:00-10:45 – Lecture 13. Luca Lanzanó: Fundamentals of Super-resolution microscopy and its combination with FLIM-Phasors.

10:45-11:30 – Lecture 14. Fernando Stefani. Far-field fluorescence nanoscopy with sub-10 nm resolution.

11:30-12:15 – Lecture 15. Leonel Malacrida: The single plane illumination microscopy and its applications.asurements

Virtual coffee break and meet with the instructors

13:30-14:15 – Lecture 16. Enrico Gratton: The DIVER microscope for deep tissue imaging.

14:15-15:00 – Lecture 17. Lorenzo Scipioni. The Phasor S-FLIM Microscope for multiplexing microscopy.

15:00-15:45 – Lecture 18. Alexander Vallmitjana: 3D-Single particle tracking and its applications.

Virtual lunch break and meet with the instructors

16:15 – 16:40 – Application talk #7 Francesco Cardarelli: iMSD application for molecular intracellular diffusion studies.

16:40 – 17:05 – Application talk #8. Lorenzo Scipioni: Comprehensive correlation analysis for super-resolution dynamic fingerprinting of cellular compartments using the Zeiss Airyscan detector.

17:05 – 17:30 – Application talk #9. Suman Ranjit: Applications of the DIVER microscope for biomedical imaging.

Virtual coffee break and meet with the instructors


Thursday, November 26

10:00 – 10:25 – Application talk #10 Valeria Levi: Applications of FCS to study the organization of GR in the nucleus.

10:25 – 10:50 – Application talk #11. Luis Bagatolli: Uses of solvatochromic probes for water dynamics in yeast.

10:50 – 11:15 – Application talk #12. Germán Gunther: Development and application of CAPRYDAA for in vivo membrane dynamics.

11:15 – 11:40 – Application talk #13 Federico Lecumberry: Applications of imaging processing and AI in advanced fluorescence microscopy.

11:40-12:05 – Application talk #14. Florencia Irigoín. The primary cillium membrane organization studied by spectral phasors and LAURDAN.

Virtual lunch break and meet with the instructors

13:30 – 13:55 – Application talk #15. Francesco Palomba: Dimethylaminonaphtalen (DAN) probes and liquid phase separation.

13:55 – 14:20 – Application talk #16. Belen Torrado: Study of protein transport in the primary cilium using FRAP and pCF.

14:20-14:45 – Application talk #17. Ariel Fernánadez: Snapshot polarimetric and phase quantitative microscopy.

14:45-15:10 – Application talk #18. Michelle Digman: Evaluation of pre-implantation embryos by FLIM and autofluorescence.

Virtual coffee break and meet with the instructors

15:40 – 16:40 – Lecture 19: Workshop close and special lecture. David Jameson: A nano-history of fluorescence.

16:40 – 17:30 – Workshop closing and virtual coffee break with instructors


Friday, November 27

10:00 -12:00 Breakout rooms and discussions (All participants will have the chance to rotate between two sections.).

  1. What is fluorescence and harmonic generation? (Enrico Gratton)
  2. Can we see a single molecule? Why is this important? (Francesco Palomba)
  3. What is optical super-resolution? (Alexander Vallmitjiana)
  4. How we can observe a tumor in patients using fluorescence? (Suman Ranjit and Belen Torrado)
  5. Why do phasors plots analysis for FLIM and hyperspectral imaging? Why is this important? (Leonel Malacrida)
  6. Why and when SPIM is better than regular raster scanning microscopy? (Per Niklas Hedde)

Virtual lunch break and meet with the instructors

13:30 – 15:30 – Virtual practical section (20 total presentation):

Two topics (total 10 students by subgroup)

  • RICS and N&B-EGFP-PaxEGFP (Leonel Malacrida, Per Niklas Hedde and Marcela Diaz)
  • FLIM-Phasor-Autofluorescence and metabolism//NuBlue fluorescence and nuclear compaction (Belén Torrado, Alex Vallmitjana and Francesco Palomba)

Virtual coffee break and meet with the instructors

16:00-17:30 – Final discussion