Organizers
Paola Scavone (uy) / Steffen Härtel (cl)
Format
The Binational Postgraduate Course is a free course consisting of a total of 121 hours, of which 30 hours correspond to lectures in online synchronous/asynchronous format, 60 hours to the study of secondary materials, 16 hours to training with asynchronous materials, and 26 hours to practical sessions and presentation of results.
Theoretical Sessions (October 13th–17th, 2025): The theoretical sessions will be held online, in both synchronous and asynchronous formats, during the first week of the course.
Practical Sessions: A one-week practical session will take place for students at the IIBCE (October 20th–24th, 2025, Montevideo, Uruguay), including biofilm culture and manipulation, visualization of biofilms using confocal microscopy, and image processing and analysis for the extraction of quantitative parameters.
Locations
First Week: On-Line Format (Octuber 13th-17th)
Second Week: Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay (October 20th- 24th)
Teachers and Instructors
Paola Scavone (uy) / Steffen Härtel (cl) / Pablo Zunino (uy) / Jorge Jara (cl) / Eduardo de Mello (uy) / Erlen Cruz (uy) / Nicole Canales (cl) / Nicolás Navarro (uy) / Karina Palma (cl) / Luciana Robino (uy) / Dante Castagnini (cl) / Maria José González (uy) / Juan Eduardo Rodriguez (cl) / Angela Cabezas (uy)
Topics
Development of Microbial Biofilms
Biofilm Relevance and Resistance
Nanotechnology as a Solution for Biofilm Control
Dual Role of Biofilms in Industry and Medicine
Advanced Microscopy Techniques for Biofilm Study
Course Program and Lectures
Program & Calendar LINK
Monday 13th
Introduction to the Course and Activities
Microbial Biofilms Formation: Stages, Matrix, Gene Expression, Quorum Sensing (PS) PDF Document
Microscopy Introduction I (SH) PDF Document
Microscopy Introduction II (SH) PDF Document
Tutorials and Manuals Review (JJW – KP)
Software Installation and Configuration (JJW – KP)
Thuesday 14th
Microscopy, Image Acquisition and Analysis Applied to Microbiology I (SH) PDF Document
Microscopy, Image Acquisition and Analysis Applied to Microbiology II (SH) PDF Document
Importance of Biofilms in Wastewater Treatment Systems I (AC) PDF Document
Charla Virtual: Biofilm & Health Process (LR) PDF Document
I: https://drive.google.com/file/d/1qZCdwJ5JkgFCNAIuhfSxEy9c3b09RGJc/view?usp=sharing
II: https://drive.google.com/file/d/1lwXiIhD89_q1TazC6JO7rPjaooSvyBfd/view?usp=sharing
Tutorials and Manuals Review
Software Installation and Configuration
Wednesday 15th
Bacteriophages for Biofilm Control (EM) PDF Document
Light Sheet Microscopy applied to Microbiology (JER) PDF Document
Light Sheet Microscopy applied to Biofilms (NC) PDF Document
Image Processing I & II (JJW) PDF Document
Biofilms Study Models (MJG) PDF Document
Tutorials and Manuals Review
Software Installation and Configuration
Thursday 16th
Deconvolution Introduction I (SH) PDF Document
Deconvolution Introduction II / Image Processing III (JJW) PDF Document
Biofilms and the Health-Disease Process (discussion session) (LR/PZ/PS) PDF Document
Tutorial Deconvolution in Bacterial Images (NC) PDF Document
Review of Biofilm Formation Protocols
Deconvolution
Friday 17th
Expansion Microscopy in Bacteria and Biofilms (DC) PDF Document
Nanotechnology Applied to Biofilms I (ECJ/NNM) PDF Document
Image Processing IV (JJW) PDF Document
Image Processing V (JJW) PDF Document
Examen
Manuals and Protocols
Bacterial Protocols PDF Document
Eradication Trial Exercise XLS Document
Inhibition Assay Exercise XLS Document
Huygens Professional_SVI Manual PDF Document
Practical Session Image Processing I PDF Document
Practical Session Image Processing II PDF Document
Image Pre-bExM ZIP File
Image Post-bExM ZIP File
Huygens Instalation Tutorial PDF Documents
Relevant Link
Global Bioimaging : https://globalbioimaging.org/
Latin American Bioimaging: https://labi.lat/es
La Red de Equipamiento Científico Avanzado: https://redeca.med.uchile.cl
Microscopy Australia: https://myscope.training
The Scale of the Universe: https://htwins.net/scale2
Photomultiplier: www.olympus-lifescience.com/en/microscope-resource
/primer/digitalimaging/concepts/photomultipliers
Chrome Spectra Viewer: www.chroma.com/spectra-viewer
Thermo Fisher Spectra: www.thermofisher.com/order/spectra-viewer
Software to Download and Install
- Huygens Deconvolution (SVI): https://svi.nl/tiki-login_scr.php
- FIJI, … is an image processing package: https://fiji.sc
- Icy, … an open community platform for bioimage informatics: http://icy.bioimageanalysis.org
Groups
On Line Sessions
Literature
Dolan _ Costerton 2002_Biofilms Survival Mechanisms of Clinically Relevant Microorganisms PDF Document
Jonkman et al 2020_Tutorial guidance for quantitative confocal microscopy PDF Document
North 2006_Seeing is believing PDF Document
Pearson 2007_The Good The Bad and The Ugly PDF Document
Scavone et al 2016_Fimbriae have distinguishable roles in Proteus mirabilis PDF Document
Schlapp et al 2011_Development of 3D architecture of uropathogenic Proteus mirabilis batch culture PDF Document
Sweldlow et al 2021_A global view of standards for open image data formats and repositories PDF Document
Castañeda et al 2014_Computational Methods for Analysis of Dynamic Events in Cell PDF Document
Guzman Soto et al-2021_Mimicking biofilm formation PDF Document
Sauer et al 2022_The biofilm life cycle – Expanding the conceptual model of biofilm formation PDF Document
Azeredo et al 2017_Critical review on biofilm methods PDF Document
Merrit et al 2011_Growing and Analyzing Static Biofilms PDF Document
Class Literature – Eduardo de Mello
Nobrega et al 2015_Revisiting phage terapy PDF Document
Torres-Barceló & Hochberg 2016_Evolutionary Rationale for Phage PDF Document
Milho et al 2019_Antimicrobial assessment of phage terapy… PDF Document
Pires et al 2022_An overview of the current state of phage teraphy… PDF Document
Gorski et al 2020_Phage Therapy… PDF Document
Furfaro et al 2018_Bacteriophage Teraphy… PDF Document
Chang et al 2022_Bacteriophage-Mediated Control of Biofilms… PDF Document
D’Accolti et al 2023_Potential Use of a Combined Bacteriophage-Probiotic Sanitation… PDF Document
Brives & Pourraz 2020_Phage Terapy… PDF Document
Hitchcock et al 2023_Current Clinical Lanscape… PDF Document