Modules

Module 1 : RECONSTRUCTION AND STATISTICAL ANALYSIS OF THE CELL LINEAGE TREE

FROM 3D+TIME IMAGING OF DEVELOPING MODEL ORGANISMS

Fri, 5 July 2013

 

Module leader: Nadine Peyrieras (CNRS, Gif-sur-Yvette)

Other teachers: N. Peyrieras team & BioEmergences platform task force (Emmanuel Faure, Barbara Rizzi, Julien Dumont, Julien Delile, Gaëlle Recher; CNRS, Gif-sur-Yvette); Pierre Suret (PhLAM, Lille)

6 hours of courses (2 teachers)

  • Engineering embryos for multicolor in vivo 3D+time imaging
  •  Multimodal and multiscale in vivo and in toto 3D+time imaging of developing model organisms
  • -Pipelining the algorithmic reconstruction of digital specimens

Workshops (3 teachers)

  • Mounting embryos (zebrafish, sea urchin, mouse) for in vivo 3D+time imaging
  • SPIM/DSLM and MLSM multicolor in vivo 3D+time imaging for the cell lineage reconstruction

Data processing and analysis (2 teachers)

  • SPIM/DSLM multiviews fusion
  • Data processing for nucleus center detection cell tracking and shapes segmentation
  • Digital specimens visualization and validation
  • Data analysis, cell clonal analysis, statistical analysis,
  • Biomechanical modeling and parameters space exploration

Module 2 : DYNAMICS OF MEMBRANE PROTEINS IN PLANT CELLS

 

Fri, 5 July 2013

 

Module leader: Béatrice Satiat-Jeunemaître (CNRS, Gif-sur-Yvette)

Other teachers: Beatrice Satiat-Jeunemaître team & Imagif Cell Biology Pole task force (Spencer Brown, Jim Dompierre, Sébastien Bellow, Claire Boulogne, ISV/Imagif, CNRS Gif-sur-Yvette); Samantha Vernhettes (IJPB, Versailles)

6 hours of courses (4 teachers)

  • Plant cell compartmentation and associated molecular machineries: an overview
  • Cell wall morphogenesis and trafficking events at the cell surface
  • Tracking of Morphogenesis of endomembrane compartments
  • Membranes and Microtubules
  • Tips and Tricks in plant cell Bio-Imaging
  • Choice of the optical system according to the biological question

Workshops (5 teachers, 12 hours)

  • Tags and markers for plant cells (immunocytochemistry, stable and transient expressions)
  • FRAP
  • TIRF and Super-resolution approaches in plants
  • Measurement and data analysis for FLIM
  • Correlative microscopy
  • Image analyses

Data processing and analysis (2 teachers, 4 hours)

  • Unsupervised machine learning for comparison and classification of signal behavior
  • Common Courses or Worshops or Data reading/processing with other modules

Module 3 : REAL TIME KINASE ACTIVITY MEASUREMENTS OF CELL CYCLE REGULATORS IN CELLULO AND IN EMBRYO

 

Fri, 5 July 2013

 

Module leaders: Olivier Gavet (Institut Curie/ UPMC, Paris); Franck Riquet (Univ Lille1, Lille)

Other teachers: Pierre Vincent (CNRS – UMR 7102, Paris), Elvire Guiot (CNRS – UMR 7102, Paris), Fabienne Merola (Univ Paris Sud, Orsay), Marc Tramier (UMR 6290 CNRS, Rennes), Aymeric Leray (CNRS- BCF IRI USR3078, Villeneuve d’Ascq),

– Common Courses or Worshops or Data reading/processing with other modules

6 hours of courses (6 teachers)

  • Introduction to Biosensing (P. Vincent)
  • Introduction to cell cycle regulation
  •  Dynamic of MPF activity during entry into mitosis (O. Gavet)
  •  Dynamics of MAPK/ERK in cell cycle context (F.Riquet)
  • Design and Optimization of Genetically Encoded KARs (F.Riquet)
  • FRET Measurements: Methods and Instrumentation (A. Leray & M. Tramier)
  • Biophysics of fluorophores (F. Merola)

Workshops (5 teachers)

  • Measurement of biological activities using genetically encoded biosensors by fluorescence intensity and lifetime-based imaging methods in cellulo and in a tissue context
  • Embryo mounting approaches depending on the biological characteristics and presentation of imaging set-ups

Data reading and processing (3 teachers)

Presentation of the different analysis strategies as a function of imaging methods

  • Raw and reconstructed data visualization and quantification
  • Analysis of data in embryos

Module 4 : MOLECULAR DYNAMICS AND INTERACTIONS FOR STUDYING TRANSCRIPTION COMPLEX ASSEMBLIES IN LIVE CELLS

 

Fri, 5 July 2013

 

Module leaders: Aymeric Leray (CNRS- BCF IRI USR3078, Villeneuve d’Ascq), Marc Tramier (UMR 6290 CNRS,Rennes)

Other teachers: Sandrine Lêvéque-Fort (CLUPS/ISMO, Orsay); Gaétan Herbomel (Rennes); Mariano Gonzalez Pisfil (Villeneuve d’Ascq), Catherine Souchier (Grenoble) and Laurent Héliot (Villeneuve d’Ascq)Objectives:

The main objective of this tutorial is to present and describe the protocols used for studying the interactions and molecular dynamics in living cells. The participants will learn how to employ appropriate techniques and analysis methods specifically developed for extracting the molecular dynamics information obtained from complementary techniques at different time and space scales. Complexes involved in transcriptional regulation will be used as supports for exploring the different techniques for molecular dynamics studies.

Keys words: Molecular dynamics, FRET, FLIM, FastFLIM, FCS, FCCS, single particle detections (SPT-PALM), Molecular dynamic analysis and modeling,

6 hours of courses (2 teachers)

  • Introduction to the studies of molecular dynamics and interactions: a biological perspective
  • Introduction to the tools for the investigation of molecular dynamics in live cells (FRAP, FCS, SPT): concepts, comparison and complementarities
  • Introduction to the tools for the investigation of protein-protein interactions in live cells (FRET by FLIM, two-color FCS): concepts, comparison and complementarities
  • Presentation of the strategies for the analysis of raw data and modelisation

Workshops (2 teachers)

Studies of molecular dynamics and interactions by using FRAP, FRET/FLIM, FCS, two-color FCS, SPT-PALM

Data reading and processing (2 teachers)Use of the analysis strategies on datasets acquired by the participants

Module 5 : super-resolution imaging

 

Fri, 5 July 2013

Module 6 : FROM BIOIMAGE PROCESSING TO BIO-IMAGE INFORMATICS FOR TWO STUDY CASES IN CELL BIOLOGY

 

Fri, 5 July 2013

 

Module leader: Charles Kervrann (INRIA, Rennes)

Other teachers (to be confirmed): J. Boulanger (CNRS Institut Curie, Paris), Thomas Walter (Ecole des Mines, Institut Curie, Paris), Patrick Bouthemy (INRIA Rennes), Perrine Paul-Gilloteaux (CNRS, Institut Curie, Paris), Thierry Pecot (INRIA Rennes), Prenom Nom (Bio-Image Group, Institut Pasteur)

Objectives: application of image processing and machine learning techniques for deciphering processes and mechanisms in cell biology.

Background: some experience in image processing, applied mathematics and computer science

Tools:

  • Image processing software: ImageJ, ICY
  • Computer Science: CImg, Python, C++, Java
  • Applied mathematics: R, Matlab

Organization:

Data and biological study cases (N0 teachers)

  • Mitocheck data and cell division phenotype analysis
  • Spatial location of genes and transcription factors
  • Vesicle trafficking and membrane transport analysis

Basics in image processing (N1 teachers)

  • Introduction to software and computer science tools
  • Introduction to image data, storage and algorithms for fluorescence microscopy

Inverse problems and tracking problems in fluorescence microscopy (N2 teachers)

  • Low-level image processing: deconvolution and denoising
  • Object detection and segmentation
  • Motion analysis, registration and object tracking

Phenotypes clustering, machine learning and classification (N3 teachers)

  • Introduction to image descriptors and dimension reduction
  • Basics in clustering and classification of descriptors
  • Machine learning and optimization methods for bio-image informatics

Workshop and applications (N4 teachers)

  • Presentation of workflows and demonstration of algorithms
  • Experiments on biological study cases
  • Visualization and analysis of classification results

References: Ateliers MiFoBio (P. Paul-Gilloteaux, J. Boulanger), Cours EMBO (T. Walter, P. Paul-Gilloteaux,Prenom Nom (Bio-Image Group, Institut Pasteur)), BIAT 2011 (J. Boulanger), Cours Telecom Physique Strasbourg (T. Walter, J. Boulanger, C. Kervrann, P. Bouthemy)