15th-17th OCTOBER, 2025

A 2.5 DAY WORKSHOP on the use of artificial intelligence and machine learning of the analysis of single-cell spatial transcriptomics, in Lyon, France.

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The analysis of data from single-cell, potentially spatial, transcriptomics, increasingly relies on artificial intelligence (AI) or machine learning (ML) computer tools. Beyond the familiar clustering of single-cells, they promise to offer access to a wide spectrum of far-reaching biological information, including the inference of cell-cell interactions, lineage reconstructions or the 3d spatial organisation of the tissue.

The workshop will deliver both general introductions targeting the non-expert biologist who plans to start using these algorithms, and state-of-the-art methodology-oriented talks for a more expert audience. 

The Workshop will take place in the Conference Room of the

Science University Library of Université Claude Bernard Lyon 1 (BU Sciences)

on the Lyon La Doua Campus. 

Address:  Domaine de la Doua - 20 avenue Gaston Berger, 69622 Villeurbanne Cedex, France. GPS: 45.78203257421637, 4.870511781811795

 Lunches will be at the nearby Domus Restaurant (see the map below).

How to get there (see the map below):

• Access by train or plane
  • From Lyon St-Exupery (LYS) airport : Take the airport shuttle Rhone-Express to Lyon City Center. Exit at Part-Dieu train station.
  • From Part-Dieu train station: take Tramway line T1 for "IUT Feyssine" and exit at station "Université Lyon 1" or "Gaston Berger". 
  • From Perrache train station: Take metro line A (for "Laurent Bonnevay") and exit at Station "Charpennes". There, take Tramway line T1 (for "IUT Feyssine") and exit at station "Université Lyon 1" or "Gaston Berger". 
• Access by car: 
  • Arriving by the East By-Pass ("Rocade Est") : take exit 1B then exit "Croix Luizet". Follow "La Doua" then "Domaine Scientifique de la Doua"
  • Arriving by Laurent Bonnevay Boulevard: take exit 6 ("Porte de Croix Luizet"), then follow "Domaine Scientifique de la Doua"
• Public transportation in Lyon: www.tcl.fr
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The program of the workshop is available here and via the "Program" link top of the left column. 

Confirmed invited speakers:

• Xiang Zhou, University of Michigan, Ann Arbor, USA
• Genevieve Stein O’Brien, Johns Hopkins University, USA
• Sergio Sarnataro, Ecole Normale Supérieure, Lyon, France 
• Yvan Saeys, Ghent University, Belgium
• Marianna Rapsomaniki, Lausanne University Hospital, Switzerland 
• Franck Picard, Ecole Normale Supérieure, Lyon, France
• Guillaume Marcy, Université Claude Bernard Lyon 1, France
• Laura Cantini, Pasteur Institute, Paris, France
• Quentin Blampey, Paris-Saclay University, France

The workshop features both general introductory talks and expert-level methodology-oriented presentations. As well as live sessions demos of application packages for concrete illustration of use cases!

This event is organized by Université Claude Bernard Lyon 1, with support from the Spatial-Cell-ID national equipment.

Thanks to the wonderous work of its local program committee:

Hugues Berry, AIstroSight, Inria

Olivier Gandrillon, Lab. Biology and Modelling of the Cell

Guillaume Marcy, Lyon Neuroscience research Center 

Sophie Pantalacci, Lab. Biology and Modelling of the Cell 

Franck Picard, Lab. Biology and Modelling of the Cell  

Olivier Raineteau, Stem-cell & Brain Research Institute

Sergio Sarnataro, Spatial-Cell-ID 

Marie Sémon, Lab. Biology and Modelling of the Cell