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.

REGISTRATION IS NOW OPEN (see below)

A CALL FOR CONTRIBUTIONS IS ALSO OPEN (see below)

REGISTRATION IS FREE BUT MANDATORY

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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. 

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To register: first click on "My registration" (left column, top). Then register using your sciencesconf account (create one if need be).

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The exact venue in Lyon will be specified at a later date, as we intend to adjust it according to the number of registrants.

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Assembly of the program is on-going, but confirmed invited speakers include:

• Xiang Zhou, University of Michigan, Ann Arbor, USA
• Per Uhlén, Karolinska Institute, Stockholm, Sweden
• 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 program will feature 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!

Call for contributions

We solicit the submission of contributed talks and live sessions to be considered for presentation at the symposium, related :

• to the development of new AI or ML approaches for the analysis of single-cell, potentially spatial, transcriptomics, or
• to the application of AI or ML approaches in a new context related to single-cell, potentially spatial, transcriptomics

Submissions will be selected by the program committee (see below). 

A) Contributed talks: the slots for contributed talks will be 15 min + 5 min questions.

B) Contributed live sessions: live demos of application packages for concrete illustration of use cases. Each live session will last 10 min, questions included.

Submission Format

Contributed talks or live sessions are to be submitted online, after the registration process (click on "My submissions", left column, top after login to your account).

For both types of submissions, please provide a short abstract describing the topics of your talk or session, together with a link to your code repository for live sessions. 

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