VIB Hackathon on spatial omics tools and methods

Abstract

During a three-day hackathon, work was performed on various topics within the field of spatial omics data analysis. The topics were organized in five workgroups and included benchmarking, pipelines, spatial transcriptomics, spatial proteomics, spatial multi-omics and cell-cell communication. Most tools and methods were considered in the context of the Python ecosystem for spatial (SpatialData) and single-cell (scverse) data analysis.

Authors 39

1. Benjamin Rombaut

   Ghent University · VIB-UGent Center for Inflammation Research · VIB.AI

   Affiliation as printed

   Data Mining and Modelling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium

   Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

   VIB Center for AI and Computational Biology, Ghent, Belgium

2. Lotte Pollaris

   Ghent University · VIB-UGent Center for Inflammation Research · VIB.AI

   Affiliation as printed

   Data Mining and Modelling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium

   Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

   VIB Center for AI and Computational Biology, Ghent, Belgium

3. Chananchida Sang-aram

   Ghent University · VIB-UGent Center for Inflammation Research · VIB.AI

   Affiliation as printed

   Data Mining and Modelling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium

   Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

   VIB Center for AI and Computational Biology, Ghent, Belgium

4. Michiel Ver Cruysse

   VIB-UGent Center for Inflammation Research · VIB.AI

   Affiliation as printed

   Data Mining and Modelling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium

   VIB Center for AI and Computational Biology, Ghent, Belgium

5. Robrecht Cannoodt

   Ghent University · VIB-UGent Center for Inflammation Research

   Affiliation as printed

   Data Mining and Modelling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium

   Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

6. Frank Vernaillen
   Affiliation as printed

   VIB Spatial Catalyst 5 Data Intuitive, Lebbeke, Belgium

7. Arne Defauw
   Affiliation as printed

   VIB Spatial Catalyst 5 Data Intuitive, Lebbeke, Belgium

8. Julien Mortier
   Affiliation as printed

   VIB Spatial Catalyst 5 Data Intuitive, Lebbeke, Belgium

9. Mayar Ali

   Helmholtz Munich · Institute of Computational Biology

   Affiliation as printed

   Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Munich, Neuherberg, Germany

   Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany

10. Kresimir Bestak

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany

11. Quentin Blampey

    Université Paris-Saclay · CentraleSupélec

    Affiliation as printed

    MICS Laboratory, CentraleSupélec, Paris-Saclay University, Paris, France

12. Michele Bortolomeazzi

    German Cancer Research Center

    Affiliation as printed

    German Cancer Research Center (DKFZ), Heidelberg, Germany

    ScOpen Lab,

13. Paula Maglio Cauhy

    UK Dementia Research Institute · University College London

    Affiliation as printed

    UK Dementia Research Institute, University College London, WC1E 6BT, London, UK

14. Miraj Cetin

    German Cancer Research Center

    Affiliation as printed

    Systems Immunology and Single-Cell Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany

15. Daniel Dimitrov

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany

16. Francesca Drummer

    Helmholtz Munich · LMU Klinikum · Institut für Schlaganfall- und Demenzforschung · Institute of Computational Biology · Ludwig-Maximilians-Universität München

    Affiliation as printed

    Institute for Stroke and Dementia Research, Klinikum Der Universität München, Ludwig-Maximilians-Universität, Munich, Germany

    Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany

17. Lorenzo Giordani

    Inserm · Sorbonne Université · Institut de Myologie · Centre de Recherche en Myologie

    Affiliation as printed

    Sorbonne Université, INSERM UMRS 974, Association Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France

18. Aroj Hada

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    AI-Health Innovation Cluster, Heidelberg, Germany

    Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany

19. Luuk Harbers

    VIB-KU Leuven Center for Cancer Biology

    Affiliation as printed

    VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium

20. Migual A. Ibarra-Arellano

    Heidelberg University · University Hospital Heidelberg

    Affiliation as printed

    Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany

21. Paul Kießling Aachen

    Universitätsklinikum Aachen · RWTH Aachen University

    Affiliation as printed

    RWTH Aachen, University Hospital

22. Laurens Lehner

    Helmholtz Munich · Institute of Computational Biology

    Affiliation as printed

    Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany

23. Susmita Mandal

    Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Institute of Pathology at Charité -Universitätsmedizin Berlin, Germany

24. Benedetta Manzato Aachen Department of Human Genetics

    Leiden University Medical Center

    Affiliation as printed

    Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands

25. Luca Marconato

    European Molecular Biology Laboratory

    Affiliation as printed

    European Molecular Biology Laboratorium, Heidelberg, Germany

26. Claudio Novella-Rausell Aachen Department of Human Genetics

    Leiden University Medical Center

    Affiliation as printed

    Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands

27. Anastasiia Okhtienko

    Technical University of Munich

    Affiliation as printed

    Institute of Virology, Technical University of Munich, Munich, Germany

28. Giovanni Palla

    Helmholtz Munich · Institute of Computational Biology

    Affiliation as printed

    Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany

29. Daryna Pikulska Aachen

    Universitätsklinikum Aachen · RWTH Aachen University

    Affiliation as printed

    RWTH Aachen, University Hospital

30. Carlos Ariel Pulido-Vicuña
31. Guillaume Sacchetti

    VIB-KU Leuven Center for Cancer Biology · KU Leuven

    Affiliation as printed

    KU Leuven, Leuven, Belgium

    Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology,

    VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium

32. Alexander Sudy

    Berlin Institute of Health at Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Center of Digital Health, Berlin Institute of Health at Charité -Universitätsmedizin Berlin, Germany

33. Lotte Van de Vreken

    VIB-UGent Center for Plant Systems Biology

    Affiliation as printed

    VIB-UGent Center for Plant Systems Biology, Ghent, Belgium

34. Wouter-Michiel Vierdag

    European Molecular Biology Laboratory

    Affiliation as printed

    European Molecular Biology Laboratorium, Heidelberg, Germany

35. Vladislav Vlasov

    Vrije Universiteit Brussel

    Affiliation as printed

    Brain and Systems Immunology Lab, Brussels Center for Immunology, Vrije Universiteit Brussel

36. Sai Nirmayi Yasa

    VIB-KU Leuven Center for Cancer Biology

    Affiliation as printed

    VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium

    VIB Hackathon on spatial omics Ghent, Belgium, 2024

37. Estella Yixing Dong

    Centre Hospitalier Universitaire Vaudois · University of Lausanne

    Affiliation as printed

    Biomedical Data Science Center, Lausanne University Hospital;

    University of Lausanne, Lausanne, Switzerland

38. Ruth Seurinck

    Ghent University · VIB-UGent Center for Inflammation Research · VIB.AI

    Affiliation as printed

    Data Mining and Modelling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium

    Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

    VIB Center for AI and Computational Biology, Ghent, Belgium

39. Yvan Saeys

    Ghent University · VIB-UGent Center for Inflammation Research · VIB.AI

    Affiliation as printed

    Data Mining and Modelling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium

    Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

    VIB Center for AI and Computational Biology, Ghent, Belgium