At the Montefiore Institute (University of Liège, Belgium), we are researchers developing machine learning algorithms and big data software modules to make life easier for multidisciplinary teams who have to deal with very large images. We contribute to the Cytomine open-source project initiated by our research unit in 2010 and now managed by Cytomine cooperative (social enterprise).

The Cytomine software is a rich internet application using modern web technologies, databases, and machine learning to foster active and distributed collaboration and ease large-scale image exploitation. The software can be used by life scientists to help them better evaluate drug treatments or understand biological processes directly from whole-slide tissue images, by pathologists to share and ease their diagnosis, and by teachers and students for image-based training purposes (e.g. histology courses).

Our main research interests are:

  • Development of efficient workflows and novel algorithms (tree-based machine learning and deep learning) for object detection, recognition, and segmentation in very large images
  • Development of novel algorithms and web user interfaces for multimodal imaging data
  • Benchmarking of algorithms on realistic datasets
  • Development of novel algorithms for user behavior analytics
  • Applications in biomedical domain with a specific focus on digital pathology
  • Applications in any other domain with large sets of large images (geology, astronomy, art history, ...).

  • Here is an overview of our research results. In addition to our open-access scientific publications, these results are distributed through the Cytomine open-source software repository.

    • Image segmentation techniques for the quantification of whole tissue slides prepared with various protocols (Hematoxylin & Eosin staining, Immunohistochemistry, ...) (collaboration with laboratory of Tumor and Development Biology at GIGA).
      See e.g. Marée et al. ISBI 2014.

    • Workflows for sorting various types of cells, e.g. detect abnormal cells for early cytological diagnosis (collaboration with various labs).
      See e.g. Delga et al., Acta Cytologica 2014; Mormont et al., 2016.

    • Cell counting algorithms in specific regions of interests within tissues (collaborations with researchers at GIGA).
      See e.g. Rubens et al. (in preparation).

    • Image classification and object recognition algorithms for diagnostic of for phenotyping, e.g. in developmental and toxicological studies (collaboration with laboratory of Molecular Biology and Genetic Engineering at GIGA).
      See e.g. Marée et al., Pattern Recognition Letters 2016; ISBI 2016 ; Jeanray et al., PLOS One 2015.

    • Interest point detection algorithms for morphometric change measurements e.g. in developmental and toxicological studies (collaboration with laboratory of Molecular Biology and Genetic Engineering at GIGA).
      See e.g. IEEE TMI 2015; Vandaele et al. 2017 (accepted).

    • Applications in various domains (see publications).

    (15 Sept. 2017) Grégoire, Christopher, and Renaud are now working for Cytomine.coop, a social cooperative to manage the open-source community and to provide services on top of Cytomine open-source software. Learn more about their services and their open company philosophy on Cytomine.coop.

    (Sept. 2017) The first worldwide massive online course (MOOC) in french on histology is over. It was a great success ! It will come back next year. It was organized by University of Liege and the FUN platform. More info, course teaser, and registration.

    (May 2016) Thanks to Regional-IT, Daily Science, and Le 15e jour for press coverage of our project and open-source release party.

    (Jan. 2016) Our Cytomine paper is formally accepted for publication in Bioinformatics journal.
    Cytomine is now released under an open-source software license and available on Github (see instructions below).
    You can still request an account on our demo server.

    (Sept. 2014) A vulgarization of some our research is available on University of Liege Reflexions website

    (Oct. 2010) Cytomine kick-off.

    The main Cytomine publication is (Marée et al., 2016). We list here all related publications.

    We release our research results mainly through the Cytomine open-source software. To install and use it you can read installation instructions and its full documentation wiki (it includes guides for administrators, developers, and a Cytomine guide for end-users).
    Cytomine can be installed on large servers for large-scale studies but also on laptops for small-scale works. You can also check the Cytomine user guide to get access information on the demo server using default accounts.

    We kindly ask you to cite Cytomine website url (www.cytomine.be) and our main publication (Marée et al., Bioinformatics 2016) when you use our software in your own work.

    Raphaël Marée initiated the Cytomine research project in 2010, he now coordinates the Cytomine research and development activities @ULiège and he is a researcher in machine learning/big data/computer vision.

    Romain Mormont (PhD Student) is a researcher in machine learning (deep learning, interactive learning).

    Rémy Vandaele (PhD Student) is a researcher in machine learning (tree-based methods).

    Ulysse Rubens is a software developer (Cytomine modules and machine learning).

    Prof. Pierre Geurts and Prof. Louis Wehenkel are long-term machine learning collaborators.


    Previous contributors (from our team or students) include: Loic Rollus (2010-2015), Benjamin Stevens (2010-2014), Renaud Hoyoux (2014-2017, now at Cytomine cooperative), Gilles Louppe (2013), Jean-Michel Begon (2014), Pierre Ansen, Julien Confetti, Olivier Caubo, Thomas Vessiere, Laurent Vanosmael.

    For any questions related to our research activities or for potential research collaborations or internships @ ULiège, feel free to contact us:
    Raphaël Marée
    Quartier Polytech 1, 10, Allée de la découverte
    Montefiore Institute (B28)
    Tel. : +32 4 366 26 44

    For Cytomine open-source project issues, post an issue into the Cytomine Github repository.

    To ask for a specific demo account, to support the open-source project, or for service requests (e.g. installation, hosting, maintenance, trainings, specific software developments, slide scanning), please contact Cytomine cooperative.

    We are currently involved in the following projects:

  • NEUBIAS (2016-2020) funded by EU COST Action.
  • ADRIC (2017-2021) funded by Pole Mecatech, by Wallonia/DGO6.

  • Previous projects:

  • HISTOWEB (2014-2017) research grant n°1318185 funded by Wallonia/DGO6.
  • SMASH (2012-2014) research grant n°1217606 funded by Wallonia/DGO6.
  • CYTOMINE (2010-2016) research grant n°1017072 funded by Wallonia/DG06.
            Wallonia         University of Liege