Publications

Have also a look at the list of external publications we know where collaborators or external teams were using the Cytomine software or algorithm variants.
Navdeep Kumar, Raphaël Marée, Pierre Geurts, Marc Muller (2023). Recent Advances in Bioimage Analysis Methods for Detecting Skeletal Deformities in Biomedical and Aquaculture Fish Species. Biomolecules.

Open Access (MDPI)

Allyson Fries, Marie Pirotte, Laurent Vanhee, Pierre Bonnet, Pascale Quatresooz, Christophe Debruyne, Raphaël Marée, Valérie Defaweux (2023). Validating instructional design and predicting student performance in histology education- Using machine learning via virtual microscopy.. Anatomical Sciences Education.

Open Access (ORBI)

Romain Mormont, Mehdi Testouri, Raphaël Marée, Pierre Geurts (2022). Relieving pixel-wise labeling effort for pathology image segmentation with self-training. ECCV workshop on AI-enabled medical image analysis: Digital Pathology & Radiology/COVID19.

Open Access (ORBI)

Navdeep Kumar, Claudia Di Biagio, Zachary Dellacqua, Ratish Raman, Arianna Martini, Clara Boglione, Marc Muller, Pierre Geurts, Raphaël Marée (2022). Empirical Evaluation of Deep Learning Approaches for Landmark Detection in Fish Bioimages. ECCV workshop on BioImage Computing.

Open Access (ORBI) Code

Navdeep Kumar, Alessio Carletti, Paulo Gavaia, Marc Muller, Leonor Cancela, Pierre Geurts, Raphaël Marée (2021). Deep Learning approaches for Head and Operculum Segmentation in Zebrafish Microscopy Images. CAIP 2021.

Code

Perrine Paul-Gilloteaux, Sébastien Tosi, Jean-Karim Hériché, Alban Gaignard, Hervé Ménager, Raphaël Marée, Volker Baecker, Anna Klemm, Matúš Kalaš, Chong Zhang, Kota Miura, Julien Colombelli (2021). Bioimage analysis workflows: community resources to navigate through a complex ecosystem. F1000Research.

PDF Cite DOI

Ulysse Rubens, Romain Mormont, Lassi Paavolainen, Volker Bäcker, Benjamin Pavie, Leandro A. Scholz, Gino Michiels, Martin Maška, Devrim Ünay, Graeme Ball, Renaud Hoyoux, Rémy Vandaele, Ofra Golani, Stefan G. Stanciu, Natasa Sladoje, Perrine Paul-Gilloteaux, Raphaël Marée, Sébastien Tosi (2020). BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows. Patterns.

PDF Cite DOI

Romain Mormont, Pierre Geurts, Raphaël Marée (2020). Multi-task pre-training of deep neural networks for digital pathology. IEEE Journal of Biomedical and Health Informatics.

PDF Cite DOI Code

Raphaël Marée (2019). Open Practices and Resources for Collaborative Digital Pathology. Frontiers in Medicine.

PDF Cite DOI

Ulysse Rubens, Renaud Hoyoux, Laurent Vanosmael, Mehdy Ouras, Maxime Tasset, Christopher Hamilton, Rémi Longuespée, Raphaël Marée (2019). Cytomine: Toward an Open and Collaborative Software Platform for Digital Pathology Bridged to Molecular Investigations. PROTEOMICS – Clinical Applications.

PDF Cite DOI Open Access (ORBI)

Laurent Vanhee, Ulysse Rubens, Alodie Weatherspoon, Laurence Pesesse, Pascale Quatresooz, Sylvie Multon, Valérie Defaweux, Pierre Geurts, Raphaël Marée (2018). New Cytomine modules for user behavior analytics in digital pathology. 14th European Congress on Digital Pathology, Journal of Pathology Informatics.

PDF Cite DOI

Romain Mormont, Pierre Geurts, Raphaël Marée (2018). Comparison of Deep Transfer Learning Strategies for Digital Pathology. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW).

PDF Cite DOI Open Access (ORBI)

Rémy Vandaele, Jessica Aceto, Marc Muller, Frédérique Péronnet, Vincent Debat, Ching-Wei Wang, Cheng-Ta Huang, Sébastien Jodogne, Philippe Martinive, Pierre Geurts, Raphaël Marée (2018). Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach. Scientific Reports.

PDF Cite DOI

Raphaël Marée (2017). The need for careful data collection for pattern recognition in digital pathology. Journal of Pathology Informatics.

PDF Cite DOI

Romain Mormont, Jean-Michel Begon, Renaud Hoyoux, Raphaël Marée (2016). SLDC: an open-source workflow for object detection in multi-gigapixel images. The 25th Belgian-Dutch Conference on Machine Learning (Benelearn).

PDF Cite Code

Raphaël Marée, Pierre Geurts, Louis Wehenkel (2016). Towards generic image classification using tree-based learning: An extensive empirical study. Pattern Recognition Letters.

PDF Cite DOI Open Access (ORBI)

Raphaël Marée, Stéphane Dallongeville, Jean-Christophe Olivo-Marin, Vannary Meas-Yedid (2016). An approach for detection of glomeruli in multisite digital pathology. 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI).

PDF Cite DOI Open Access (ORBI)

Raphaël Marée, Loic Rollus, Benjamin Stevens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts, Louis Wehenkel (2016). Collaborative analysis of multi-gigapixel imaging data using Cytomine. Bioinformatics.

PDF Cite DOI

Ching-Wei Wang, Cheng-Ta Huang, Meng-Che Hsieh, Chung-Hsing Li, Sheng-Wei Chang, Wei-Cheng Li, Rémy Vandaele, Raphaël Marée, Sébastien Jodogne, Pierre Geurts, Cheng Chen, Guoyan Zheng, Chengwen Chu, Hengameh Mirzaalian, Ghassan Hamarneh, Tomaz Vrtovec, Bulat Ibragimov (2015). Evaluation and Comparison of Anatomical Landmark Detection Methods for Cephalometric X-Ray Images: A Grand Challenge. IEEE Transactions on Medical Imaging.

PDF Cite DOI Open Access (ORBI)

Raphaël Marée, Loic Rollus, Benjamin Stevens, Gilles Louppe, Olivier Caubo, Natacha Rocks, Sandrine Bekaert, Didier Cataldo, Louis Wehenkel (2014). A hybrid human-computer approach for large-scale image-based measurements using web services and machine learning. 2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI).

PDF Cite DOI

Raphaël Marée, Benjamin Stevens, Loic Rollus, Natacha Rocks, Xavier Moles Lopez, Isabelle Salmon, Didier Cataldo, Louis Wehenkel (2013). A rich internet application for remote visualization and collaborative annotation of digital slides in histology and cytology. Diagnostic Pathology.

PDF Cite DOI

Raphaël Marée, Louis Wehenkel, Pierre Geurts (2013). Extremely Randomized Trees and Random Subwindows for Image Classification, Annotation, and Retrieval. Decision Forests for Computer Vision and Medical Image Analysis.

Cite