On in-vitro and in-vivo IVUS data fusion. - Francesco Ciompi; Oriol Pujol; Oriol Rodriguez-Leor; Angel Serrano Vida; Josepa Mauri; Petia Radeva (CCIA, 2009)

Enhancing In-Vitro IVUS Data for Tissue Characterization. - Francesco Ciompi; Oriol Pujol; Oriol Rodriguez-Leor; Carlo Gatta; Angel Serrano Vida; Petia Radeva (IbPRIA, 2009)

Toward Robust Myocardial Blush Grade Estimation in Contrast Angiography. - Carlo Gatta; Juan Diego Gomez Valencia; Francesco Ciompi; Oriol Rodriguez-Leor; Petia Radeva (IbPRIA, 2009)

ECOC Random Fields for Lumen Segmentation in Radial Artery IVUS Sequences. - Francesco Ciompi; Oriol Pujol; Eduard Fernández-Nofrerías; Josepa Mauri; Petia Radeva (MICCAI (1), 2009)

A Meta-Learning Approach to Conditional Random Fields Using Error-Correcting Output Codes. - Francesco Ciompi; Oriol Pujol; Petia Radeva (ICPR, 2010)

Ultrasonographic plaque characterization using a Rayleigh mixture model. - José C. R. Seabra; João M. Sanches; Francesco Ciompi; Petia Radeva (ISBI, 2010)

Real-Time Gating of IVUS Sequences Based on Motion Blur Analysis: Method and Quantitative Validation. - Carlo Gatta; Simone Balocco; Francesco Ciompi; Rayyan Hemetsberger; Oriol Rodriguez-Leor; Petia Radeva (MICCAI (2), 2010)

Automatic Branching Detection in IVUS Sequences. - Marina Alberti; Carlo Gatta; Simone Balocco; Francesco Ciompi; Oriol Pujol; Joana Silva; Xavier Carrillo; Petia Radeva (IbPRIA, 2011)

Combining Growcut and Temporal Correlation for IVUS Lumen Segmentation. - Simone Balocco; Carlo Gatta; Francesco Ciompi; Oriol Pujol; Xavier Carrillo; Josepa Mauri; Petia Radeva (IbPRIA, 2011)

A Holistic Approach for the Detection of Media-Adventitia Border in IVUS. - Francesco Ciompi; Oriol Pujol; Carlo Gatta; Xavier Carrillo; Josepa Mauri; Petia Radeva (MICCAI (3), 2011)

Rayleigh Mixture Model for Plaque Characterization in Intravascular Ultrasound. - José C. R. Seabra; Francesco Ciompi; Oriol Pujol; Josepa Mauri; Petia Radeva; João M. Sanches (IEEE Trans. Biomed. Eng., 2011)

HoliMAb: A holistic approach for Media-Adventitia border detection in intravascular ultrasound. - Francesco Ciompi; Oriol Pujol; Carlo Gatta; Marina Alberti; Simone Balocco; Xavier Carrillo; Josepa Mauri-Ferre; Petia Radeva (Medical Image Anal., 2012)

Automatic Bifurcation Detection in Coronary IVUS Sequences. - Marina Alberti; Simone Balocco; Carlo Gatta; Francesco Ciompi; Oriol Pujol; Joana Silva; Xavier Carrillo; Petia Radeva (IEEE Trans. Biomed. Eng., 2012)

Learning to Detect Stent Struts in Intravascular Ultrasound. - Francesco Ciompi; Rui Hua; Simone Balocco; Marina Alberti; Oriol Pujol; Carles Caus; Josepa Mauri; Petia Radeva (IbPRIA, 2013)

Stent Shape Estimation through a Comprehensive Interpretation of Intravascular Ultrasound Images. - Francesco Ciompi; Simone Balocco; Carles Caus; Josepa Mauri; Petia Radeva (MICCAI (2), 2013)

Standardized evaluation methodology and reference database for evaluating IVUS image segmentation. - Simone Balocco; Carlo Gatta; Francesco Ciompi; Andreas Wahle; Petia Radeva; Stéphane G. Carlier; Gözde B. Ünal; Elias Sanidas; Josepa Mauri; Xavier Carrillo; Tomas Kovarnik; Ching-Wei Wang; et al. (Comput. Medical Imaging Graph., 2014)

Stacked Sequential Scale-SpaceTaylor Context. - Carlo Gatta; Francesco Ciompi (IEEE Trans. Pattern Anal. Mach. Intell., 2014)

ECOC-DRF: Discriminative random fields based on error correcting output codes. - Francesco Ciompi; Oriol Pujol; Petia Radeva (Pattern Recognit., 2014)

Off-the-shelf convolutional neural network features for pulmonary nodule detection in computed tomography scans. - Bram van Ginneken; Arnaud A. A. Setio; Colin Jacobs; Francesco Ciompi (ISBI, 2015)

Automatic detection of spiculation of pulmonary nodules in computed tomography images. - Francesco Ciompi; Colin Jacobs; Ernst Th. Scholten; Sarah J. van Riel; Mathilde M. W. Wille; Mathias Prokop; Bram van Ginneken (Computer-Aided Diagnosis, 2015)

Computer-aided detection of lung cancer: combining pulmonary nodule detection systems with a tumor risk prediction model. - Arnaud A. A. Setio; Colin Jacobs; Francesco Ciompi; Sarah J. van Riel; Mathilde Marie Winkler Wille; Asger Dirksen; Eva M. van Rikxoort; Bram van Ginneken (Computer-Aided Diagnosis, 2015)

Automatic classification of pulmonary peri-fissural nodules in computed tomography using an ensemble of 2D views and a convolutional neural network out-of-the-box. - Francesco Ciompi; Bartjan de Hoop; Sarah J. van Riel; Kaman Chung; Ernst Th. Scholten; Matthijs Oudkerk; Pim A. de Jong; Mathias Prokop; Bram van Ginneken (Medical Image Anal., 2015)

Bag-of-Frequencies: A Descriptor of Pulmonary Nodules in Computed Tomography Images. - Francesco Ciompi; Colin Jacobs; Ernst Th. Scholten; Mathilde M. W. Wille; Pim A. de Jong; Mathias Prokop; Bram van Ginneken (IEEE Trans. Medical Imaging, 2015)

Deep convolutional neural networks for automatic coronary calcium scoring in a screening study with low-dose chest CT. - Nikolas Leßmann; Ivana Isgum; Arnaud A. A. Setio; Bob D. de Vos; Francesco Ciompi; Pim A. de Jong; Matthijs Oudkerk; W. P. Th. M. Mali; Max A. Viergever; Bram van Ginneken (Computer-Aided Diagnosis, 2016)

Towards automatic pulmonary nodule management in lung cancer screening with deep learning. - Francesco Ciompi; Kaman Chung; Sarah J. van Riel; Arnaud Arindra Adiyoso Setio; Paul K. Gerke; Colin Jacobs; Ernst Th. Scholten; Cornelia Schaefer-Prokop; Mathilde M. W. Wille; Alfonso Marchiano; Ugo Pastorino; Mathias Prokop; et al. (CoRR, 2016)

Automatic Pulmonary Artery-Vein Separation and Classification in Computed Tomography Using Tree Partitioning and Peripheral Vessel Matching. - Jean-Paul Charbonnier; Monique Brink; Francesco Ciompi; Ernst Th. Scholten; Cornelia Schaefer-Prokop; Eva M. van Rikxoort (IEEE Trans. Medical Imaging, 2016)

Pulmonary Nodule Detection in CT Images: False Positive Reduction Using Multi-View Convolutional Networks. - Arnaud Arindra Adiyoso Setio; Francesco Ciompi; Geert Litjens 001; Paul K. Gerke; Colin Jacobs; Sarah J. van Riel; Mathilde Marie Winkler Wille; Matiullah Naqibullah; Clara I. Sánchez; Bram van Ginneken (IEEE Trans. Medical Imaging, 2016)

Comparison of different methods for tissue segmentation in histopathological whole-slide images. - Péter Bándi; Rob van de Loo; Milad Intezar; Daan Geijs; Francesco Ciompi; Bram van Ginneken; Jeroen van der Laak; Geert Litjens 001 (ISBI, 2017)

The importance of stain normalization in colorectal tissue classification with convolutional networks. - Francesco Ciompi; Oscar Geessink; Babak Ehteshami Bejnordi; Gabriel Silva de Souza; Alexi Baidoshvili; Geert Litjens 001; Bram van Ginneken; Iris Nagtegaal; Jeroen van der Laak (ISBI, 2017)

Intra-coronary Stent Localization in Intravascular Ultrasound Sequences, A Preliminary Study. - Simone Balocco; Francesco Ciompi; Juan Rigla; Xavier Carrillo; Josepa Mauri; Petia Radeva (CVII-STENT/LABELS@MICCAI, 2017)

Improving airway segmentation in computed tomography using leak detection with convolutional networks. - Jean-Paul Charbonnier; Eva M. van Rikxoort; Arnaud A. A. Setio; Cornelia Schaefer-Prokop; Bram van Ginneken; Francesco Ciompi (Medical Image Anal., 2017)

A survey on deep learning in medical image analysis. - Geert Litjens 001; Thijs Kooi; Babak Ehteshami Bejnordi; Arnaud Arindra Adiyoso Setio; Francesco Ciompi; Mohsen Ghafoorian; Jeroen A. W. M. van der Laak; Bram van Ginneken; Clara I. Sánchez (Medical Image Anal., 2017)

Automatic Detection of Tumor Budding in Colorectal Carcinoma with Deep Learning. - John-Melle Bokhorst; Lucia Rijstenberg; Danny Goudkade; Iris Nagtegaal; Jeroen van der Laak; Francesco Ciompi (COMPAY/OMIA@MICCAI, 2018)

H&E stain augmentation improves generalization of convolutional networks for histopathological mitosis detection. - David Tellez; Maschenka Balkenhol; Nico Karssemeijer; Geert Litjens 001; Jeroen van der Laak; Francesco Ciompi (Digital Pathology, 2018)

Predicting breast tumor proliferation from whole-slide images: the TUPAC16 challenge. - Mitko Veta; Yujing J. Heng; Nikolas Stathonikos; Babak Ehteshami Bejnordi; Francisco Beca; Thomas Wollmann; Karl Rohr; Manan A. Shah; Dayong Wang; Mikaël Rousson; Martin Hedlund; David Tellez; et al. (CoRR, 2018)

Whole-Slide Mitosis Detection in H&E Breast Histology Using PHH3 as a Reference to Train Distilled Stain-Invariant Convolutional Networks. - David Tellez; Maschenka Balkenhol; Irene Otte-Höller; Rob van de Loo; Rob Vogels; Peter Bult; Carla Wauters; Willem Vreuls; Suzanne Mol; Nico Karssemeijer; Geert Litjens 001; Jeroen van der Laak; et al. (IEEE Trans. Medical Imaging, 2018)

Learning from sparsely annotated data for semantic segmentation in histopathology images. - John-Melle Bokhorst; Hans Pinckaers; Peter van Zwam; Iris Nagtegaal; Jeroen van der Laak; Francesco Ciompi (MIDL, 2019)

Needles in Haystacks: On Classifying Tiny Objects in Large Images. - Nick Pawlowski; Suvrat Bhooshan; Nicolas Ballas; Francesco Ciompi; Ben Glocker; Michal Drozdzal (CoRR, 2019)

Learning to detect lymphocytes in immunohistochemistry with deep learning. - Zaneta Swiderska-Chadaj; Hans Pinckaers; Mart van Rijthoven; Maschenka Balkenhol; Margarita Melnikova; Oscar Geessink; Quirine Manson; Mark Sherman 003; António Polónia; Jeremy Parry; Mustapha Abubakar; Geert Litjens 001; et al. (Medical Image Anal., 2019)

Quantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathology. - David Tellez; Geert Litjens 001; Péter Bándi; Wouter Bulten; John-Melle Bokhorst; Francesco Ciompi; Jeroen van der Laak (Medical Image Anal., 2019)

Predicting breast tumor proliferation from whole-slide images: The TUPAC16 challenge. - Mitko Veta; Yujing J. Heng; Nikolas Stathonikos; Babak Ehteshami Bejnordi; Francisco Beca; Thomas Wollmann; Karl Rohr; Manan A. Shah; Dayong Wang; Mikaël Rousson; Martin Hedlund; David Tellez; et al. (Medical Image Anal., 2019)

Virtual Staining for Mitosis Detection in Breast Histopathology. - Caner Mercan; G. C. A. M. Mooij; David Tellez; Johannes Lotz 002; Nick Weiss; Marcel van Gerven; Francesco Ciompi (ISBI, 2020)

Extending Unsupervised Neural Image Compression With Supervised Multitask Learning. - David Tellez; Diederik Höppener; Cornelis Verhoef; Dirk J. Grünhagen; Pieter Nierop; Michal Drozdzal; Jeroen van der Laak; Francesco Ciompi (MIDL, 2020)

A deep learning approach to assess the predominant tumor growth pattern in whole-slide images of lung adenocarcinoma. - Zaneta Swiderska-Chadaj; Karolina Nurzynska; Bartlomiej Grala; Katrien Grunberg; Lieke van der Woude; Monika Looijen-Salamon; Ann E. Walts; Tomasz Markiewicz; Francesco Ciompi; Arkadiusz Gertych (Digital Pathology, 2020)

Virtual staining for mitosis detection in Breast Histopathology. - Caner Mercan; Germonda Reijnen-Mooij; David Tellez Martin; Johannes Lotz 002; Nick Weiss; Marcel van Gerven; Francesco Ciompi (CoRR, 2020)

Automated Scoring of Nuclear Pleomorphism Spectrum with Pathologist-level Performance in Breast Cancer. - Caner Mercan; Maschenka Balkenhol; Roberto Salgado; Mark Sherman 003; Philippe Vielh; Willem Vreuls; António Polónia; Hugo M. Horlings; Wilko Weichert; Jodi M. Carter; Peter Bult; Matthias Christgen; et al. (CoRR, 2020)

Multi-Scale Task Multiple Instance Learning for the Classification of Digital Pathology Images with Global Annotations. - Niccolò Marini; Sebastian Otálora; Francesco Ciompi; Gianmaria Silvello; Stefano Marchesin 001; Simona Vatrano; Genziana Buttafuoco; Manfredo Atzori; Henning Müller (COMPAY@MICCAI, 2021)

A Partial Label-Based Machine Learning Approach For Cervical Whole-Slide Image Classification: The Winning TissueNet Solution*. - Rutger H. J. Fick; Brice Tayart; Capucine Bertrand; Solene Chan-Lang; Tina Rey; Francesco Ciompi; Cyprien Tilmant; Isabelle Farré; Saima Ben Hadj (EMBC, 2021)

Neural image compression for non-small cell lung cancer subtype classification in H&E stained whole-slide images. - Witali Aswolinskiy; David Tellez; Gabriel Raya; Lieke van der Woude; Monika Looijen-Salamon; Jeroen van der Laak; Katrien Grunberg; Francesco Ciompi (Digital Pathology, 2021)

Few-shot weakly supervised detection and retrieval in histopathology whole-slide images. - Mart van Rijthoven; Maschenka Balkenhol; Manfredo Atzori; Peter Bult; Jeroen van der Laak; Francesco Ciompi (Digital Pathology, 2021)

Quantifying the Scanner-Induced Domain Gap in Mitosis Detection. - Marc Aubreville; Christof Bertram; Mitko Veta; Robert Klopfleisch; Nikolas Stathonikos; Katharina Breininger; Natalie D. ter Hoeve; Francesco Ciompi; Andreas Maier 001 (CoRR, 2021)

Automated risk classification of colon biopsies based on semantic segmentation of histopathology images. - John-Melle Bokhorst; Iris D. Nagtegaal; Filippo Fraggetta; Simona Vatrano; Wilma Mesker; Michael Vieth; Jeroen van der Laak; Francesco Ciompi (CoRR, 2021)

Multi_Scale_Tools: A Python Library to Exploit Multi-Scale Whole Slide Images. - Niccolò Marini; Sebastian Otálora; Damian Podareanu; Mart van Rijthoven; Jeroen van der Laak; Francesco Ciompi; Henning Müller; Manfredo Atzori (Frontiers Comput. Sci., 2021)

HookNet: Multi-resolution convolutional neural networks for semantic segmentation in histopathology whole-slide images. - Mart van Rijthoven; Maschenka Balkenhol; Karina Silina; Jeroen van der Laak; Francesco Ciompi (Medical Image Anal., 2021)

Neural Image Compression for Gigapixel Histopathology Image Analysis. - David Tellez; Geert Litjens 001; Jeroen van der Laak; Francesco Ciompi (IEEE Trans. Pattern Anal. Mach. Intell., 2021)

Editorial Computational Pathology. - Francesco Ciompi; Mitko Veta; Jeroen van der Laak; Nasir M. Rajpoot (IEEE J. Biomed. Health Informatics, 2021)

Mitosis domain generalization in histopathology images - The MIDOG challenge. - Marc Aubreville; Nikolas Stathonikos; Christof A. Bertram; Robert Klopfleisch; Natalie D. ter Hoeve; Francesco Ciompi; Frauke Wilm; Christian Marzahl; Taryn A. Donovan; Andreas K. Maier; Jack Breen; Nishant Ravikumar; et al. (CoRR, 2022)

Seeded iterative clustering for histology region identification. - Eduard Chelebian; Francesco Ciompi; Carolina Wählby (CoRR, 2022)

Unleashing the potential of digital pathology data by training computer-aided diagnosis models without human annotations. - Niccolò Marini; Stefano Marchesin 001; Sebastian Otálora; Marek Wodzinski; Alessandro Caputo; Mart van Rijthoven; Witali Aswolinskiy; John-Melle Bokhorst; Damian Podareanu; Edyta Petters; Svetla Boytcheva; Genziana Buttafuoco; et al. (npj Digit. Medicine, 2022)

Abstract: the MIDOG Challenge 2021 - Mitosis Domain Generalization in Histopathology Images. - Marc Aubreville; Nikolas Stathonikos; Christof A. Bertram; Robert Klopfleisch; Natalie D. ter Hoeve; Francesco Ciompi; Frauke Wilm; Christian Marzahl; Taryn A. Donovan; Andreas K. Maier; Mitko Veta; Katharina Breininger (Bildverarbeitung für die Medizin, 2023)

nnUNet meets pathology: Bridging the gap for application to whole slide images and computational biomarkers. - Joey Spronck; Thijs Gelton; Leander van Eekelen; Joep Bogaerts; Leslie Tessier; Mart van Rijthoven; Lieke van der Woude; Michel van den Heuvel; Willemijn Theelen; Jeroen van der Laak; Francesco Ciompi (MIDL, 2023)

LYSTO: The Lymphocyte Assessment Hackathon and Benchmark Dataset. - Yiping Jiao; Jeroen van der Laak; Shadi Albarqouni; Zhang Li; Tao Tan; Abhir Bhalerao; Jiabo Ma; Jiamei Sun; Johnathon Pocock; Josien P. W. Pluim; Navid Alemi Koohbanani; Raja Muhammad Saad Bashir; et al. (CoRR, 2023)

Mitosis domain generalization in histopathology images - The MIDOG challenge. - Marc Aubreville; Nikolas Stathonikos; Christof A. Bertram; Robert Klopfleisch; Natalie D. ter Hoeve; Francesco Ciompi; Frauke Wilm; Christian Marzahl; Taryn A. Donovan; Andreas K. Maier; Jack Breen; Nishant Ravikumar; et al. (Medical Image Anal., 2023)

Histopathobiome - integrating histopathology and microbiome data via multimodal deep learning. - Agata Polejowska; Annemarie Boleij; Francesco Ciompi (COMPAY@MICCAI, 2024)

Scoring Tumor-Infiltrating Lymphocytes in breast DCIS: A guideline-driven artificial intelligence approach. - Matteo Pozzi; Natalie Klubickova; Michela Campora; Frédérique Meeuwsen; Joey Spronck; Carlijn M. Lems; Michelle Stegeman; Leslie Tessier; Mattia Barbareschi; Jeroen van der Laak; Giuseppe Jurman; Francesco Ciompi (COMPAY@MICCAI, 2024)

Benchmarking Hierarchical Image Pyramid Transformer for the Classification of Colon Biopsies and Polyps Histopathology Images. - Nohemí Sofia León Contreras; Clément Grisi; Witali Aswolinskiy; Simona Vatrano; Filippo Fraggetta; Iris Nagtegaal; Marina D'Amato; Francesco Ciompi (ISBI, 2024)

Color Deconvolution for Color-Agnostic and Cross-Modality Analysis of Immunohistochemistry Whole-Slide Images with Deep Learning. - Carlijn M. Lems; Daan J. Geijs; John-Melle Bokhorst; Maxime Sülter; Leander van Eekelen; Francesco Ciompi (ISBI, 2024)

"HoVer-UNet": Accelerating Hovernet with Unet-Based Multi-Class Nuclei Segmentation Via Knowledge Distillation. - Cristian Tommasino; Cristiano Russo; Antonio Maria Rinaldi; Francesco Ciompi (ISBI, 2024)

Hitchhiker's guide to cancer-associated lymphoid aggregates in histology images: manual and deep learning-based quantification approaches. - Karina Silina; Francesco Ciompi (CoRR, 2024)

Uncertainty-guided annotation enhances segmentation with the human-in-the-loop. - Nadieh Khalili; Joey Spronck; Francesco Ciompi; Jeroen van der Laak; Geert Litjens 001 (CoRR, 2024)

Multimodal representations of biomedical knowledge from limited training whole slide images and reports using deep learning. - Niccolò Marini; Stefano Marchesin 001; Marek Wodzinski; Alessandro Caputo; Damian Podareanu; Bryan Cardenas Guevara; Svetla Boytcheva; Simona Vatrano; Filippo Fraggetta; Francesco Ciompi; Gianmaria Silvello; Henning Müller; et al. (Medical Image Anal., 2024)

DEPICTER: Deep representation clustering for histology annotation. - Eduard Chelebian; Christophe Avenel; Francesco Ciompi; Carolina Wählby (Comput. Biol. Medicine, 2024)

LYSTO: The Lymphocyte Assessment Hackathon and Benchmark Dataset. - Yiping Jiao; Jeroen van der Laak; Shadi Albarqouni; Zhang Li; Tao Tan; Abhir Bhalerao; Shenghua Cheng; Jiabo Ma; John Pocock; Josien P. W. Pluim; Navid Alemi Koohbanani; Raja Muhammad Saad Bashir; et al. (IEEE J. Biomed. Health Informatics, 2024)

The DRAGON benchmark for clinical NLP. - Joeran S. Bosma; Koen Dercksen; Luc Builtjes; Romain André; Christian Roest; Stefan J. Fransen; Constant R. Noordman; Mar Navarro-Padilla; Judith Lefkes; Natália Alves; Max J. J. de Grauw; Leander van Eekelen; et al. (npj Digit. Medicine, 2025)

"No negatives needed": weakly-supervised regression for interpretable tumor detection in whole-slide histopathology images. - Marina D'Amato; Jeroen van der Laak; Francesco Ciompi (CoRR, 2025)

A tissue and cell-level annotated H&E and PD-L1 histopathology image dataset in non-small cell lung cancer. - Joey Spronck; Leander van Eekelen; Dominique van Midden; Joep Bogaerts; Leslie Tessier; Valerie Dechering; Muradije Demirel-Andishmand; Gabriel Silva de Souza; Roland Nemeth; Enrico Munari; Giuseppe Bogina; Ilaria Girolami; et al. (CoRR, 2025)