Towards Spatial Correspondence between Specimen and In-vivo Breast Imaging. - Thomy Mertzanidou; John H. Hipwell; Mehmet Dalmis; Bram Platel; Jeroen van der Laak; Ritse Mann; Nico Karssemeijer; Peter Bult; David J. Hawkes (Digital Mammography / IWDM, 2014)

Quantitative analysis of stain variability in histology slides and an algorithm for standardization. - Babak Ehteshami Bejnordi; Nadya Timofeeva; Irene Otte-Höller; Nico Karssemeijer; Jeroen A. W. M. van der Laak (Digital Pathology, 2014)

A multi-scale superpixel classification approach to the detection of regions of interest in whole slide histopathology images. - Babak Ehteshami Bejnordi; Geert Litjens 001; Meyke Hermsen; Nico Karssemeijer; Jeroen A. W. M. van der Laak (Digital Pathology, 2015)

Automated detection of prostate cancer in digitized whole-slide images of H and E-stained biopsy specimens. - Geert Litjens 001; Babak Ehteshami Bejnordi; Nadya Timofeeva; G. Swadi; Iringo Kovacs; Christina A. Hulsbergen van de Kaa; Jeroen van der Laak (Digital Pathology, 2015)

Minimum slice spacing required to reconstruct 3D shape for serial sections of breast tissue for comparison with medical imaging. - Sara Reis; Björn Eiben; Thomy Mertzanidou; John H. Hipwell; Meyke Hermsen; Jeroen van der Laak; Sarah E. Pinder; Peter Bult; David J. Hawkes (Digital Pathology, 2015)

Variational Weakly Supervised Gaussian Processes. - Melih Kandemir; Manuel Haußmann; Ferran Diego; Kumar T. Rajamani; Jeroen van der Laak; Fred A. Hamprecht (BMVC, 2016)

Whole Mastectomy Volume Reconstruction from 2D Radiographs and Its Mapping to Histology. - Thomy Mertzanidou; John H. Hipwell; Sara Reis; Babak Ehteshami Bejnordi; Meyke Hermsen; Mehmet Dalmis; Suzan Vreemann; Bram Platel; Jeroen van der Laak; Nico Karssemeijer; Ritse Mann; Peter Bult; et al. (Digital Mammography / IWDM, 2016)

A generic nuclei detection method for histopathological breast images. - Henning Kost; André Homeyer; Peter Bult; Maschenka C. A. Balkenhol; Jeroen A. W. M. van der Laak; Horst K. Hahn (Digital Pathology, 2016)

A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry. - Bonnie Nijhof; Anna Castells-Nobau; Louis Wolf; Jolanda M. Scheffer-de Gooyert; Ignacio Monedero; Laura Torroja; Lluís Coromina; Jeroen A. W. M. van der Laak; Annette Schenck (PLoS Comput. Biol., 2016)

Automated Detection of DCIS in Whole-Slide H&E Stained Breast Histopathology Images. - Babak Ehteshami Bejnordi; Maschenka Balkenhol; Geert Litjens 001; Roland Holland; Peter Bult; Nico Karssemeijer; Jeroen A. W. M. van der Laak (IEEE Trans. Medical Imaging, 2016)

Stain Specific Standardization of Whole-Slide Histopathological Images. - Babak Ehteshami Bejnordi; Geert Litjens 001; Nadya Timofeeva; Irene Otte-Höller; André Homeyer; Nico Karssemeijer; Jeroen A. W. M. van der Laak (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)

Deep learning-based assessment of tumor-associated stroma for diagnosing breast cancer in histopathology images. - Babak Ehteshami Bejnordi; Jimmy Lin; Ben Glass; Maeve Mullooly; Gretchen L. Gierach; Mark E. Sherman; Nico Karssemeijer; Jeroen van der Laak; Andrew H. Beck (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)

Evaluation of tongue squamous cell carcinoma resection margins using ex-vivo MR. - Stefan C. A. Steens; Elise M. Bekers; Willem L. J. Weijs; Geert J. S. Litjens; Andor Veltien; Arie Maat; Guido B. van den Broek; Jeroen A. W. M. van der Laak; Jurgen J. Fütterer; Christina A. Hulsbergen van de Kaa; Matthias A. W. Merkx; Robert P. Takes (Int. J. Comput. Assist. Radiol. Surg., 2017)

Context-aware stacked convolutional neural networks for classification of breast carcinomas in whole-slide histopathology images. - Babak Ehteshami Bejnordi; Guido C. A. Zuidhof; Maschenka Balkenhol; Meyke Hermsen; Peter Bult; Bram van Ginneken; Nico Karssemeijer; Geert Litjens 001; Jeroen van der Laak (CoRR, 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)

Stain normalization of histopathology images using generative adversarial networks. - Farhad Ghazvinian Zanjani; Svitlana Zinger; Babak Ehteshami Bejnordi; Jeroen A. W. M. van der Laak; Peter H. N. de With (ISBI, 2018)

Structure Instance Segmentation in Renal Tissue: A Case Study on Tubular Immune Cell Detection. - Thomas de Bel; Meyke Hermsen; Geert Litjens 001; Jeroen van der Laak (COMPAY/OMIA@MICCAI, 2018)

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)

Automatic segmentation of histopathological slides of renal tissue using deep learning. - Thomas de Bel; Meyke Hermsen; Bart Smeets; Luuk Hilbrands; Jeroen van der Laak; Geert Litjens 001 (Digital Pathology, 2018)

Automated segmentation of epithelial tissue in prostatectomy slides using deep learning. - Wouter Bulten; Christina A. Hulsbergen van de Kaa; Jeroen van der Laak; Geert J. S. Litjens (Digital Pathology, 2018)

Automatic color unmixing of IHC stained whole slide images. - Daan J. Geijs; Milad Intezar; Jeroen A. W. M. van der Laak; Geert J. S. Litjens (Digital Pathology, 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)

Epithelium segmentation using deep learning in H&E-stained prostate specimens with immunohistochemistry as reference standard. - Wouter Bulten; Péter Bándi; Jeffrey Hoven; Rob van de Loo; Johannes Lotz 002; Nick Weiss; Jeroen van der Laak; Bram van Ginneken; Christina A. Hulsbergen van de Kaa; Geert Litjens 001 (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)

Stain-Transforming Cycle-Consistent Generative Adversarial Networks for Improved Segmentation of Renal Histopathology. - Thomas de Bel; Meyke Hermsen; Jesper Kers; Jeroen van der Laak; Geert Litjens 001 (MIDL, 2019)

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)

Automated Gleason Grading of Prostate Biopsies using Deep Learning. - Wouter Bulten; Hans Pinckaers; Hester van Boven; Robert Vink; Thomas de Bel; Bram van Ginneken; Jeroen van der Laak; Christina A. Hulsbergen van de Kaa; Geert Litjens 001 (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)

From Detection of Individual Metastases to Classification of Lymph Node Status at the Patient Level: The CAMELYON17 Challenge. - Péter Bándi; Oscar Geessink; Quirine Manson; Marcory Van Dijk; Maschenka Balkenhol; Meyke Hermsen; Babak Ehteshami Bejnordi; Byungjae Lee; Kyunghyun Paeng; Aoxiao Zhong; Quanzheng Li; Farhad Ghazvinian Zanjani; et al. (IEEE Trans. Medical Imaging, 2019)

Efficient Out-of-Distribution Detection in Digital Pathology Using Multi-Head Convolutional Neural Networks. - Jasper Linmans; Jeroen van der Laak; Geert Litjens 001 (MIDL, 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)

Artificial Intelligence Assistance Significantly Improves Gleason Grading of Prostate Biopsies by Pathologists. - Wouter Bulten; Maschenka Balkenhol; Jean-Joël Awoumou Belinga; Américo Brilhante; Asli Çakir; Xavier Farré; Katerina Geronatsiou; Vincent Molinié; Guilherme Pereira; Paromita Roy; Günter Saile; Paulo Salles; et al. (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)

Tailoring automated data augmentation to H&E-stained histopathology. - Khrystyna Faryna; Jeroen van der Laak; Geert Litjens 001 (MIDL, 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)

Computational Pathology: What is the way forward? - Jeroen A. W. M. van der Laak (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)

High-resolution Image Registration of Consecutive and Re-stained Sections in Histopathology. - Johannes Lotz 002; Nick Weiss; Jeroen van der Laak; Stefan Heldmann (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)

Residual cyclegan for robust domain transformation of histopathological tissue slides. - Thomas de Bel; John-Melle Bokhorst; Jeroen van der Laak; Geert Litjens 001 (Medical Image Anal., 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)

Detection of Prostate Cancer in Whole-Slide Images Through End-to-End Training With Image-Level Labels. - Hans Pinckaers; Wouter Bulten; Jeroen van der Laak; Geert Litjens 001 (IEEE Trans. Medical Imaging, 2021)

HyReCo - Hybrid re-stained and consecutive histological serial sections. - Jeroen van der Laak; Johannes Lotz 002; Nick Weiss; Stefan Heldmann (IEEE DataPort, 2021)

Domain adaptation strategies for cancer-independent detection of lymph node metastases. - Péter Bándi; Maschenka Balkenhol; Marcory Van Dijk; Bram van Ginneken; Jeroen van der Laak; Geert Litjens 001 (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)

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)

Hierarchical Vision Transformers for Context-Aware Prostate Cancer Grading in Whole Slide Images. - Clément Grisi; Geert Litjens 001; Jeroen van der Laak (CoRR, 2023)

Predictive uncertainty estimation for out-of-distribution detection in digital pathology. - Jasper Linmans; Stefan Elfwing; Jeroen van der Laak; Geert Litjens 001 (Medical Image Anal., 2023)

Continual learning strategies for cancer-independent detection of lymph node metastases. - Péter Bándi; Maschenka Balkenhol; Marcory Van Dijk; Michel Kok; Bram van Ginneken; Jeroen van der Laak; Geert Litjens 001 (Medical Image Anal., 2023)

Gigapixel end-to-end training using streaming and attention. - Stephan Dooper; Hans Pinckaers; Witali Aswolinskiy; Konnie M. Hebeda; Sofia Jarkman; Jeroen van der Laak; Geert Litjens 001 (Medical Image Anal., 2023)

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)

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)

Masked Attention as a Mechanism for Improving Interpretability of Vision Transformers. - Clément Grisi; Geert Litjens 001; Jeroen van der Laak (CoRR, 2024)

Improving Quality Control of Whole Slide Images by Explicit Artifact Augmentation. - Artur Jurgas; Marek Wodzinski; Marina D'Amato; Jeroen van der Laak; Manfredo Atzori; Henning Müller (CoRR, 2024)

Diffusion models for out-of-distribution detection in digital pathology. - Jasper Linmans; Gabriel Raya; Jeroen van der Laak; Geert Litjens 001 (Medical Image Anal., 2024)

The Latent Doctor Model for Modeling Inter-Observer Variability. - Jasper Linmans; Emiel Hoogeboom; Jeroen van der Laak; Geert Litjens 001 (IEEE J. Biomed. Health Informatics, 2024)

Automatic data augmentation to improve generalization of deep learning in H&E stained histopathology. - Khrystyna Faryna; Jeroen van der Laak; Geert Litjens 001 (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)

Deep learning-based histopathologic segmentation of peritubular capillaries in kidney transplant biopsies. - Dominique van Midden; Linda Studer; Meyke Hermsen; Eric J. Steenbergen; Jesper Kers; Nicolas Kozakowski; Zeljko Kikic; Luuk Hilbrands; Jeroen A. W. M. van der Laak (Comput. Biol. Medicine, 2025)

Hierarchical Vision Transformers for prostate biopsy grading: Towards bridging the generalization gap. - Clément Grisi; Kimmo Kartasalo; Martin Eklund; Lars Egevad; Jeroen van der Laak; Geert Litjens 001 (Medical Image Anal., 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)