D. Höppener, W. Aswolinskiy, Z. Qian, D. Tellez, P. Nierop, M. Starmans, I. Nagtegaal, M. Doukas, J. de Wilt, D. Grünhagen, J. van der Laak, P. Vermeulen, F. Ciompi and C. Verhoef, "Classifying histopathological growth patterns for resected colorectal liver metastasis with a deep learning analysis",
BJS Open,
2024;8.
A. Jurgas, M. Wodzinski, M. D'Amato, J. van der Laak, M. Atzori and H. Müller, "Improving quality control of whole slide images by explicit artifact augmentation",
Scientific Reports,
2024;14.
K. Faryna, L. Tessier, J. Retamero, S. Bonthu, P. Samanta, N. Singhal, S. Kammerer-Jacquet, C. Radulescu, V. Agosti, A. Collin, X. Farre', J. Fontugne, R. Grobholz, A. Hoogland, K. Leite, M. Oktay, A. Polonia, P. Roy, P. Salles, T. van der Kwast, J. van Ipenburg, J. van der Laak and G. Litjens, "Evaluation of AI-based Gleason grading algorithms "in the wild"",
Modern Pathology,
2024:100563.
J. An, Y. Wang, Q. Cai, G. Zhao, S. Dooper, G. Litjens and Z. Gao, "Transformer-Based Weakly Supervised Learning for Whole Slide Lung Cancer Image Classification",
IEEE Journal of Biomedical and Health Informatics,
2024:1-14.
A. Saha, J.S. Bosma, J. Twilt, B. van Ginneken, A. Bjartell, A. Padhani, D. Bonekamp, G. Villeirs, G. Salomon, G. Giannarini, J. Kalpathy-Cramer, J. Barentsz, K. Maier-Hein, M. Rusu, O. Rouviere, R. van den Bergh, V. Panebianco, V. Kasivisvanathan, N. Obuchowski, D. Yakar, M. Elschot, J. Veltman, J. Futterer, C. Noordman, I. Slootweg, C. Roest, S. Fransen, M. Sunoqrot, T. Bathen, D. Rouw, J. Immerzeel, J. Geerdink, C. van Run, M. Groeneveld, J. Meakin, A. Karagoz, A. Bone, A. Routier, A. Marcoux, C. Abi-Nader, C. Li, D. Feng, D. Alis, E. Karaarslan, E. Ahn, F. Nicolas, G. Sonn, I. Bhattacharya, J. Kim, J. Shi, H. Jahanandish, H. An, H. Kan, I. Oksuz, L. Qiao, M. Rohe, M. Yergin, M. Khadra, M. Seker, M. Kartal, N. Debs, R. Fan, S. Saunders, S. Soerensen, S. Moroianu, S. Vesal, Y. Yuan, A. Malakoti-Fard, A. Maciunien, A. Kawashima, A. de de Machadov, A. Moreira, A. Ponsiglione, A. Rappaport, A. Stanzione, A. Ciuvasovas, B. Turkbey, B. de Keyzer, B. Pedersen, B. Eijlers, C. Chen, C. Riccardo, D. Alis, E. Courrech Staal, F. Jaderling, F. Langkilde, G. Aringhieri, G. Brembilla, H. Son, H. Vanderlelij, H. Raat, I. Pikuniene, I. Macova, I. Schoots, I. Caglic, J. Zawaideh, J. Wallstrom, L. Bittencourt, M. Khurram, M. Choi, N. Takahashi, N. Tan, P. Franco, P. Gutierrez, P. Thimansson, P. Hanus, P. Puech, P. Rau, P. de Visschere, R. Guillaume, R. Cuocolo, R. Falcao, R. van Stiphout, R. Girometti, R. Briediene, R. Grigiene, S. Gitau, S. Withey, S. Ghai, T. Penzkofer, T. Barrett, V. Tammisetti, V. Logager, V. Cerny, W. Venderink, Y. Law, Y. Lee, M. de Rooij and H. Huisman, "Artificial intelligence and radiologists in prostate cancer detection on MRI (PI-CAI): an international, paired, non-inferiority, confirmatory study",
The Lancet Oncology,
2024;25(7):879-887.
E. Smeets, M. Trajkovic-Arsic, D. Geijs, S. Karakaya, M. van Zanten, L. Brosens, B. Feuerecker, M. Gotthardt, J. Siveke, R. Braren, F. Ciompi and E. Aarntzen, "Histology-Based Radiomics for [18F]FDG PET Identifies Tissue Heterogeneity in Pancreatic Cancer",
Journal of Nuclear Medicine,
2024:jnumed.123.266262.
P. Vendittelli, J. Bokhorst, E. Smeets, V. Kryklyva, L. Brosens, C. Verbeke and G. Litjens, "Automatic quantification of tumor-stroma ratio as a prognostic marker for pancreatic cancer",
PLOS ONE,
2024;19:e0301969.
R. Leon-Ferre, J. Carter, D. Zahrieh, J. Sinnwell, R. Salgado, V. Suman, D. Hillman, J. Boughey, K. Kalari, F. Couch, J. Ingle, M. Balkenhol, F. Ciompi, J. van der Laak and M. Goetz, "Automated mitotic spindle hotspot counts are highly associated with clinical outcomes in systemically untreated early-stage triple-negative breast cancer",
npj Breast Cancer,
2024;10.
V. Eekelen, Leander, J. Spronck, M. Looijen-Salamon, S. Vos, E. Munari, I. Girolami, A. Eccher, B. Acs, C. Boyaci, G. de Souza, M. Demirel-Andishmand, L. Meesters, D. Zegers, L. van der Woude, W. Theelen, M. van den Heuvel, K. Grünberg, B. van Ginneken, J. van der Laak and F. Ciompi, "Comparing deep learning and pathologist quantification of cell-level PD-L1 expression in non-small cell lung cancer whole-slide images",
Scientific Reports,
2024;14.
A. Vos, L. Pijnenborg, S. van Vliet, L. Kodach, F. Ciompi, R. van der Post, F. Simmer and I. Nagtegaal, "Biological background of colorectal polyps and carcinomas with heterotopic ossification: A national study and literature review",
Human Pathology,
2024;145:34-41.
L. Maier-Hein, A. Reinke, P. Godau, M. Tizabi, F. Buettner, E. Christodoulou, B. Glocker, F. Isensee, J. Kleesiek, M. Kozubek, M. Reyes, M. Riegler, M. Wiesenfarth, A. Kavur, C. Sudre, M. Baumgartner, M. Eisenmann, D. Heckmann-Nötzel, T. Rädsch, L. Acion, M. Antonelli, T. Arbel, S. Bakas, A. Benis, M. Blaschko, M. Cardoso, V. Cheplygina, B. Cimini, G. Collins, K. Farahani, L. Ferrer, A. Galdran, B. van Ginneken, R. Haase, D. Hashimoto, M. Hoffman, M. Huisman, P. Jannin, C. Kahn, D. Kainmueller, B. Kainz, A. Karargyris, A. Karthikesalingam, F. Kofler, A. Kopp-Schneider, A. Kreshuk, T. Kurc, B. Landman, G. Litjens, A. Madani, K. Maier-Hein, A. Martel, P. Mattson, E. Meijering, B. Menze, K. Moons, H. Müller, B. Nichyporuk, F. Nickel, J. Petersen, N. Rajpoot, N. Rieke, J. Saez-Rodriguez, C. Sánchez, S. Shetty, M. van Smeden, R. Summers, A. Taha, A. Tiulpin, S. Tsaftaris, B. Van Calster, G. Varoquaux and P. Jäger, "Metrics reloaded: recommendations for image analysis validation",
Nature Methods,
2024;21:195-212.
A. Reinke, M. Tizabi, M. Baumgartner, M. Eisenmann, D. Heckmann-Nötzel, A. Kavur, T. Rädsch, C. Sudre, L. Acion, M. Antonelli, T. Arbel, S. Bakas, A. Benis, F. Buettner, M. Cardoso, V. Cheplygina, J. Chen, E. Christodoulou, B. Cimini, K. Farahani, L. Ferrer, A. Galdran, B. van Ginneken, B. Glocker, P. Godau, D. Hashimoto, M. Hoffman, M. Huisman, F. Isensee, P. Jannin, C. Kahn, D. Kainmueller, B. Kainz, A. Karargyris, J. Kleesiek, F. Kofler, T. Kooi, A. Kopp-Schneider, M. Kozubek, A. Kreshuk, T. Kurc, B. Landman, G. Litjens, A. Madani, K. Maier-Hein, A. Martel, E. Meijering, B. Menze, K. Moons, H. Müller, B. Nichyporuk, F. Nickel, J. Petersen, S. Rafelski, N. Rajpoot, M. Reyes, M. Riegler, N. Rieke, J. Saez-Rodriguez, C. Sánchez, S. Shetty, R. Summers, A. Taha, A. Tiulpin, S. Tsaftaris, B. Van Calster, G. Varoquaux, Z. Yaniv, P. Jäger and L. Maier-Hein, "Understanding metric-related pitfalls in image analysis validation",
Nature Methods,
2024;21:182-194.
E. Chelebian, C. Avenel, F. Ciompi and C. Wählby, "DEPICTER: Deep representation clustering for histology annotation",
Computers in Biology and Medicine,
2024;170:108026.
K. Faryna, J. van der Laak and G. Litjens, "Automatic data augmentation to improve generalization of deep learning in H&E stained histopathology",
Computers in Biology and Medicine,
2024;170:108018.
D. Schouten, J. van der Laak, B. van Ginneken and G. Litjens, "Full resolution reconstruction of whole-mount sections from digitized individual tissue fragments",
Scientific Reports,
2024;14.
C. Jahangir, D. Page, G. Broeckx, C. Gonzalez, C. Burke, C. Murphy, J. Reis-Filho, A. Ly, P. Harms, R. Gupta, M. Vieth, A. Hida, M. Kahila, Z. Kos, P. van Diest, S. Verbandt, J. Thagaard, R. Khiroya, K. Abduljabbar, G. Acosta Haab, B. Acs, S. Adams, J. Almeida, I. Alvarado-Cabrero, F. Azmoudeh-Ardalan, S. Badve, N. Baharun, E. Bellolio, V. Bheemaraju, K. Blenman, L. Mendonça Botinelly Fujimoto, O. Burgues, A. Chardas, M. Cheang, F. Ciompi, L. Cooper, A. Coosemans, G. Corredor, F. Dantas Portela, F. Deman, S. Demaria, S. Dudgeon, M. Elghazawy, C. Fernandez-Martín, S. Fineberg, S. Fox, J. Giltnane, S. Gnjatic, P. Gonzalez-Ericsson, A. Grigoriadis, N. Halama, M. Hanna, A. Harbhajanka, S. Hart, J. Hartman, S. Hewitt, H. Horlings, Z. Husain, S. Irshad, E. Janssen, T. Kataoka, K. Kawaguchi, A. Khramtsov, U. Kiraz, P. Kirtani, L. Kodach, K. Korski, G. Akturk, E. Scott, A. Kovács, A. L\aenkholm , C. Lang-Schwarz, D. Larsimont, J. Lennerz, M. Lerousseau, X. Li, A. Madabhushi, S. Maley, V. Manur Narasimhamurthy, D. Marks, E. McDonald, R. Mehrotra, S. Michiels, D. Kharidehal, F. Minhas, S. Mittal, D. Moore, S. Mushtaq, H. Nighat, T. Papathomas, F. Penault-Llorca, R. Perera, C. Pinard, J. Pinto-Cardenas, G. Pruneri, L. Pusztai, N. Rajpoot, B. Rapoport, T. Rau, J. Ribeiro, D. Rimm, A. Vincent-Salomon, J. Saltz, S. Sayed, E. Hytopoulos, S. Mahon, K. Siziopikou, C. Sotiriou, A. Stenzinger, M. Sughayer, D. Sur, F. Symmans, S. Tanaka, T. Taxter, S. Tejpar, J. Teuwen, E. Thompson, T. Tramm, W. Tran, J. van der Laak, G. Verghese, G. Viale, N. Wahab, T. Walter, Y. Waumans, H. Wen, W. Yang, Y. Yuan, J. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, E. Specht Stovgaard, R. Salgado, W. Gallagher and A. Rahman, "Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer",
The Journal of Pathology,
2024;262:271-288.
J. Linmans, G. Raya, J. van der Laak and G. Litjens, "Diffusion models for out-of-distribution detection in digital pathology",
Medical Image Analysis,
2024;93:103088.
D. Geijs, S. Dooper, W. Aswolinskiy, L. Hillen, A. Amir and G. Litjens, "Detection and subtyping of basal cell carcinoma in whole-slide histopathology using weakly-supervised learning",
Medical Image Analysis,
2024;93:103063.
M. van Rijthoven, S. Obahor, F. Pagliarulo, V. den Maries, P. Schraml, H. Moch, J. van der Laak, F. Ciompi and K. Silina, "Multi-resolution deep learning characterizes tertiary lymphoid structures and their prognostic relevance in solid tumors",
Communications Medicine,
2024.
S. Vermorgen, T. Gelton, P. Bult, H. Kusters-Vandevelde, J. Hausnerová, K. de Van Vijver, B. Davidson, I. Stefansson, L. Kooreman, A. Qerimi, J. Huvila, B. Gilks, M. Shahi, S. Zomer, C. Bartosch, J. Pijnenborg, J. Bulten, F. Ciompi and M. Simons, "Endometrial Pipelle Biopsy Computer-Aided Diagnosis: A Feasibility Study",
Modern Pathology,
2024;37:100417.
G. Solé-Guardia, M. Luijten, B. Geenen, J. Claassen, G. Litjens, F. de Leeuw, M. Wiesmann and A. Kiliaan, "Three-dimensional identification of microvascular pathology and neurovascular inflammation in severe white matter hyperintensity: a case report",
Scientific Reports,
2024;14.
M. Ilié, V. Lake, E. de Alava, S. Bonin, S. Chlebowski, A. Delort, E. Dequeker, R. Al-Dieri, A. Diepstra, O. Carpén, C. Eloy, A. Fassina, F. Fend, P. Fernandez, G. Gorkiewicz, S. Heeke, R. Henrique, G. Hoefler, P. Huertas, M. Hummel, K. Kashofer, J. van der Laak, R. de Pablos, F. Schmitt, E. Schuuring, G. Stanta, W. Timens, B. Westphalen and P. Hofman, "Standardization through education of molecular pathology: a spotlight on the European Masters in Molecular Pathology",
Virchows Archiv,
2024;485:761-775.
N. Marini, S. Marchesin, M. Wodzinski, A. Caputo, D. Podareanu, B. Guevara, S. Boytcheva, S. Vatrano, F. Fraggetta, F. Ciompi, G. Silvello, H. Müller and M. Atzori, "Multimodal representations of biomedical knowledge from limited training whole slide images and reports using deep learning",
Medical Image Analysis,
2024;97:103303.
F. Khoraminia, F. de Jong, F. Akram, G. Litjens, M. Jansen, A. Gonzalez, D. Lichtenburg, A. Stubbs, N. Khalili and T. Zuiverloon, "Abstract B004: Deep learning unveils molecular footprints in histology: predicting molecular subtypes from bladder cancer histology slides",
Clinical Cancer Research,
2024;30:B004-B004.
G. Solé-Guardia, M. Luijten, E. Janssen, R. Visch, B. Geenen, B. Küsters, J. Claassen, G. Litjens, F. de Leeuw, M. Wiesmann and A. Kiliaan, "Deep learning-based segmentation in MRI-(immuno)histological examination of myelin and axonal damage in normal-appearing white matter and white matter hyperintensities",
Brain Pathology,
2024.
C. Grisi, G. Litjens and J. van der Laak, "Masked Attention as a Mechanism for Improving Interpretability of Vision Transformers",
arXiv:2404.18152,
2024.
K. Silina and F. Ciompi, "Hitchhiker's guide to cancer-associated lymphoid aggregates in histology images: manual and deep learning-based quantification approaches",
arXiv:2403.04142,
2024.
N. Khalili, J. Spronck, F. Ciompi, J. van der Laak and G. Litjens, "Uncertainty-guided annotation enhances segmentation with the human-in-the-loop",
arXiv:2404.07208,
2024.
L. Borras Ferris, S. Püttmann, N. Marini, S. Vatrano, F. Fragetta, A. Caputo, F. Ciompi, M. Atzori and H. Müller, "A full pipeline to analyze lung histopathology images",
Medical Imaging 2024: Digital and Computational Pathology,
2024.
C. Tommasino, C. Russo, A. Rinaldi and F. Ciompi, ""HoVer-UNet": Accelerating Hovernet with Unet-Based Multi-Class Nuclei Segmentation Via Knowledge Distillation",
2024 IEEE International Symposium on Biomedical Imaging (ISBI),
2024:1-4.
K. Faryna, J. van der Laak and G. Litjens, "Towards embedding stain-invariance in convolutional neural networks for H&E-stained histopathology",
Medical Imaging 2024: Digital and Computational Pathology,
2024.
N. Contreras, C. Grisi, W. Aswolinskiy, S. Vatrano, F. Fraggetta, I. Nagtegaal, M. D'Amato and F. Ciompi, "Benchmarking Hierarchical Image Pyramid Transformer for the Classification of Colon Biopsies and Polyps Histopathology Images",
2024 IEEE International Symposium on Biomedical Imaging (ISBI),
2024:1-4.
S. Püttmann, L. Borras Ferris, N. Marini, W. Aswolinsky, S. Vatrano, F. Fragetta, I. Nagtegaal, C. van der Post, F. Ciompi, M. Atzori, C. Friedrich and H. Müller, "Automated classification of celiac disease in histopathological images: a multi-scale approach",
Medical Imaging 2024: Computer-Aided Diagnosis,
2024.
C. Lems, D. Geijs, J. Bokhorst, M. Sülter, L. van Eekelen and F. Ciompi, "Color Deconvolution for Color-Agnostic and Cross-Modality Analysis of Immunohistochemistry Whole-Slide Images with Deep Learning",
2024 IEEE International Symposium on Biomedical Imaging (ISBI),
2024:1-4.
L. Tessier, C. Gonzalez-Gonzalo, D. Tellez, W. Bulten and M. van der Laak, "Large-scale validation of AI-assisted mitosis counting in breast cancer",
European Congress on Digital Pathology,
2024.
M. D'Amato, A. Boden, P. van Diest, N. Stathonikos, H. Hoefling, F. Versaevel, G. Litjens, F. Ciompi and J. van der Laak, "Automated Quality Control in Histopathology through Artifact Segmentation",
European Congress on Digital Pathology,
2024.
D. Schouten, N. Khalili, J. van der Laak and G. Litjens, "Full Resolution Three-Dimensional Reconstruction of Non-Serial Prostate Whole-Mounts: Pilot Validation and Initial Results",
European Congress on Digital Pathology,
2024.
A. Polejowska, F. Ayatollahi, A. Erdogan, F. Ciompi and A. Boleij, "Spirochetosis detection in colon histopathology images via fine-tuning and boosting techniques using foundation models",
Medical Imaging with Deep Learning 2024,
2024.
S. de Jong, M. Groot, R. Verhoeven, E. van der Heijden and F. Ciompi, "Weakly supervised lung cancer detection on label-free intraoperative microscopy with higher harmonic generation",
Medical Imaging with Deep Learning 2024,
2024.
M. Stegeman, G. Bogina, E. Munari, J. van der Laak and F. Ciompi, "Vision Language Foundation Models for Scoring Tumor-Infiltrating Lymphocytes in Breast Cancer through Text Prompting",
European Congress on Digital Pathology,
2024.
D. Midden, L. Studer, M. Hermsen, N. Kozakowski, J. Kers, L. Hilbrands and J. van der Laak, "Deep learning-based segmentation of peritubular capillaries in kidney transplant biopsies.",
European Congress on Digital Pathology,
2024.
L. Eekelen, G. den Heuvel, L. Studer, J. Spronck, K. Grünberg, D. Zegers, J. der Laak, M. den Heuvel and F. Ciompi, "Immunotherapy response prediction for non-small cell lung cancer is improved by using cell-graphs of the tumor microenvironment",
European Congress on Digital Pathology,
2024.
D. Midden, L. Studer, M. Hermsen, A. Farris, J. Kers, L. Hilbrands and J. van der Laak, "Introducing the MONKEY Challenge: Machine-learning for Optimal detection of iNflammatory cells in the KidnEY",
European Congress on Digital Pathology,
2024.
B. Sturm, P. Lock, J. Westerga, W. Blokx and J. van der Laak, "Deep learning predicts the effect of neo-adjuvant chemotherapy for patients with triple negative breast cancer",
European Congress on Digital Pathology,
2024.