francescociompi.com | 2025
* shared authorship
M. D'Amato, J. van der Laak and F. Ciompi, ""No negatives needed": weakly-supervised regression for interpretable tumor detection in whole-slide histopathology images", arXiv:2502.21109, 2025. [Preprint]
Witali Aswolinskiy, Rachel S van der Post, Michiel Simons, Enrico Munari, Michela Campora, Carla Baronchelli, Laura Ardighieri, Simona Vatrano, Iris Nagtegaal, Jeroen van der Laak, Francesco Ciompi, "Attention-based whole-slide image compression achieves pathologist-level pre-screening of multi-organ routine histopathology biopsies", https://doi.org/10.1101/2024.12.17.24319180, 2025. [Preprint]
M. van Rijthoven, W. Aswolinskiy, L. Tessier, M. Balkenhol, J. Bogaerts, D. Drubay, L. Blesa, D. Peeters, E. Stovgaard, A. L\aenkholm , H. Haynes, L. Craciun, D. Larsimont, M. Amgad, L. Cooper, C. de Kock, V. Dechering, J. Lotz, N. Weiss, M. van Bockstal, C. Galant, E. Lips, H. Horlings, J. Wesseling, L. Mulder, S. van den Belt, K. Weber, P. Jank, C. Denkert, E. Munari, G. Bogina, C. Russ, A. Lemm, S. Loi, J. Douglas, S. Michiels, H. Joensuu, M. Fan, D. Lee, J. Ye, K. Byun, J. Kim, S. Xu, Z. Ji, F. Xie, J. Kuang, X. Chen, L. Chen, A. Tsakiroglou, R. Byers, M. Fergie, V. Ramanathan, A. Martel, A. Shephard, S. Ahmed Raza, M. Jahanifar, N. Rajpoot, S. Cho, D. Kim, H. Jang, C. Park, K. Kim, R. Donders, S. Maurits, M. Groeneveld, A. Mickan, J. Meakin, B. van Ginneken, R. Salgado, J. van der Laak and F. Ciompi, "Tumor-infiltrating lymphocytes in breast cancer through artificial intelligence: biomarker analysis from the results of the TIGER challenge", https://doi.org/10.1101/2025.02.28.25323078, 2025. [Preprint]
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.
N. Khalili and F. Ciompi, "Scaling data toward pan-cancer foundation models", Trends in Cancer, 2024;10:871-872.
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.
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.
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.
E. Chelebian, C. Avenel, F. Ciompi and C. Wählby, "DEPICTER: Deep representation clustering for histology annotation", Computers in Biology and Medicine, 2024;170:108026. [Code]
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.
L. van Eekelen, J. Spronck, M. Looijen-Salamon, S. Vos, E. Munari, I. Girolami, A. Eccher, B. Acs, C. Boyaci, G. Silva de Souza, M. Demirel-Andishmand, L. Dulce 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", Nature Scientific Reports 14, 7136 (2024).
S. Vermorgen, T. Gelton, P. Bult, H. V.N. Kusters-Vandevelde, J. Hausnerová, K. Van de Vijver, B. Davidson, I. Marie Stefansson, L. F.S. Kooreman, A. Qerimi, J. Huvila, B. Gilks, M. Shahi, S. Zomer, C. Bartosch, J. M.A. Pijnenborg, J. Bulten, F. Ciompi* and M. Simons*, "Endometrial Pipelle Biopsy Computer-Aided Diagnosis: A Feasibility Study", Modern Pathology, Volume 37, Issue 2, 2024. [Data] [Evaluation platform]
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", Nature Communications Medicine, 2024. [Code] [Annotations] [Masks] [Model weights]
W. Aswolinskiy, E. Munari, H. Horlings, L. Mulder, G. Bogina, J. Sanders, Y. Liu, A. van den Belt-Dusebout, L. Tessier, M. Balkenhol, M. Stegeman, J. Hoven, J. Wesseling, J. van der Laak, E. Lips and F. Ciompi, "PROACTING: predicting pathological complete response to neoadjuvant chemotherapy in breast cancer from routine diagnostic histopathology biopsies with deep learning", Breast Cancer Research, 2023;25. [Algorithm]
Y. Jiao, J. van der Laak, S. Albarqouni, Z. Li, T. Tan, A. Bhalerao, J. Ma, J. Sun, J. Pocock, J. Pluim, N. Koohbanani, R. Bashir, S. Raza, S. Liu, S. Graham, S. Wetstein, S. Khurram, T. Watson, N. Rajpoot, M. Veta and F. Ciompi, "LYSTO: The Lymphocyte Assessment Hackathon and Benchmark Dataset", IEEE Journal of Biomedical and Health Informatics, 2023:1-12. [Hackathon website] [Data]
J. Bokhorst, I. Nagtegaal, F. Fraggetta, S. Vatrano, W. Mesker, M. Vieth, J. van der Laak and F. Ciompi, "Deep learning for multi-class semantic segmentation enables colorectal cancer detection and classification in digital pathology images", Nature Scientific Reports, 2023;13:8398. [Algorithm]
J. Bokhorst, I. Nagtegaal, I. Zlobec, H. Dawson, K. Sheahan, F. Simmer, R. Kirsch, M. Vieth, A. Lugli, J. van der Laak and F. Ciompi, "Semi-Supervised Learning to Automate Tumor Bud Detection in Cytokeratin-Stained Whole-Slide Images of Colorectal Cancer", Cancers, 2023;15(7):2079. [Algorithm]
N. Brouwer, A. Khan, J. Bokhorst, F. Ayatollahi, J. Hay, F. Ciompi, F. Simmer, N. Hugen, J. de Wilt, M. Berger, A. Lugli, I. Zlobec, J. Edwards and I. Nagtegaal, "The complexity of shapes; how the circularity of tumor nodules impacts prognosis in colorectal cancer", Modern Pathology, 2023:100376.
J. Bokhorst, F. Ciompi, S. Öztürk, A. Oguz Erdogan, M. Vieth, H. Dawson, R. Kirsch, F. Simmer, K. Sheahan, A. Lugli, I. Zlobec, J. van der Laak and I. Nagtegaal, "Fully Automated Tumor Bud Assessment in Hematoxylin and Eosin-Stained Whole Slide Images of Colorectal Cancer", Modern Pathology, 2023;36:100233.
M. Smit, F. Ciompi, J. Bokhorst, G. van Pelt, O. Geessink, H. Putter, R. Tollenaar, J. van Krieken, W. Mesker and J. van der Laak, "Deep learning based tumor-stroma ratio scoring in colon cancer correlates with microscopic assessment", Journal of Pathology Informatics, 2023.
J. Thagaard, G. Broeckx, D. Page, C. Jahangir, S. Verbandt, Z. Kos, R. Gupta, R. Khiroya, K. Abduljabbar, G. Acosta Haab, B. Acs, G. Akturk, J. Almeida, I. Alvarado-Cabrero, M. Amgad, F. Azmoudeh-Ardalan, S. Badve, N. Baharun, E. Balslev, E. Bellolio, V. Bheemaraju, K. Blenman, L. Mendonça Botinelly Fujimoto, N. Bouchmaa, O. Burgues, A. Chardas, M. U Chon Cheang, F. Ciompi, L. Cooper, A. Coosemans, G. Corredor, A. Dahl, F. Dantas Portela, F. Deman, S. Demaria, J. Doré Hansen, S. Dudgeon, T. Ebstrup, M. Elghazawy, C. Fernandez-Martín, S. Fox, W. Gallagher, J. Giltnane, S. Gnjatic, P. Gonzalez-Ericsson, A. Grigoriadis, N. Halama, M. Hanna, A. Harbhajanka, S. Hart, J. Hartman, S. Hauberg, S. Hewitt, A. Hida, H. Horlings, Z. Husain, E. Hytopoulos, S. Irshad, E. Janssen, M. Kahila, T. Kataoka, K. Kawaguchi, D. Kharidehal, A. Khramtsov, U. Kiraz, P. Kirtani, L. Kodach, K. Korski, A. Kovács, A. Laenkholm, C. Lang-Schwarz, D. Larsimont, J. Lennerz, M. Lerousseau, X. Li, A. Ly, A. Madabhushi, S. Maley, V. Manur Narasimhamurthy, D. Marks, E. McDonald, R. Mehrotra, S. Michiels, 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, A. Rahman, N. Rajpoot, B. Rapoport, T. Rau, J. Reis-Filho, J. Ribeiro, D. Rimm, A. Roslind, A. Vincent-Salomon, M. Salto-Tellez, J. Saltz, S. Sayed, E. Scott, K. Siziopikou, C. Sotiriou, A. Stenzinger, M. Sughayer, D. Sur, S. Fineberg, F. Symmans, S. Tanaka, T. Taxter, S. Tejpar, J. Teuwen, E. Thompson, T. Tramm, W. Tran, J. van der Laak, P. van Diest, G. Verghese, G. Viale, M. Vieth, N. Wahab, T. Walter, Y. Waumans, H. Wen, W. Yang, Y. Yuan, R. Zin, S. Adams, J. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, R. Salgado and E. Specht Stovgaard, "Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer", The Journal of Pathology, 2023;260:498-513.
D. Page, G. Broeckx, C. Jahangir, S. Verbandt, R. Gupta, J. Thagaard, R. Khiroya, Z. Kos, K. Abduljabbar, G. Acosta Haab, B. Acs, G. Akturk, J. Almeida, I. Alvarado-Cabrero, F. Azmoudeh-Ardalan, S. Badve, N. Baharun, E. Bellolio, V. Bheemaraju, K. Blenman, L. Mendonça Botinelly Fujimoto, N. Bouchmaa, O. Burgues, M. Cheang, F. Ciompi, L. Cooper, A. Coosemans, G. Corredor, F. Dantas Portela, F. Deman, S. Demaria, S. Dudgeon, M. Elghazawy, S. Ely, C. Fernandez-Martín, S. Fineberg, S. Fox, W. Gallagher, J. Giltnane, S. Gnjatic, P. Gonzalez-Ericsson, A. Grigoriadis, N. Halama, M. Hanna, A. Harbhajanka, A. Hardas, S. Hart, J. Hartman, S. Hewitt, A. Hida, H. Horlings, Z. Husain, E. Hytopoulos, S. Irshad, E. Janssen, M. Kahila, T. Kataoka, K. Kawaguchi, D. Kharidehal, A. Khramtsov, U. Kiraz, P. Kirtani, L. Kodach, K. Korski, A. Kovács, A. Laenkholm, C. Lang-Schwarz, D. Larsimont, J. Lennerz, M. Lerousseau, X. Li, A. Ly, A. Madabhushi, S. Maley, V. Manur Narasimhamurthy, D. Marks, E. McDonald, R. Mehrotra, S. Michiels, 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, A. Rahman, N. Rajpoot, B. Rapoport, T. Rau, J. Reis-Filho, J. Ribeiro, D. Rimm, A. Vincent-Salomon, M. Salto-Tellez, J. Saltz, S. Sayed, 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, P. van Diest, G. Verghese, G. Viale, M. Vieth, N. Wahab, T. Walter, Y. Waumans, H. Wen, W. Yang, Y. Yuan, S. Adams, J. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, R. Salgado and E. Specht Stovgaard, "Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer", The Journal of Pathology, 2023;260:514-532.
L. Menotti, G. Silvello, M. Atzori, S. Boytcheva, F. Ciompi, G. Di Nunzio, F. Fraggetta, F. Giachelle, O. Irrera, S. Marchesin, N. Marini, H. Müller and T. Primov, "Modelling digital health data: The ExaMode ontology for computational pathology", Journal of Pathology Informatics, 2023;14:100332.
M. Aubreville, N. Stathonikos, C. Bertram, R. Klopfleisch, N. Ter Hoeve, F. Ciompi, F. Wilm, C. Marzahl, T. Donovan, A. Maier, J. Breen, N. Ravikumar, Y. Chung, J. Park, R. Nateghi, F. Pourakpour, R. Fick, S. Ben Hadj, M. Jahanifar, A. Shephard, J. Dexl, T. Wittenberg, S. Kondo, M. Lafarge, V. Koelzer, J. Liang, Y. Wang, X. Long, J. Liu, S. Razavi, A. Khademi, S. Yang, X. Wang, R. Erber, A. Klang, K. Lipnik, P. Bolfa, M. Dark, G. Wasinger, M. Veta and K. Breininger, "Mitosis domain generalization in histopathology images - The MIDOG challenge.", Medical Image Analysis, 2022;84:102699.
C. Mercan, M. Balkenhol, R. Salgado, M. Sherman, P. Vielh, W. Vreuls, A. Polonia, H. Horlings, W. Weichert, J. Carter, P. Bult, M. Christgen, C. Denkert, K. van de Vijver, J. Bokhorst, J. van der Laak and F. Ciompi, "Deep learning for fully-automated nuclear pleomorphism scoring in breast cancer.", NPJ breast cancer,2022;8(1):120.
S. Marchesin, F. Giachelle, N. Marini, M. Atzori, S. Boytcheva, G. Buttafuoco, F. Ciompi, G. Di Nunzio, F. Fraggetta, O. Irrera, H. Muller, T. Primov, S. Vatrano and G. Silvello, "Empowering digital pathology applications through explainable knowledge extraction tools.", Journal of pathology informatics,2022;13:100139.
E. Munari, G. Querzoli, M. Brunelli, M. Marconi, M. Sommaggio, M. Cocchi, G. Martignoni, G. Netto, A. Calio, L. Quatrini, F. Mariotti, C. Luchini, I. Girolami, A. Eccher, D. Segala, F. Ciompi, G. Zamboni, L. Moretta and G. Bogina, "Comparison of three validated PD-L1 immunohistochemical assays in urothelial carcinoma of the bladder: interchangeability and issues related to patient selection.", Frontiers in immunology,2022;13:954910.
N. Marini, S. Marchesin, S. Otalora, M. Wodzinski, A. Caputo, M. van Rijthoven, W. Aswolinskiy, J. Bokhorst, D. Podareanu, E. Petters, S. Boytcheva, G. Buttafuoco, S. Vatrano, F. Fraggetta, J. van der Laak, M. Agosti, F. Ciompi, G. Silvello, H. Muller and M. Atzori, "Unleashing the potential of digital pathology data by training computer-aided diagnosis models without human annotations.", NPJ digital medicine,2022;5(1):102.
M. Hermsen, F. Ciompi, A. Adefidipe, A. Denic, A. Dendooven, B. Smith, D. van Midden, J. Brasen, J. Kers, M. Stegall, P. Bándi, T. Nguyen, Z. Swiderska-Chadaj, B. Smeets, L. Hilbrands and J. van der Laak, "Convolutional neural networks for the evaluation of chronic and inflammatory lesions in kidney transplant biopsies", American Journal of Pathology, 2022;192(10):1418-1432.
G. Litjens, F. Ciompi and J. van der Laak, "A Decade of GigaScience: The Challenges of Gigapixel Pathology Images.", GigaScience, 2022;11.
S. Satturwar, I. Girolami, E. Munari, F. Ciompi, A. Eccher and L. Pantanowitz, "Program death ligand-1 immunocytochemistry in lung cancer cytological samples: A systematic review.", Diagnostic cytopathology, 2022;50(6):313-323.
E. Munari, M. Marconi, G. Querzoli, G. Lunardi, P. Bertoglio, F. Ciompi, A. Tosadori, A. Eccher, N. Tumino, L. Quatrini, P. Vacca, G. Rossi, A. Cavazza, G. Martignoni, M. Brunelli, G. Netto, L. Moretta, G. Zamboni and G. Bogina, "Impact of PD-L1 and PD-1 Expression on the Prognostic Significance of CD8+, Tumor-Infiltrating Lymphocytes in Non-Small Cell Lung Cancer.", Frontiers in immunology, 2021;12:680973.
E. Munari, F. Mariotti, L. Quatrini, P. Bertoglio, N. Tumino, P. Vacca, A. Eccher, F. Ciompi, M. Brunelli, G. Martignoni, G. Bogina and L. Moretta, "PD-1/PD-L1 in Cancer: Pathophysiological, Diagnostic and Therapeutic Aspects.", International journal of molecular sciences, 2021;22(10).
J. van der Laak, G. Litjens and F. Ciompi, "Deep learning in histopathology: the path to the clinic.", Nature Medicine, 2021;27(5):775-784. [Download]
F. Faita, T. Oranges, N. Di Lascio, F. Ciompi, S. Vitali, G. Aringhieri, A. Janowska, M. Romanelli and V. Dini, "Ultra-high-frequency ultrasound and machine learning approaches for the differential diagnosis of melanocytic lesions.", Experimental Dermatology, 2021.
M. Balkenhol, F. Ciompi, Z. Swiderska-Chadaj, R. van de Loo, M. Intezar, I. Otte-Holler, D. Geijs, J. Lotz, N. Weiss, T. de Bel, G. Litjens, P. Bult and J. van der Laak, "Optimized tumour infiltrating lymphocyte assessment for triple negative breast cancer prognostics.", The Breast, 2021;56:78-87.
M. van Rijthoven, M. Balkenhol, K. Silina, J. van der Laak and F. Ciompi, "HookNet: Multi-resolution convolutional neural networks for semantic segmentation in histopathology whole-slide images", Medical Image Analysis, 2021;68:101890.
D. Tellez, G. Litjens, J. van der Laak and F. Ciompi, "Neural Image Compression for Gigapixel Histopathology Image Analysis.", IEEE Transactions on Pattern Analysis and Machine Intelligence,2021;43(2):567-578.
F. Ciompi, M. Veta, J. van der Laak and N. Rajpoot, "Editorial Computational Pathology", IEEE Journal of Biomedical and Health Informatics, 2021;25(2):303-306.
N. Marini, S. Otálora, D. Podareanu, M. van Rijthoven, J. van der Laak, F. Ciompi, H. Muller and M. Atzori, "Multi_Scale_Tools: A Python Library to Exploit Multi-Scale Whole Slide Images", Frontiers in Computer Science, 2021;3.
Z. Kos, A. Roblin, R. Kim, S. Michiels, B. Gallas, W. Chen, K. van de Vijver, S. Goel, S. Adams, S. Demaria, G. Viale, T. Nielsen, S. Badve, W. Symmans, C. Sotiriou, D. Rimm, S. Hewitt, C. Denkert, S. Loibl, S. Luen, J. Bartlett, P. Savas, G. Pruneri, D. Dillon, M. Cheang, A. Tutt, J. Hall, M. Kok, H. Horlings, A. Madabhushi, J. van der Laak, F. Ciompi, A. Laenkholm, E. Bellolio, T. Gruosso, S. Fox, J. Araya, G. Floris, J. Hudeček, L. Voorwerk, A. Beck, J. Kerner, D. Larsimont, S. Declercq, G. den Eynden, L. Pusztai, A. Ehinger, W. Yang, K. AbdulJabbar, Y. Yuan, R. Singh, C. Hiley, M. al Bakir, A. Lazar, S. Naber, S. Wienert, M. Castillo, G. Curigliano, M. Dieci, F. André, C. Swanton, J. Reis-Filho, J. Sparano, E. Balslev, I. Chen, E. Stovgaard, K. Pogue-Geile, K. Blenman, F. Penault-Llorca, S. Schnitt, S. Lakhani, A. Vincent-Salomon, F. Rojo, J. Braybrooke, M. Hanna, M. Soler-Monsó, D. Bethmann, C. Castaneda, K. Willard-Gallo, A. Sharma, H. Lien, S. Fineberg, J. Thagaard, L. Comerma, P. Gonzalez-Ericsson, E. Brogi, S. Loi, J. Saltz, F. Klaushen, L. Cooper, M. Amgad, D. Moore and R. Salgado, "Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer", npj Breast Cancer, 2020;6(1).
M. Amgad, A. Stovgaard, E. Balslev, J. Thagaard, W. Chen, S. Dudgeon, A. Sharma, J. Kerner, C. Denkert, Y. Yuan, K. AbdulJabbar, S. Wienert, P. Savas, L. Voorwerk, A. Beck, A. Madabhushi, J. Hartman, M. Sebastian, H. Horlings, J. Hudeček, F. Ciompi, D. Moore, R. Singh, E. Roblin, M. Balancin, M. Mathieu, J. Lennerz, P. Kirtani, I. Chen, J. Braybrooke, G. Pruneri, S. Demaria, S. Adams, S. Schnitt, S. Lakhani, F. Rojo, L. Comerma, S. Badve, M. Khojasteh, W. Symmans, C. Sotiriou, P. Gonzalez-Ericsson, K. Pogue-Geile, R. Kim, D. Rimm, G. Viale, S. Hewitt, J. Bartlett, F. Penault-Llorca, S. Goel, H. Lien, S. Loibl, Z. Kos, S. Loi, M. Hanna, S. Michiels, M. Kok, T. Nielsen, A. Lazar, Z. Bago-Horvath, L. Kooreman, J. van der Laak, J. Saltz, B. Gallas, U. Kurkure, M. Barnes, R. Salgado and L. Cooper, "Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group", npj Breast Cancer, 2020;6(1).
J. Bokhorst, A. Blank, A. Lugli, I. Zlobec, H. Dawson, M. Vieth, L. Rijstenberg, S. Brockmoeller, M. Urbanowicz, J. Flejou, R. Kirsch, F. Ciompi, J. van der Laak and I. Nagtegaal, "Assessment of individual tumor buds using keratin immunohistochemistry: moderate interobserver agreement suggests a role for machine learning", Modern Pathology, 2019.
J. van der Laak, F. Ciompi and G. Litjens, "No pixel-level annotations needed", Nature Biomedical Engineering, 2019;3(11):855-856.
Z. Swiderska-Chadaj, H. Pinckaers, M. van Rijthoven, M. Balkenhol, M. Melnikova, O. Geessink, Q. Manson, M. Sherman, A. Polonia, J. Parry, M. Abubakar, G. Litjens, J. van der Laak and F. Ciompi, "Learning to detect lymphocytes in immunohistochemistry with deep learning", Medical Image Analysis, 2019;58:101547.
D. Tellez, G. Litjens, P. Bándi, W. Bulten, J. Bokhorst, F. Ciompi and J. van der Laak, "Quantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathology", Medical Image Analysis, 2019;58:101544.
G. Litjens, F. Ciompi, J. Wolterink, B. de Vos, T. Leiner, J. Teuwen and I. Isgum, "State-of-the-Art Deep Learning in Cardiovascular Image Analysis", JACC Cardiovascular Imaging, 2019;12(8 Pt 1):1549-1565.
M. Balkenhol, D. Tellez, W. Vreuls, P. Clahsen, H. Pinckaers, F. Ciompi, P. Bult and J. van der Laak, "Deep learning assisted mitotic counting for breast cancer", Laboratory Investigation, 2019.
M. Balkenhol, P. Bult, D. Tellez, W. Vreuls, P. Clahsen, F. Ciompi and J. van der Laak, "Deep learning and manual assessment show that the absolute mitotic count does not contain prognostic information in triple negative breast cancer", Cellular Oncology, 2019;42:4555-4569.
M. Veta, Y. Heng, N. Stathonikos, B. Bejnordi, F. Beca, T. Wollmann, K. Rohr, M. Shah, D. Wang, M. Rousson, M. Hedlund, D. Tellez, F. Ciompi, E. Zerhouni, D. Lanyi, M. Viana, V. Kovalev, V. Liauchuk, H. Phoulady, T. Qaiser, S. Graham, N. Rajpoot, E. Sjoblom, J. Molin, K. Paeng, S. Hwang, S. Park, Z. Jia, E. Chang, Y. Xu, A. Beck, P. van Diest and J. Pluim, "Predicting breast tumor proliferation from whole-slide images: the TUPAC16 challenge", Medical Image Analysis, 2019;54(5):111-121.
O. Geessink, A. Baidoshvili, J. Klaase, B. Ehteshami Bejnordi, G. Litjens, G. van Pelt, W. Mesker, I. Nagtegaal, F. Ciompi and J. van der Laak, "Computer aided quantification of intratumoral stroma yields an independent prognosticator in rectal cancer", Cellular Oncology, 2019:1-11.
S. Balocco, F. Ciompi, J. Rigla, X. Carrillo, J. Mauri and P. Radeva, "Assessment Of Intra-coronary Stent Location And Extension In Intravascular Ultrasound Sequences", Medical Physics, 2018;46(2):484-493.
M. Silva, M. Prokop, C. Jacobs, G. Capretti, N. Sverzellati, F. Ciompi, B. van Ginneken, C. Schaefer-Prokop, C. Galeone, A. Marchiano and U. Pastorino, "Long-term Active Surveillance of Screening Detected Subsolid Nodules is a Safe Strategy to Reduce Overtreatment", Journal of Thoracic Oncology, 2018;13:1454-1463.
D. Tellez, M. Balkenhol, I. Otte-Holler, R. van de Loo, R. Vogels, P. Bult, C. Wauters, W. Vreuls, S. Mol, N. Karssemeijer, G. Litjens, J. van der Laak and F. Ciompi, "Whole-Slide Mitosis Detection in H&E Breast Histology Using PHH3 as a Reference to Train Distilled Stain-Invariant Convolutional Networks", IEEE Transactions on Medical Imaging, 2018;37(9):2126 - 2136.
M. Silva, C. Schaefer-Prokop, C. Jacobs, G. Capretti, F. Ciompi, B. van Ginneken, U. Pastorino and N. Sverzellati, "Detection of Subsolid Nodules in Lung Cancer Screening: Complementary Sensitivity of Visual Reading and Computer-Aided Diagnosis", Investigative Radiology, 2018;53(8):441-449.
K. Chung, F. Ciompi, J. Scholten E. Th. Goo, M. Prokop, C. Jacobs, B. van Ginneken and C. Schaefer-Prokop, "Visual Discrimination of Screen-detected Persistent from Transient Subsolid Nodules: an Observer Study", PLoS One, 2018;13(2):e0191874.
J. Charbonnier, K. Chung, E. Scholten, E. van Rikxoort, C. Jacobs, N. Sverzellati, M. Silva, U. Pastorino, B. van Ginneken and F. Ciompi, "Automatic segmentation of the solid core and enclosed vessels in subsolid pulmonary nodules", Nature Scientific Reports, 2018;8(1):646.
S. van Riel, F. Ciompi, M. Winkler Wille, A. Dirksen, S. Lam, E. Scholten, S. Rossi, N. Sverzellati, M. Naqibullah, R. Wittenberg, M. Hovinga-de Boer, M. Snoeren, L. Peters-Bax, O. Mets, M. Brink, M. Prokop, C. Schaefer-Prokop and B. van Ginneken, "Malignancy risk estimation of pulmonary nodules in screening CTs: Comparison between a computer model and human observers", PLoS One, 2017;12(11):e0185032.
F. Ciompi, K. Chung, S. van Riel, A. Setio, P. Gerke, C. Jacobs, E. Scholten, C. Schaefer-Prokop, M. Wille, A. Marchiano, U. Pastorino, M. Prokop and B. van Ginneken, "Towards automatic pulmonary nodule management in lung cancer screening with deep learning", Nature Scientific Reports, 2017(46479).
G. Litjens, T. Kooi, B. Ehteshami Bejnordi, A. Setio, F. Ciompi, M. Ghafoorian, J. van der Laak, B. van Ginneken and C. Sánchez, "A Survey on Deep Learning in Medical Image Analysis", Medical Image Analysis, 2017;42:60-88.
K. Chung, C. Jacobs, E. Scholten, J. Goo, H. Prosch, N. Sverzellati, F. Ciompi, O. Mets, P. Gerke, M. Prokop, B. van Ginneken and C. Schaefer-Prokop, "Lung-RADS Category 4X: Does It Improve Prediction of Malignancy in Subsolid Nodules?", Radiology, 2017;284(1):264-271.
S. van Riel, F. Ciompi, C. Jacobs, M. Winkler Wille, E. Scholten, M. Naqibullah, S. Lam, M. Prokop, C. Schaefer-Prokop and B. van Ginneken, "Malignancy risk estimation of screen-detected nodules at baseline CT: comparison of the PanCan model, Lung-RADS and NCCN guidelines", European Radiology, 2017;27(10):4019-4029.
J. Charbonnier, E. van Rikxoort, A. Setio, C. Schaefer-Prokop, B. van Ginneken and F. Ciompi, "Improving Airway Segmentation in Computed Tomography using Leak Detection with Convolutional Networks", Medical Image Analysis, 2017;36:52-60.
F. Ciompi, S. Balocco, J. Rigla, X. Carrillo, J. Mauri and P. Radeva, "Computer-aided detection of intracoronary stent in intravascular ultrasound sequences", Medical Physics, 2016;43(10):5616.
A. Setio, F. Ciompi, G. Litjens, P. Gerke, C. Jacobs, S. van Riel, M. Wille, M. Naqibullah, C. Sánchez and B. van Ginneken, "Pulmonary nodule detection in CT images: false positive reduction using multi-view convolutional networks", IEEE Transactions on Medical Imaging, 2016;35(5):1160-1169.
J. Charbonnier, M. Brink, F. Ciompi, E. Scholten, C. Schaefer-Prokop and E. van Rikxoort, "Automatic Pulmonary Artery-Vein Separation and Classification in Computed Tomography Using Tree Partitioning and Peripheral Vessel Matching", IEEE Transactions on Medical Imaging, 2016:882-892.
F. Ciompi, B. de Hoop, S. van Riel, K. Chung, E. Scholten, M. Oudkerk, P. de Jong, M. Prokop and B. van Ginneken, "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", Medical Image Analysis, 2015;26(1):195-202.
F. Ciompi, C. Jacobs, E. Scholten, M. Winkler Wille, P. de Jong, M. Prokop and B. van Ginneken, "Bag of frequencies: a descriptor of pulmonary nodules in Computed Tomography images", IEEE Transactions on Medical Imaging, 2015;34(4):1-12.
C. Gatta and F. Ciompi, "Stacked sequential scale-space Taylor context", IEEE Transactions on Pattern Analysis and Machine Intelligence, 2014;36(8):1694-1700.
S. Balocco, C. Gatta, F. Ciompi, A. Wahle, P. Radeva, S. Carlier, G. Unal, E. Sanidas, J. Mauri, X. Carillo, T. Kovarnik, C. Wang, H. Chen, T. Exarchos, D. Fotiadis, F. Destrempes, G. Cloutier, O. Pujol, M. Alberti, E. Mendizabal-Ruiz, M. Rivera, T. Aksoy, R. Downe and I. Kakadiaris, "Standardized evaluation methodology and reference database for evaluating IVUS image segmentation", Computerized Medical Imaging and Graphics, 2014;38:70-90.
F. Ciompi, O. Pujol and P. Radeva, "ECOC-DRF: Discriminative Random Fields based on Error-Correcting Output Codes", Pattern Recognition, 2014;47:2193-2204.
F. Ciompi, O. Pujol, C. Gatta, M. Alberti, S. Balocco, X. Carrillo, J. Mauri-Ferre and P. Radeva, "HoliMAb: A holistic approach for Media--Adventitia border detection in intravascular ultrasound", Medical Image Analysis, 2012.
M. Alberti, S. Balocco, C. Gatta, F. Ciompi, O. Pujol, J. Silva, X. Carrillo and P. Radeva, "Automatic bifurcation detection in coronary IVUS sequences", IEEE Transactions on Biomedical Engineering, 2012;59(4):1022-1031.
X. Carrillo, E. Fernandez-Nofrerias, F. Ciompi, O. Rodriguez-Leor, P. Radeva, N. Salvatella, O. Pujol, J. Mauri and A. Bayes-Genis, "Changes in radial artery volume assessed using intravascular ultrasound: a comparison of two vasodilator regimens in transradial coronary interventions", Journal of Invasive Cardiology, 2011;23(10):401-404.
J. Seabra, F. Ciompi, O. Pujol, J. Mauri, P. Radeva and J. Sanches, "Rayleigh mixture model for plaque characterization in intravascular ultrasound", IEEE Transactions on Biomedical Engineering, 2011;58(5):1314-1324.
F. Ciompi, O. Pujol, C. Gatta, O. Rodriguez-Leor, J. Mauri-Ferre and P. Radeva, "Fusing in-vitro and in-vivo intravascular ultrasound data for plaque characterization", International Journal of Cardiac Imaging, 2010;26(7):763-779.