Publications
2019
Papers in international journals
- P. Bándi, M. Balkenhol, B. van Ginneken, J. van der Laak and G. Litjens, "Resolution-agnostic tissue segmentation in whole-slide histopathology images with convolutional neural networks", PeerJ, 2019;7:e8242.
- 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.
- A. Patel, F. Schreuder, C. Klijn, M. Prokop, B. van Ginneken, H. Marquering, Y. Roos, M. Baharoglu, F. Meijer and R. Manniesing, "Intracerebral haemorrhage segmentation in non-contrast CT", Scientific Reports, 2019;9(1):17858.
- J. Bleker, T. Kwee, R. Dierckx, I. de Jong, H. Huisman and D. Yakar, "Multiparametric MRI and auto-fixed volume of interest-based radiomics signature for clinically significant peripheral zone prostate cancer", European Radiology, 2019.
- M. Bakker, S. de Lange, R. Pijnappel, R. Mann, P. Peeters, E. Monninkhof, M. Emaus, C. Loo, R. Bisschops, M. Lobbes, M. de Jong, K. Duvivier, J. Veltman, N. Karssemeijer, H. de Koning, P. van Diest, W. Mali, M. van den Bosch, W. Veldhuis, C. van Gils and D. Group, "Supplemental MRI Screening for Women with Extremely Dense Breast Tissue", New England Journal of Medicine, 2019;381(22):2091-2102.
- O. Debats, G. Litjens and H. Huisman, "Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks", PeerJ, 2019;7:e8052.
- M. Mullooly, B. Ehteshami Bejnordi, R. Pfeiffer, S. Fan, M. Palakal, M. Hada, P. Vacek, D. Weaver, J. Shepherd, B. Fan, A. Mahmoudzadeh, J. Wang, S. Malkov, J. Johnson, S. Herschorn, B. Sprague, S. Hewitt, L. Brinton, N. Karssemeijer, J. van der Laak, A. Beck, M. Sherman and G. Gierach, "Application of convolutional neural networks to breast biopsies to delineate tissue correlates of mammographic breast density", NPJ Breast Cancer, 2019;5:43.
- J. van der Laak, F. Ciompi and G. Litjens, "No pixel-level annotations needed", Nature Biomedical Engineering, 2019;3(11):855-856.
- C. Balta, R. Bouwman, M. Broeders, N. Karssemeijer, W. Veldkamp, I. Sechopoulos and R. van Engen, "Optimization of the difference-of-Gaussian channel sets for the channelized Hotelling observer", Journal of Medical Imaging, 2019;6(3):035501.
- A. Hering, S. Kuckertz, S. Heldmann and M. Heinrich, "Memory-efficient 2.5D convolutional transformer networks for multi-modal deformable registration with weak label supervision applied to whole-heart CT and MRI scans", Computer Assisted Radiology and Surgery, 2019.
- K. Wiegertjes, A. ter Telgte, P. Oliveira, E. van Leijsen, M. Bergkamp, I. van Uden, M. Ghafoorian, H. van der Holst, D. Norris, B. Platel, C. Klijn, A. Tuladhar and F. de Leeuw, "The role of small diffusion-weighted imaging lesions in cerebral small vessel disease", Neurology, 2019;93:e1627-e1634.
- D. Valkenburg, E. Runhart, N. Bax, B. Liefers, S. Lambertus, C. Sánchez, F. Cremers and C. Hoyng, "Highly variable disease courses in siblings with Stargardt disease", Ophthalmology, 2019;126(12):1712-1721.
- M. Hermsen, T. de Bel, M. den Boer, E. Steenbergen, J. Kers, S. Florquin, J. Roelofs, M. Stegall, M. Alexander, B. Smith, B. Smeets, L. Hilbrands and J. van der Laak, "Deep-learning based histopathologic assessment of kidney tissue", Journal of the American Society of Nephrology, 2019;30(10):1968-1979.
- 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.
- N. deSouza, E. Achten, A. Alberich-Bayarri, F. Bamberg, R. Boellaard, O. Clement, L. Fournier, F. Gallagher, X. Golay, C. Heussel, E. Jackson, R. Manniesing, M. Mayerhofer, E. Neri, J. O'Connor, K. Oguz, A. Persson, M. Smits, E. van Beek, C. Zech and E. of Radiology, "Validated imaging biomarkers as decision-making tools in clinical trials and routine practice: current status and recommendations from the EIBALL* subcommittee of the European Society of Radiology (ESR)", Insights into Imaging, 2019;10(1):87.
- 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.
- R. Philipsen, C. Sánchez, J. Melendez, W. Lew and B. van Ginneken, "Automated chest X-ray reading for tuberculosis in the Philippines to improve case detection: a cohort study", International Journal of Tuberculosis and Lung Disease, 2019;23(7):805-810.
- A. Halilovic, D. Verweij, A. Simons, M. Stevens-Kroef, S. Vermeulen, J. Elsink, B. Tops, I. Otte-Holler, J. van der Laak, C. van de Water, O. Boelens, M. Schlooz-Vries, J. Dijkstra, I. Nagtegaal, J. Tol, P. van Cleef, P. Span and P. Bult, "HER2, chromosome 17 polysomy and DNA ploidy status in breast cancer; a translational study", Scientific Reports, 2019;9(1):11679.
- G. Aresta, C. Jacobs, T. Araujo, A. Cunha, I. Ramos, B. van Ginneken and A. Campilho, "iW-Net: an automatic and minimalistic interactive lung nodule segmentation deep network", Scientific Reports, 2019;9(1):11591.
- M. Meijs, S. Pegge, K. Murayama, H. Boogaarts, M. Prokop, P. Willems, R. Manniesing and F. Meijer, "Color mapping of 4D-CTA for the detection of cranial arteriovenous shunts", American Journal of Neuroradiology, 2019;40(9):1498-1504.
- 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.
- V. Schreur, A. de Breuk, F. Venhuizen, C. Sánchez, C. Tack, B. Klevering, E. de Jong and C. Hoyng, "Retinal hyperreflective foci in type 1 diabetes mellitus", Retina, 2019.
- E. Abels, L. Pantanowitz, F. Aeffner, M. Zarella, J. van der Laak, M. Bui, V. Vemuri, A. Parwani, J. Gibbs, E. Agosto-Arroyo, A. Beck and C. Kozlowski, "Computational pathology definitions, best practices, and recommendations for regulatory guidance: a white paper from the Digital Pathology Association", Journal of Pathology, 2019;249(3):286-294.
- H. Huisman, "Solid Science of AI Supporting Bladder Cancer CT Reading", Academic Radiology, 2019;26(9):1146-1147.
- C. Jacobs and B. van Ginneken, "Google's lung cancer AI: a promising tool that needs further validation", Nature Reviews Clinical Oncology, 2019;16(9):532-533.
- 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.
- S. Saadatmand, H. Geuzinge, E. Rutgers, R. Mann, D. de van Roy Zuidewijn, H. Zonderland, R. Tollenaar, M. Lobbes, M. Ausems, M. van 't Riet, M. Hooning, I. Mares-Engelberts, E. Luiten, E. Heijnsdijk, C. Verhoef, N. Karssemeijer, J. Oosterwijk, I. Obdeijn, H. de Koning, M. Tilanus-Linthorst and F. study group, "MRI versus mammography for breast cancer screening in women with familial risk (FaMRIsc): a multicentre, randomised, controlled trial", Lancet Oncology, 2019;20(8):1136-1147.
- N. Khalili, N. Lessmann, E. Turk, N. Claessens, R. de Heus, T. Kolk, M. Viergever, M. Benders and I. Išgum, "Automatic brain tissue segmentation in fetal MRI using convolutional neural networks", Magnetic Resonance Imaging, 2019;64:77-89.
- I. Munsterman, M. Van Erp, G. Weijers, C. Bronkhorst, C. de Korte, J. Drenth, J. van der Laak and E. Tjwa, "A Novel Automatic Digital Algorithm that Accurately Quantifies Steatosis in NAFLD on Histopathological Whole-Slide Images", Cytometry Part B-Clinical Cytometry, 2019.
- E. van Leijsen, M. Bergkamp, I. van Uden, S. Cooijmans, M. Ghafoorian, H. van der Holst, D. Norris, R. Kessels, B. Platel, A. Tuladhar and F. de Leeuw, "Cognitive consequences of regression of cerebral small vessel disease", European Stroke Journal, 2019;4(1):85-89.
- G. Chlebus, H. Meine, S. Thoduka, N. Abolmaali, B. van Ginneken, H. Hahn and A. Schenk, "Reducing inter-observer variability and interaction time of MR liver volumetry by combining automatic CNN-based liver segmentation and manual corrections", PLoS One, 2019;14(5):e0217228.
- D. Grob, E. Smit, J. Prince, J. Kist, L. Stöger, B. Geurts, M. Snoeren, R. van Dijk, L. Oostveen, M. Prokop, C. Schaefer-Prokop, I. Sechopoulos and M. Brink, "Iodine Maps from Subtraction CT or Dual-Energy CT to Detect Pulmonary Emboli with CT Angiography: A Multiple-Observer Study", Radiology, 2019;292:197-205.
- W. Sanderink, B. Laarhuis, L. Strobbe, I. Sechopoulos, P. Bult, N. Karssemeijer and R. Mann, "A systematic review on the use of the breast lesion excision system in breast disease", Insights into Imaging, 2019;10(1):49.
- T. Heesterbeek, E. de Jong, I. Acar, J. Groenewoud, B. Liefers, C. Sánchez, T. Peto, C. Hoyng, D. Pauleikhoff, H. Hense and A. den Hollander, "Genetic risk score has added value over initial clinical grading stage in predicting disease progression in age-related macular degeneration", Scientific Reports, 2019;9(1):6611.
- J. Luiten, B. Korte, A. Voogd, W. Vreuls, E. Luiten, L. Strobbe, M. Rutten, M. Plaisier, P. Lohle, M. Hooijen, V. Tjan-Heijnen and L. Duijm, "Trends in frequency and outcome of high-risk breast lesions at core needle biopsy in women recalled at biennial screening mammography, a multiinstitutional study", International Journal of Cancer, 2019;145:2720-2727.
- A. Rodriguez-Ruiz, K. Lang, A. Gubern-Merida, J. Teuwen, M. Broeders, G. Gennaro, P. Clauser, T. Helbich, M. Chevalier, T. Mertelmeier, M. Wallis, I. Andersson, S. Zackrisson, I. Sechopoulos and R. Mann, "Can we reduce the workload of mammographic screening by automatic identification of normal exams with artificial intelligence? A feasibility study", European Radiology, 2019;29(9):4825-4832.
- L. Aprupe, G. Litjens, T. Brinker, J. van der Laak and N. Grabe, "Robust and accurate quantification of biomarkers of immune cells in lung cancer micro-environment using deep convolutional neural networks", PeerJ, 2019;7:e6335.
- 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.
- B. Sturm, D. Creytens, M. Cook, J. Smits, M. van Dijk, E. Eijken, E. Kurpershoek, H. Kusters-Vandevelde, A. Ooms, C. Wauters, W. Blokx and J. van der Laak, "Validation of Whole-slide Digitally Imaged Melanocytic Lesions: Does Z-Stack Scanning Improve Diagnostic Accuracy?", Journal of Pathology Informatics, 2019;10:6.
- M. Maas, G. Litjens, A. Wright, U. Attenberger, M. Haider, T. Helbich, B. Kiefer, K. Macura, D. Margolis, A. Padhani, K. Selnaes, G. Villeirs, J. Futterer and T. Scheenen, "A Single-Arm, Multicenter Validation Study of Prostate Cancer Localization and Aggressiveness With a Quantitative Multiparametric Magnetic Resonance Imaging Approach", Investigative Radiology, 2019.
- 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.
- D. Grob, E. Smit, L. Oostveen, M. Snoeren, M. Prokop, C. Schaefer-Prokop, I. Sechopoulos and M. Brink, "Image Quality of Iodine Maps for Pulmonary Embolism: A Comparison of Subtraction CT and Dual-Energy CT", American Journal of Roentgenology, 2019;212:1253-1259.
- H. Bogunovic, F. Venhuizen, S. Klimscha, S. Apostolopoulos, A. Bab-Hadiashar, U. Bagci, M. Beg, L. Bekalo, Q. Chen, C. Ciller, K. Gopinath, A. Gostar, K. Jeon, Z. Ji, S. Kang, D. Koozekanani, D. Lu, D. Morley, K. Parhi, H. Park, A. Rashno, M. Sarunic, S. Shaikh, J. Sivaswamy, R. Tennakoon, S. Yadav, S. De Zanet, S. Waldstein, B. Gerendas, C. Klaver, C. Sánchez and U. Schmidt-Erfurth, "RETOUCH: The Retinal OCT Fluid Detection and Segmentation Benchmark and Challenge", IEEE Transactions on Medical Imaging, 2019;38(8):1858-1874.
- 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.
- J. Gómez-Valverde, A. Antón, G. Fatti, B. Liefers, A. Herranz, A. Santos, C. Sánchez and M. Ledesma-Carbayo, "Automatic glaucoma classification using color fundus images based on convolutional neural networks and transfer learning", Biomedical Optics Express, 2019;10(2):892-913.
- S. Vreemann, M. Dalmis, P. Bult, N. Karssemeijer, M. Broeders, A. Gubern-Mérida and R. Mann, "Amount of fibroglandular tissue FGT and background parenchymal enhancement BPE in relation to breast cancer risk and false positives in a breast MRI screening program", European Radiology, 2019;29:4678-4690.
- A. Schreuder, C. Jacobs, L. Gallardo-Estrella, M. Prokop, C. Schaefer-Prokop and B. van Ginneken, "Predicting all-cause and lung cancer mortality using emphysema score progression rate between baseline and follow-up chest CT images: A comparison of risk model performances", PLoS One, 2019;14(2):e0212756.
- N. Lessmann, B. van Ginneken, P. de Jong and I. Išgum, "Iterative fully convolutional neural networks for automatic vertebra segmentation and identification", Medical Image Analysis, 2019;53:142-155.
- G. Napolitano, E. Lynge, M. Lillholm, I. Vejborg, C. van Gils, M. Nielsen and N. Karssemeijer, "Change in mammographic density across birth cohorts of Dutch breast cancer screening participants", International Journal of Cancer, 2019;145(11):2954-2962.
- W. Bulten, P. Bándi, J. Hoven, R. van de Loo, J. Lotz, N. Weiss, J. van der Laak, B. van Ginneken, C. Hulsbergen-van de Kaa and G. Litjens, "Epithelium segmentation using deep learning in H&E-stained prostate specimens with immunohistochemistry as reference standard", Scientific Reports, 2019;9(1).
- J. Charbonnier, E. Pompe, C. Moore, S. Humphries, B. van Ginneken, B. Make, E. Regan, J. Crapo, E. van Rikxoort and D. Lynch, "Airway wall thickening on CT: Relation to smoking status and severity of COPD", Respiratory Medicine, 2019;146:36-41.
- N. Lessmann, P. de Jong, C. Celeng, R. Takx, M. Viergever, B. van Ginneken and I. Išgum, "Sex Differences in Coronary Artery and Thoracic Aorta Calcification and Their Association With Cardiovascular Mortality in Heavy Smokers", JACC Cardiovascular Imaging, 2019;12:1808-1817.
- M. Dalmis, A. Gubern-Mérida, S. Vreemann, P. Bult, N. Karssemeijer, R. Mann and J. Teuwen, "Artificial Intelligence Based Classification of Breast Lesions Imaged With a Multi-Parametric Breast MRI Protocol With ultrafast DCE-MRI, T2 and DWI", Investigative Radiology, 2019;56(6):325-332.
- T. van den Heuvel, H. Petros, S. Santini, C. de Korte and B. van Ginneken, "Automated Fetal Head Detection and Circumference Estimation from Free-Hand Ultrasound Sweeps Using Deep Learning in Resource-Limited Countries", Ultrasound in Medicine and Biology, 2019;45(3):773-785.
- C. Balta, R. Bouwman, I. Sechopoulos, M. Broeders, N. Karssemeijer, R. van Engen and W. Veldkamp, "Can a channelized Hotelling observer assess image quality in acquired mammographic images of an anthropomorphic breast phantom including image processing?", Medical Physics, 2019;46:714-725.
- M. Bergkamp, A. Tuladhar, H. van der Holst, E. van Leijsen, M. Ghafoorian, I. van Uden, E. van Dijk, D. Norris, B. Platel, R. Esselink and F. Leeuw, "Brain atrophy and strategic lesion location increases risk of parkinsonism in cerebral small vessel disease", Parkinsonism & Related Disorders, 2019;61:94-100.
- B. van Ginneken, "Deep Learning for Triage of Chest Radiographs: Should Every Institution Train Its Own System?", Radiology, 2019;290:545-546.
- M. Tammemagi, A. Ritchie, S. Atkar-Khattra, B. Dougherty, C. Sanghera, J. Mayo, R. Yuan, D. Manos, A. McWilliams, H. Schmidt, M. Gingras, S. Pasian, L. Stewart, S. Tsai, J. M.Seely, P. Burrowes, R. Bhatia, E. A.Haider, C. Boylan, C. Jacobs, B. van Ginneken, M. Tsao, S. Lam and the Pan-Canadian Early Detection of Lung Cancer Study Group, "Predicting Malignancy Risk of Screen Detected Lung Nodules - Mean Diameter or Volume", Journal of Thoracic Oncology, 2019;14(2):203-211.
- R. Finger, S. Schmitz-Valckenberg, M. Schmid, G. Rubin, H. Dunbar, A. Tufail, D. Crabb, A. Binns, C. Sánchez, P. Margaron, G. Normand, M. Durbin, U. Luhmann, P. Zamiri, J. Cunha-Vaz, F. Asmus, F. Holz and O. behalf of the consortium, "MACUSTAR: Development and Clinical Validation of Functional, Structural, and Patient-Reported Endpoints in Intermediate Age-Related Macular Degeneration", Ophthalmologica, 2019;241(2):61-72.
- S. van Riel, C. Jacobs, E. Scholten, R. Wittenberg, M. Winkler Wille, B. de Hoop, R. Sprengers, O. Mets, B. Geurts, M. Prokop, C. Schaefer-Prokop and B. van Ginneken, "Observer variability for Lung-RADS categorisation of lung cancer screening CTs: impact on patient management", European Radiology, 2019;29(2):924-931.
- V. Schreur, A. Domanian, B. Liefers, F. Venhuizen, B. Klevering, C. Hoyng, E. de Jong and T. Theelen, "Morphological and topographical appearance of microaneurysms on optical coherence tomography angiography", British Journal of Ophthalmology, 2019;103(5):630-635.
- R. Becks, R. Manniesing, J. Vister, S. Pegge, S. Steens, E. van Dijk, M. Prokop and F. Meijer, "Brain CT Perfusion Improves Intracranial Vessel Occlusion Detection on CT Angiography", Journal of Neuroradiology, 2019;46(2):124-129.
- A. Patel, S. van de Leemput, M. Prokop, B. van Ginneken and R. Manniesing, "Image Level Training and Prediction: Intracranial Hemorrhage Identification in 3D Non-Contrast CT", IEEE Access, 2019;7(1):92355-92364.
- S. van de Leemput, J. Teuwen, B. van Ginneken and R. Manniesing, "MemCNN: A Python/PyTorch package for creating memory-efficient invertible neural networks", Journal of Open Source Software, 2019;4(39):1576.
- M. Emaus, I. Išgum, S. van Velzen, H. van den Bongard, S. Gernaat, N. Lessmann, M. Sattler, A. Teske, J. Penninkhof, H. Meijer, J. Pignol and H. Verkooijen, "Bragatston study protocol: a multicentre cohort study on automated quantification of cardiovascular calcifications on radiotherapy planning CT scans for cardiovascular risk prediction in patients with breast cancer", BMJ Open, 2019;9:e028752.
- C. Noordman and G. Vreeswijk, "Evolving novelty strategies for the Iterated Prisoner's Dilemma in deceptive tournaments", Theoretical Computer Science, 2019;785:1-16.
- B. de Vos, J. Wolterink, T. Leiner, P. de Jong, N. Lessmann and I. Isgum, "Direct automatic coronary calcium scoring in cardiac and chest CT", IEEE Transactions on Medical Imaging, 2019;38:2127-38.
- S. van de Leemput, M. Meijs, A. Patel, F. Meijer, B. van Ginneken and R. Manniesing, "Multiclass Brain Tissue Segmentation in 4D CT using Convolutional Neural Networks", IEEE Access, 2019;7(1):51557-51569.
Preprints
- P. Bilic, P. Christ, E. Vorontsov, G. Chlebus, H. Chen, Q. Dou, C. Fu, X. Han, P. Heng, J. Hesser, S. Kadoury, T. Konopczynski, M. Le, C. Li, X. Li, J. Lipkova, J. Lowengrub, H. Meine, J. Moltz, C. Pal, M. Piraud, X. Qi, J. Qi, M. Rempfler, K. Roth, A. Schenk, A. Sekuboyina, E. Vorontsov, P. Zhou, C. Hulsemeyer, M. Beetz, F. Ettlinger, F. Gruen, G. Kaissis, F. Lohofer, R. Braren, J. Holch, F. Hofmann, W. Sommer, V. Heinemann, C. Jacobs, G. Humpire Mamani, B. van Ginneken, G. Chartrand, A. Tang, M. Drozdzal, A. Ben-Cohen, E. Klang, M. Amitai, E. Konen, H. Greenspan, J. Moreau, A. Hostettler, L. Soler, R. Vivanti, A. Szeskin, N. Lev-Cohain, J. Sosna, L. Joskowicz and B. Menze, "The Liver Tumor Segmentation Benchmark (LiTS)", arXiv:1901.04056, 2019.
- R. Dilz, L. Schröder, N. Moriakov, J. Sonke and J. Teuwen, "Learned SIRT for Cone Beam Computed Tomography Reconstruction", arXiv:1908.10715, 2019.
- H. Pinckaers and G. Litjens, "Neural Ordinary Differential Equations for Semantic Segmentation of Individual Colon Glands", arXiv:1910.10470, 2019.
- K. Murphy, S. Habib, S. Zaidi, S. Khowaja, A. Khan, J. Melendez, E. Scholten, F. Amad, S. Schalekamp, M. Verhagen, R. Philipsen, A. Meijers and B. van Ginneken, "Computer aided detection of tuberculosis on chest radiographs: An evaluation of the CAD4TB v6 system", arXiv:1903.03349, 2019.
- A. Simpson, M. Antonelli, S. Bakas, M. Bilello, K. Farahani, B. van Ginneken, A. Kopp-Schneider, B. Landman, G. Litjens, B. Menze, O. Ronneberger, R. Summers, P. Bilic, P. Christ, R. Do, M. Gollub, J. Golia-Pernicka, S. Heckers, W. Jarnagin, M. McHugo, S. Napel, E. Vorontsov, L. Maier-Hein and M. Cardoso, "A large annotated medical image dataset for the development and evaluation of segmentation algorithms", arXiv:1902.09063, 2019.
- B. Liefers, J. Colijn, C. González-Gonzalo, T. Verzijden, P. Mitchell, C. Hoyng, B. van Ginneken, C. Klaver and C. Sánchez, "A deep learning model for segmentation of geographic atrophy to study its long-term natural history", arXiv:1908.05621, 2019.
- P. Putzky, D. Karkalousos, J. Teuwen, N. Moriakov, B. Bakker, M. Caan and M. Welling, "i-RIM applied to the fastMRI challenge", arXiv:1910.08952, 2019.
- N. Pawlowski, S. Bhooshan, N. Ballas, F. Ciompi, B. Glocker and M. Drozdzal, "Needles in Haystacks: On Classifying Tiny Objects in Large Images", arXiv:1908.06037, 2019.
- M. Argus, C. Schaefer-Prokop, D. Lynch and B. van Ginneken, "Function Follows Form: Regression from Complete Thoracic Computed Tomography Scans", arXiv:1909.12047, 2019.
- C. González-Gonzalo, B. Liefers, B. van Ginneken and C. Sánchez, "Iterative augmentation of visual evidence for weakly-supervised lesion localization in deep interpretability frameworks", arXiv:1910.07373, 2019.
- L. Maier-Hein, A. Reinke, M. Kozubek, A. L. Martel, T. Arbel, M. Eisenmann, A. Hanbuary, P. Jannin, H. Muller, S. Onogur, J. Saez-Rodriguez, B. van Ginneken, A. Kopp-Schneider and B. Landman, "BIAS: Transparent reporting of biomedical image analysis challenges", arXiv:1910.04071, 2019.
Papers in conference proceedings
- M. Caballo, J. Teuwen, R. Mann and I. Sechopolous, "Breast parenchyma analysis and classification for breast masses detection using texture feature descriptors and neural networks in dedicated breast CT images", Medical Imaging, 2019.
- N. Moriakov, K. Michielsen, R. Mann, J. Adler, I. Sechopolous and J. Teuwen, "Deep learning framework for digital breast tomosynthesis reconstruction", Medical Imaging, 2019.
- J. van Vugt, E. Marchiori, R. Mann, A. Gubern-Merida, N. Moriakov and J. Teuwen, "Vendor-independent soft tissue lesion detection using weakly supervised and unsupervised adversarial domain adaptation", Medical Imaging, 2019.
- N. Lessmann, J. Wolterink, M. Zreik, M. Viergever, B. van Ginneken and I. Isgum, "Vertebra partitioning with thin-plate spline surfaces steered by a convolutional neural network", Medical Imaging with Deep Learning, 2019.
- E. Calli, K. Murphy, E. Sogancioglu and B. van Ginneken, "FRODO: Free rejection of out-of-distribution samples: application to chest x-ray analysis", Medical Imaging with Deep Learning, 2019.
- A. Hering, B. van Ginneken and S. Heldmann, "mlVIRNET: Multilevel Variational Image Registration Network", Medical Image Computing and Computer-Assisted Intervention, 2019;11769:257-265.
- K. Dercksen, W. Bulten and G. Litjens, "Dealing with Label Scarcity in Computational Pathology: A Use Case in Prostate Cancer Classification", Medical Imaging with Deep Learning, 2019.
- T. van den Heuvel, C. de Korte and B. van Ginneken, "Automated interpretation of prenatal ultrasound using a predefined acquisition protocol in resource-limited countries", Medical Imaging with Deep Learning, 2019.
- J. Bokhorst, H. Pinckaers, P. van Zwam, I. Nagetgaal, J. van der Laak and F. Ciompi, "Learning from sparsely annotated data for semantic segmentation in histopathology images", Medical Imaging with Deep Learning, 2019;102:81-94.
- C. Mercan, M. Balkenhol, J. van der Laak and F. Ciompi, "From Point Annotations to Epithelial Cell Detection in Breast Cancer Histopathology using RetinaNet", Medical Imaging with Deep Learning, 2019.
- T. de Bel, M. Hermsen, J. Kers, J. van der Laak and G. Litjens, "Stain-Transforming Cycle-Consistent Generative Adversarial Networks for Improved Segmentation of Renal Histopathology", Medical Imaging with Deep Learning, 2019.
- H. Pinckaers, W. Bulten and G. Litjens, "High resolution whole prostate biopsy classification using streaming stochastic gradient descent", Medical Imaging, 2019(1).
- B. Liefers, C. González-Gonzalo, C. Klaver, B. van Ginneken and C. Sánchez, "Dense Segmentation in Selected Dimensions: Application to Retinal Optical Coherence Tomography", Medical Imaging with Deep Learning, 2019;102:337-346.
- T. van der Ouderaa, D. Worrall and B. van Ginneken, "Chest CT Super-resolution and Domain-adaptation using Memory-efficient 3D Reversible GANs", Medical Imaging with Deep Learning, 2019.
- S. van Velzen, M. Zreik, N. Lessmann, M. Viergever, P. de Jong, H. Verkooijen and I. Išgum, "Direct prediction of cardiovascular mortality from low-dose chest CT using deep learning", Medical Imaging, 2019.
- M. Kallenberg, D. Vanegas Camargo, M. Birhanu, A. Gubern-Mérida and N. Karssemeijer, "A deep learning method for volumetric breast density estimation from processed full field digital mammograms", Medical Imaging 2019: Computer-Aided Diagnosis, 2019.
- M. Hosseinzadeh, P. Brand and H. Huisman, "Effect of Adding Probabilistic Zonal Prior in Deep Learning-based Prostate Cancer Detection", Medical Imaging with Deep Learning, 2019.
- E. Calli, E. Sogancioglu, E. Scholten, K. Murphy and B. van Ginneken, "Handling label noise through model confidence and uncertainty: application to chest radiograph classification", Medical Imaging, 2019(1).
- H. Meine and A. Hering, "Efficient prealignment of CT scans for registration through a bodypart regressor", Medical Imaging with Deep Learning, 2019.
- D. Ruhe, V. Codreanu, C. van Leeuwen, D. Podareanu, V. Saletore and J. Teuwen, "Generating CT-scans with 3D Generative Adversarial Networks Using a Supercomputer", Medical Imaging meets NeurIPS, 2019.
- A. Hering and S. Heldmann, "Unsupervised Learning for Large Motion Thoracic CT Follow-Up Registration", Medical Imaging, 2019;10949:109491B.
Abstracts
- C. González-Gonzalo, B. Liefers, A. Vaidyanathan, H. van Zeeland, C. Klaver and C. Sánchez, "Opening the "black box" of deep learning in automated screening of eye diseases", Association for Research in Vision and Ophthalmology, 2019.
- S. van Velzen, N. Lessmann, M. Emaus, H. van den Bongard, H. Verkooijen and I. Isgum, "Deep learning for calcium scoring in radiotherapy treatment planning CT scans in breast cancer patients", Annual Meeting of the Radiological Society of North America, 2019.
- J. Bokhorst, H. Dawson, A. Blank, I. Zlobec, A. Lugli, M. Vieth, R. Kirsch, M. Urbanowicz, S. Brockmoeller, J. Flejou, L. Rijstenberg, J. van der Laak, F. Ciompi and I. Nagtegaal, "Assessment of tumor buds in colorectal cancer. A large-scale international digital observer study", European Congress of Pathology, 2019.
- M. Hermsen, T. de Bel, M. den Boer, E. Steenbergen, J. Kers, S. Florquin, J. Roelofs, M. Stegall, M. Alexander, B. Smith, B. Smeets, L. Hilbrands and J. van der Laak, "Deep learning-based histopathological assessment of renal tissue", American Society of Nephrology Kidney Week 2019, 2019.
- M. Silva, G. Milanese, F. Sabia, C. Jacobs, B. van Ginneken, M. Prokop, C. Schaefer-Prokop, A. Marchiano, N. Sverzellati and U. Pastorino, "Lung cancer risk after baseline round of screening: Only 20% of NLST eligibles require annual round", Annual Meeting of the European Society of Thoracic Imaging, 2019.
- M. Silva, G. Milanese, F. Sabia, C. Jacobs, B. van Ginneken, M. Prokop, C. Schaefer-Prokop, S. Sestini, A. Marchiano, N. Sverzellati and U. Pastorino, "Lung Cancer Screening in NLST Eligibles: Tailoring Annual Low-Dose Computed Tomography by Post-Test Risk Stratification", Annual Meeting of the Radiological Society of North America, 2019.
- D. Grob, L. Oostveen, C. Jacobs, M. Prokop, C. Schaefer-Prokop, I. Sechopoulos and M. Brink, "Intra-patient comparison of pulmonary nodule enhancement in subtraction CT and dual-energy CT", Annual Meeting of the European Society of Thoracic Imaging, 2019.
- W. Aswolinskiy, H. Horlings, L. Mulder, J. van der Laak, J. Wesseling, E. Lips and F. Ciompi, "Potential of an AI-based digital biomarker to predict neoadjuvant chemotherapy response from preoperative biopsies of Luminal-B breast cancer", European Congress of Pathology, 2019.
- B. Liefers, J. Colijn, C. González-Gonzalo, A. Vaidyanathan, H. van Zeeland, P. Mitchell, C. Klaver and C. Sánchez, "Prediction of areas at risk of developing geographic atrophy in color fundus images using deep learning", Association for Research in Vision and Ophthalmology, 2019.
- W. Sanderink, J. Teuwen, L. Appelman, I. Sechopoulos, N. Karssemeijer and R. Mann, "Simultaneous multi-slice single-shot DWI compared to routine read-out-segmented DWI for evaluation of breast lesions", Annual Meeting of the International Society for Magnetic Resonance in Medicine, 2019.
- H. van Zeeland, J. Meakin, B. Liefers, C. González-Gonzalo, A. Vaidyanathan, B. van Ginneken, C. Klaver and C. Sánchez, "EyeNED workstation: Development of a multi-modal vendor-independent application for annotation, spatial alignment and analysis of retinal images", Association for Research in Vision and Ophthalmology, 2019.
- W. Bulten, H. Pinckaers, C. Hulsbergen-van de Kaa and G. Litjens, "Automated Gleason Grading of Prostate Biopsies Using Deep Learning", United States and Canadian Academy of Pathology (USCAP) 108th Annual Meeting, 2019.
- G. Chlebus, G. Humpire Mamani, A. Schenk, B. van Ginneken and H. Meine, "Mimicking radiologists to improve the robustness of deep-learning based automatic liver segmentation", Annual Meeting of the Radiological Society of North America, 2019.
- N. Khalili, N. Lessmann, E. Turk, M. Viergever, M. Benders and I. Isgum, "Brain tissue segmentation in fetal MRI using convolutional neural networks with simulated intensity inhomogeneities", Annual Meeting of the International Society for Magnetic Resonance in Medicine, 2019.
- D. Valkenburg, E. Runhart, B. Liefers, S. Lambertus, C. Sánchez, F. Cremers, B. Nathalie M and C. Hoyng, "Familial discordance in disease phenotype in siblings with Stargardt disease", Association for Research in Vision and Ophthalmology, 2019.
- S. van Velzen, J. Terry, B. de Vos, N. Lessmann, S. Nair, A. Correa, H. Verkooijen, J. Carr and I. Isgum, "Automatic prediction of coronary heart disease events using coronary and thoracic aorta calcium among african americans in the Jackson Heart Study", Annual Meeting of the Radiological Society of North America, 2019.
- J. Engelberts, C. González-Gonzalo, C. Sánchez and M. van Grinsven, "Automatic Segmentation of Drusen and Exudates on Color Fundus Images using Generative Adversarial Networks", Association for Research in Vision and Ophthalmology, 2019.
- C. van 't Klooster, H. Nathoe, J. Hjortnaes, M. Bots, I. Isgum, N. Lessmann, Y. van der Graaf, T. Leiner and F. Visseren, "Prevalence and risk factors of multifocal cardiovascular calcification in patients at high cardiovascular risk", European Society of Cardiology Congress, 2019.
- T. van den Heuvel, B. van Ginneken and C. de Korte, "Improving Maternal Care In Resource-Limited Settings Using A Low-Cost Ultrasound Device And Machine Learning", Dutch Bio-Medical Engineering Conference, 2019.
- C. Jacobs, E. Scholten, A. Schreuder, M. Prokop and B. van Ginneken, "An observer study comparing radiologists with the prize-winning lung cancer detection algorithms from the 2017 Kaggle Data Science Bowl", Annual Meeting of the Radiological Society of North America, 2019.
- C. Jacobs and B. van Ginneken, "Deep learning for detection and characterization of lung nodules", Annual Meeting of the European Society of Thoracic Imaging, 2019.
- T. Haddad, N. Farahani, J. Bokhorst, F. Doubrava-Simmer, F. Ciompi, I. Nagtegaal and J. van der Laak, "A Colorectal Carcinoma in 3D: Merging Knife-Edge Scanning Microscopy and Deep Learning", EACR, 2019.
PhD theses
- E. Smit, "Feasibility of a single-acquisition CT stroke protocol", PhD thesis, 2019.
- R. Philipsen, "Automated chest radiography reading. Improvements, validation, and cost-effectiveness analysis", PhD thesis, 2019.
- A. Ruiz, "Artificial intelligence & tomosynthesis for breast cancer detection", PhD thesis, 2019.
- D. Grob, "Functional CT Imaging of the Lung: Substraction CT as a novel technique", PhD thesis, 2019.
- L. Estrella, "Quantification of COPD biomarkers in thoracic CT scans", PhD thesis, 2019.
- F. Venhuizen, "Machine Learning for Quantification of Age-Related Macular Degeneration Imaging Biomarkers in Optical Coherence Tomography", PhD thesis, 2019.
- M. Dalmis, "Automated Analysis of Breast MRI From traditional methods into deep learning", PhD thesis, 2019.
- T. van den Heuvel, "Automated low-cost ultrasound: improving antenatal care in resource-limited settings", PhD thesis, 2019.
- C. Balta, "Objective image quality assessment in X-ray breast imaging", PhD thesis, 2019.
- N. Lessmann, "Machine Learning based quantification of extrapulmonary diseases in chest CT", PhD thesis, 2019.
- J. van Zelst, "Automated 3D breast ultrasound Advances in breast cancer detection, diagnosis and screening", PhD thesis, 2019.
Master theses
- P. Sonsma, "Lymphocyte detection in hematoxylin-eosin stained histopathological images of breast cancer", Master thesis, 2019.
- T. van der Ouderaa, "Reversible Networks for Memory-efficient Image-to-Image Translation in 3D Medical Imaging", Master thesis, 2019.
- G. Mooij, "Using GANs to synthetically stain histopathological images to generate training data for automatic mitosis detection in breast tissue", Master thesis, 2019.
- E. Stoelinga, "Extracting biomarkers from hematoxylin-eosin stained histopathological images of lung cancer", Master thesis, 2019.
- D. Geijs, "Tumor segmentation in fluorescent TNBC immunohistochemical multiplex images using deep learning", Master thesis, 2019.
- J. Winkens, "Out-of-distribution detection for computational pathology with multi-head ensembles", Master thesis, 2019.
- T. Boers, "Interactive Residual 3D U-net for the Segmentation of the Pancreas in Computed Tomography Scans", Master thesis, 2019.
- L. Valacchi, "Analysis and endotracheal tube detection in chest x-rays using deep learning", Master thesis, 2019.
- M. van Rijthoven, "Cancer research in digital pathology using convolutional neural networks", Master thesis, 2019.
- K. Dercksen, "Prostate Cancer Classification and Label Scarcity", Master thesis, 2019.
- M. Kok, "Metastases Detection in Lymph Nodes using Transfer Learning", Master thesis, 2019.
Other publications
- S. Hu, D. Worrall, S. Knegt, B. Veeling, H. Huisman and M. Welling, "Supervised Uncertainty Quantification for Segmentation with Multiple Annotations", Lecture Notes in Computer Science, 2019:137-145.
- A. Hering, S. Kuckertz, S. Heldmann and M. Heinrich, "Enhancing Label-Driven Deep Deformable Image Registration with Local Distance Metrics for State-of-the-Art Cardiac Motion Tracking", Informatik aktuell, 2019:309-314.