Josien Pluim

Josien Pluim studied Computer Science at the University of Groningen and graduated in 1996, specializing in Scientific Computing and Imaging. Having done the research for her master's thesis at the Image Sciences Institute, she was bribed into staying as a PhD candidate. Her research project involved multimodality image registration, focusing on mutual information as the registration measure. In June 2001, she received her PhD degree.

She is Professor of Medical Image Analysis at Eindhoven University of Technology, in combination with a part-time position at the Image Sciences Institute. She is or was associate editor of the IEEE Transactions on Medical Imaging, IEEE Transactions on Biomedical Enigineering, Medical Physics, SPIE Journal of Medical Imaging and Medical Image Analysis. She chaired the Workshop on Biomedical Image Registration (WBIR) 2006, was programme co-chair of MICCAI 2010 and chair of the Image Processing conference of SPIE Medical Imaging (2006-2009).

Her research focusses on medical image analysis, both methodological and applied research. The main research themes are oncology, image registration and digital pathology.

Publications

• Body composition and checkpoint inhibitor treatment outcomes in advanced melanoma: a multicenter cohort study
  Schuiveling, Mark, Ter Maat, Laurens S, Van Duin, Isabella A J, Verheijden, Rik J, Troenokarso, Max F, Moeskops, Pim, Verhoeff, Joost J C, Elias, Sjoerd G, Van Amsterdam, Wouter A C, Burgers, Femke, Van Den Berkmortel, Franchette W P J, Boers-Sonderen, Marye J, Boomsma, Martijn F, De Groot, Jan Willem, Haanen, John B A G, Hospers, Geke A P, Piersma, Djura, Vreugdenhil, Gerard, Westgeest, Hans M, Kapiteijn, Ellen, Labots, Mariette, Veldhuis, Wouter B, Van Diest, Paul J, De Jong, Pim A, Pluim, Josien P W, Leiner, Tim, Veta, Mitko, Suijkerbuijk, Karijn P M Feb 2025 in Journal of the National Cancer Institute
• Influence of learned landmark correspondences on lung CT registration
  Bhat, Ishaan, Kuijf, Hugo J., Viergever, Max A., Pluim, Josien P.W. Aug 2024 in Medical Physics 51 (8), p. 5321-5336
• Deep-learning-based joint rigid and deformable contour propagation for magnetic resonance imaging-guided prostate radiotherapy
  Kolenbrander, Iris D, Maspero, Matteo, Hendriksen, Allard A, Pollitt, Ryan, van der Voort van Zyp, Jochem R N, van den Berg, Cornelis A T, Pluim, Josien P W, van Eijnatten, Maureen A J M Apr 2024 in Medical Physics 51 (4), p. 2367-2377
• Deep learning on CT scans to predict checkpoint inhibitor treatment outcomes in advanced melanoma
  Ter Maat, Laurens S, De Mooij, Rob A J, Van Duin, Isabella A J, Verhoeff, Joost J C, Elias, Sjoerd G, Leiner, Tim, van Amsterdam, Wouter A C, Troenokarso, Max F, Arntz, Eran R A N, Van den Berkmortel, Franchette W P J, Boers-Sonderen, Marye J, Boomsma, Martijn F, Van den Eertwegh, Fons J M, de Groot, Jan Willem, Hospers, Geke A P, Piersma, Djura, Vreugdenhil, Art, Westgeest, Hans M, Kapiteijn, Ellen, De Wit, Ardine A, Blokx, Willeke A M, Van Diest, Paul J, De Jong, Pim A, Pluim, Josien P W, Suijkerbuijk, Karijn P M, Veta, Mitko Dec 2024 in Scientific Reports 14 (1),
• Assessing the Robustness of Image Registration Models Under Domain Shifts with Learnable Input Images
  Kolenbrander, Iris D., Prasad, Vidya, Zikken, Leanne, van Eijnatten, Maureen A.J.M., Maspero, Matteo, Pluim, Josien P.W. oct 2024 in Assessing the Robustness of Image Registration Models Under Domain Shifts with Learnable Input Images: Biomedical Image Registration - 11th International Workshop, WBIR 2024, Held in Conjunction with MICCAI 2024, Proceedings p. 101-111 (; vol. )
• Deep learning-based recognition of key anatomical structures during robot-assisted minimally invasive esophagectomy
  den Boer, R B, Jaspers, T J M, de Jongh, C, Pluim, J P W, van der Sommen, F, Boers, T, van Hillegersberg, R, Van Eijnatten, M A J M, Ruurda, J P Jul 2023 in Surgical endoscopy 37 (7), p. 5164-5175
• CT radiomics compared to a clinical model for predicting checkpoint inhibitor treatment outcomes in patients with advanced melanoma
  Ter Maat, Laurens S, van Duin, Isabella A J, Elias, Sjoerd G, Leiner, Tim, Verhoeff, Joost J C, Arntz, Eran R A N, Troenokarso, Max F, Blokx, Willeke A M, Isgum, Ivana, de Wit, Geraldine A, van den Berkmortel, Franchette W P J, Boers-Sonderen, Marye J, Boomsma, Martijn F, van den Eertwegh, Fons J M, de Groot, Jan Willem B, Piersma, Djura, Vreugdenhil, Art, Westgeest, Hans M, Kapiteijn, Ellen, van Diest, Paul J, Pluim, Josien P W, de Jong, Pim A, Suijkerbuijk, Karijn P M, Veta, Mitko May 2023 in European Journal of Cancer 185 p. 167-177
• Reconstruction of the Corticospinal Tract in Patients with Motor-Eloquent High-Grade Gliomas Using Multilevel Fiber Tractography Combined with Functional Motor Cortex Mapping
  Zhylka, A., Sollmann, N., Kofler, F., Radwan, A., De Luca, A., Gempt, J., Wiestler, B., Menze, B., Schroeder, A., Zimmer, C., Kirschke, J. S., Sunaert, S., Leemans, A., Krieg, S. M., Pluim, J. Mar 2023 in AJNR. American journal of neuroradiology 44 (3), p. 283-290
• A Framework for Simulating Cardiac MR Images with Varying Anatomy and Contrast
  Amirrajab, Sina, Khalil, Yasmina Al, Lorenz, Cristian, Weese, Jurgen, Pluim, Josien, Breeuwer, Marcel Mar 2023 in IEEE transactions on medical imaging 42 (3), p. 726-738
• Deep learning based correction of RF field induced inhomogeneities for T2w prostate imaging at 7 T
  Harrevelt, Seb D, Meliado, Ettore F M, van Lier, Astrid L H M W, Reesink, Daan, Meijer, Richard P, Pluim, Josien P W, Raaijmakers, Alexander J E Dec 2023 in NMR in Biomedicine 36 (12),
• Bandwidth Improvement in Ultrasound Image Reconstruction Using Deep Learning Techniques
  Awasthi, Navchetan, van Anrooij, Laslo, Jansen, Gino, Schwab, Hans Martin, Pluim, Josien P.W., Lopata, Richard G.P. Jan 2023 in Healthcare (Switzerland) 11 (1), p. 1-19
• Insights from the IronTract challenge: Optimal methods for mapping brain pathways from multi-shell diffusion MRI
  Aug 2022 in NeuroImage 257 p. 1-17
• LVNet: Lightweight Model for Left Ventricle Segmentation for Short Axis Views in Echocardiographic Imaging
  Awasthi, Navchetan, Vermeer, Lars, Fixsen, Louis S., Lopata, Richard G.P., Pluim, Josien P.W. Jun 2022 in IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 69 (6), p. 2115-2128
• Automatic evaluation of graft orientation during Descemet membrane endothelial keratoplasty using intraoperative OCT
  Muijzer, Marc B., Heslinga, Friso G., Couwenberg, Floor, Noordmans, Herke Jan, Oahalou, Abdelkarim, Pluim, Josien P.W., Veta, Mitko, Wisse, Robert P.L. May 2022 in Biomedical optics express 13 (5), p. 2683-2694
• Deep learning-based breast cancer grading and survival analysis on whole-slide histopathology images
  Wetstein, Suzanne C., de Jong, Vincent M.T., Stathonikos, Nikolas, Opdam, Mark, Dackus, Gwen M.H.E., Pluim, Josien P.W., van Diest, Paul J., Veta, Mitko Dec 2022 in Scientific Reports 12 (1),
• Computer-aided anatomy recognition in intrathoracic and -abdominal surgery: a systematic review
  den Boer, R B, de Jongh, C, Huijbers, W T E, Jaspers, T J M, Pluim, J P W, van Hillegersberg, R, Van Eijnatten, M, Ruurda, J P Dec 2022 in Surgical endoscopy 36 (12), p. 8737-8752
• Imaging to predict checkpoint inhibitor outcomes in cancer. A systematic review
  Ter Maat, Laurens S, van Duin, Isabella A J, Elias, Sjoerd G, van Diest, Paul J, Pluim, Josien P W, Verhoeff, Joost J C, de Jong, Pim A, Leiner, Tim, Veta, Mitko, Suijkerbuijk, Karijn P M Nov 2022 in European Journal of Cancer 175 p. 60-76
• Label-informed cardiac magnetic resonance image synthesis through conditional generative adversarial networks
  Amirrajab, Sina, Al Khalil, Yasmina, Lorenz, Cristian, Weese, Jürgen, Pluim, Josien, Breeuwer, Marcel Oct 2022 in Computerized Medical Imaging and Graphics 101
• Generalized Probabilistic U-Net for Medical Image Segementation
  Bhat, Ishaan, Pluim, Josien P.W., Kuijf, Hugo J. 2022 in Generalized Probabilistic U-Net for Medical Image Segementation: Uncertainty for Safe Utilization of Machine Learning in Medical Imaging - 4th International Workshop, UNSURE 2022, Held in Conjunction with MICCAI 2022, Proceedings p. 113-124 (; vol. )
• Deep learning-based grading of ductal carcinoma in situ in breast histopathology images
  Wetstein, Suzanne C., Stathonikos, Nikolas, Pluim, Josien P.W., Heng, Yujing J., ter Hoeve, Natalie D., Vreuls, Celien P.H., van Diest, Paul J., Veta, Mitko Apr 2021 in Laboratory Investigation 101 (4), p. 525-533
• Using uncertainty estimation to reduce false positives in liver lesion detection
  Bhat, Ishaan, Kuijf, Hugo J., Cheplygina, Veronika, Pluim, Josien P.W. apr 2021 in Using uncertainty estimation to reduce false positives in liver lesion detection: 2021 IEEE 18th International Symposium on Biomedical Imaging, ISBI 2021 p. 663-667 (; vol. )
• Deep Learning Regression for Prostate Cancer Detection and Grading in Bi-parametric MRI
  De Vente, Coen, Vos, Pieter, Hosseinzadeh, Matin, Pluim, Josien, Veta, Mitko Feb 2021 in IEEE Transactions on Biomedical Engineering 68 (2), p. 374-383
• Roto-translation equivariant convolutional networks: Application to histopathology image analysis
  Lafarge, Maxime W, Bekkers, Erik J, Pluim, Josien P W, Duits, Remco, Veta, Mitko Feb 2021 in Medical Image Analysis 68 p. 1-12
• Tracking the Corticospinal Tract in Patients With High-Grade Glioma: Clinical Evaluation of Multi-Level Fiber Tracking and Comparison to Conventional Deterministic Approaches
  Zhylka, Andrey, Sollmann, Nico, Kofler, Florian, Radwan, Ahmed, De Luca, Alberto, Gempt, Jens, Wiestler, Benedikt, Menze, Bjoern, Krieg, Sandro M., Zimmer, Claus, Kirschke, Jan S., Sunaert, Stefan, Leemans, Alexander, Pluim, Josien P.W. Dec 2021 in Frontiers in oncology 11
• CLDICE - A novel topology-preserving loss function for tubular structure segmentation
  Shit, Suprosanna, Paetzold, Johannes C., Sekuboyina, Anjany, Ezhov, Ivan, Unger, Alexander, Zhylka, Andrey, Pluim, Josien P.W., Bauer, Ulrich, Menze, Bjoern H. 2021 in CLDICE - A novel topology-preserving loss function for tubular structure segmentation: Proceedings - 2021 IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2021 p. 16555-16564 (; vol. )
• Quantifying Graft Detachment after Descemet's Membrane Endothelial Keratoplasty with Deep Convolutional Neural Networks
  Heslinga, Friso G, Alberti, Mark, Pluim, Josien P W, Cabrerizo, Javier, Veta, Mitko Aug 2020 in Translational vision science & technology 9 (2), p. 1-9
• Correcting time-intensity curves in dynamic contrast-enhanced breast MRI for inhomogeneous excitation fields at 7T
  van Rijssel, Michael J., Pluim, Josien P.W., Chan, Hui Shan M., van den Wildenberg, Lieke, Schmitz, Alexander M.Th, Luijten, Peter R., Gilhuijs, Kenneth G.A., Klomp, Dennis W.J. Aug 2020 in Magnetic Resonance in Medicine 84 (2), p. 1000-1010
• Accelerating implant RF safety assessment using a low-rank inverse update method
  Stijnman, Peter R.S., Tokaya, Janot P., van Gemert, Jeroen, Luijten, Peter R., Pluim, Josien P.W., Brink, Wyger M., Remis, Rob F., van den Berg, Cornelis A.T., Raaijmakers, Alexander J.E. May 2020 in Magnetic Resonance in Medicine 83 (5), p. 1796-1809
• Progressively Trained Convolutional Neural Networks for Deformable Image Registration
  Eppenhof, Koen A J, Lafarge, Maxime W, Veta, Mitko, Pluim, Josien P W May 2020 in IEEE transactions on medical imaging 39 (5), p. 1594-1604
• Deep learning assessment of breast terminal duct lobular unit involution: Towards automated prediction of breast cancer risk
  Wetstein, Suzanne C, Onken, Allison M, Luffman, Christina, Baker, Gabrielle M, Pyle, Michael E, Kensler, Kevin H, Liu, Ying, Bakker, Bart, Vlutters, Ruud, van Leeuwen, Marinus B, Collins, Laura C, Schnitt, Stuart J, Pluim, Josien P W, Tamimi, Rulla M, Heng, Yujing J, Veta, Mitko Apr 2020 in PLoS ONE 15 (4), p. e0231653
• Segmentation and Classification of Melanoma and Nevus in Whole Slide Images
  Van Zon, Mike, Stathonikos, Nikolas, Blokx, Willeke A.M., Komina, Selim, Maas, Sybren L.N., Pluim, Josien P.W., Van Diest, Paul J., Veta, Mitko apr 2020 in Segmentation and Classification of Melanoma and Nevus in Whole Slide Images: ISBI 2020 - 2020 IEEE International Symposium on Biomedical Imaging p. 263-266 (; vol. )
• Fast contour propagation for MR-guided prostate radiotherapy using convolutional neural networks
  Eppenhof, K A J, Maspero, M, Savenije, M H F, de Boer, J C J, van der Voort van Zyp, J R N, Raaymakers, B W, Raaijmakers, A J E, Veta, M, van den Berg, C A T, Pluim, J P W Mar 2020 in Medical Physics 47 (3), p. 1238-1248
• Untangling the diffusion signal using the phasor transform
  van Rijssel, Michael J., Froeling, Martijn, van Lier, Astrid L.H.M.W., Verhoeff, Joost J.C., Pluim, Josien P.W. Dec 2020 in NMR in Biomedicine 33 (12), p. 1-19
• Patient-specific fine-tuning of convolutional neural networks for follow-up lesion quantification
  Jansen, Mariëlle, Kuijf, Hugo, Dhara, Ashis K., Weaver, Nick, Biessels, Geert Jan, Strand, Robin, Pluim, JPW Nov 2020 in Journal of Medical Imaging 7 (6), p. 1-15
• Automated Quantitative Measures of Terminal Duct Lobular Unit Involution and Breast Cancer Risk
  Kensler, Kevin H, Liu, Emily Z F, Wetstein, Suzanne C, Onken, Allison M, Luffman, Christina I, Baker, Gabrielle M, Collins, Laura C, Schnitt, Stuart J, Bret-Mounet, Vanessa C, Veta, Mitko, Pluim, Josien P W, Liu, Ying, Colditz, Graham A, Eliassen, A Heather, Hankinson, Susan E, Tamimi, Rulla M, Heng, Yujing J Nov 2020 in Cancer Epidemiology Biomarkers & Prevention 29 (11), p. 2358-2368
• Ultrasound Based Wall Stress Analysis of Abdominal Aortic Aneurysms using Multiperspective Imaging
  van Disseldorp, Emiel M J, van Dronkelaar, Julia J, Pluim, Josien P W, van de Vosse, Frans N, van Sambeek, Marc R H M, Lopata, Richard G P Jan 2020 in European Journal of Vascular and Endovascular Surgery 59 (1), p. 81-91
• Reducing distortions in echo-planar breast imaging at ultrahigh field with high-resolution off-resonance maps
  van Rijssel, Michael J, Zijlstra, Frank, Seevinck, Peter R, Luijten, Peter R, Gilhuijs, Kenneth G A, Klomp, Dennis W J, Pluim, Josien P W Jul 2019 in Magnetic Resonance in Medicine 82 (1), p. 425-435
• Predicting breast tumor proliferation from whole-slide images: The TUPAC16 challenge
  Veta, Mitko, Heng, Yujing J., Stathonikos, Nikolas, Bejnordi, Babak Ehteshami, Beca, Francisco, Wollmann, Thomas, Rohr, Karl, Shah, Manan A., Wang, Dayong, Rousson, Mikael, Hedlund, Martin, Tellez, David, Ciompi, Francesco, Zerhouni, Erwan, Lanyi, David, Viana, Matheus, Kovalev, Vassili, Liauchuk, Vitali, Phoulady, Hady Ahmady, Qaiser, Talha, Graham, Simon, Rajpoot, Nasir, Sjöblom, Erik, Molin, Jesper, Paeng, Kyunghyun, Hwang, Sangheum, Park, Sunggyun, Jia, Zhipeng, Chang, Eric I.Chao, Xu, Yan, Beck, Andrew H., van Diest, Paul J., Pluim, Josien P.W. May 2019 in Medical Image Analysis 54 p. 111-121
• Not-so-supervised: A survey of semi-supervised, multi-instance, and transfer learning in medical image analysis
  Cheplygina, Veronika, de Bruijne, Marleen, Pluim, Josien P.W. May 2019 in Medical Image Analysis 54 p. 280-296
• Automatic classification of focal liver lesions based on MRI and risk factors
  Jansen, MJA, Kuijf, HJ, Veldhuis, WB, Wessels, FJ, Viergever, MA, Pluim, JPW May 2019 in PLoS ONE 14 (5),
• Pulmonary CT Registration Through Supervised Learning With Convolutional Neural Networks
  Eppenhof, Koen A.J., Pluim, Josien P.W. May 2019 in IEEE transactions on medical imaging 38 (5), p. 1097-1105
• Liver segmentation and metastases detection in MR images using convolutional neural networks
  Jansen, Mariëlle J A, Kuijf, Hugo J, Niekel, Maarten, Veldhuis, Wouter B, Wessels, Frank J, Viergever, Max A, Pluim, Josien P W Oct 2019 in Journal of Medical Imaging 6 (4),
• Convolutional neural network-based regression for quantification of brain characteristics using MRI
  Fernandes, João, Alves, Victor, Khalili, Nadieh, Benders, Manon J.N.L., Išgum, Ivana, Pluim, Josien, Moeskops, Pim jan 2019 in Convolutional neural network-based regression for quantification of brain characteristics using MRI: New Knowledge in Information Systems and Technologies - Volume 2 p. 577-586 (; vol. )
• Approximation of a pipeline of unsupervised retina image analysis methods with a CNN
  Heslinga, Friso G., Pluim, Josien P.W., Dashtbozorg, Behdad, Berendschot, Tos T.J.M., Houben, A. J.H.M., Henry, Ronald M.A., Veta, Mitko jan 2019 in Approximation of a pipeline of unsupervised retina image analysis methods with a CNN: Medical Imaging 2019 p. (; vol. )
• Optimal input configuration of dynamic contrast enhanced MRI in convolutional neural networks for liver segmentation
  Jansen, MJA, Kuijf, HJ, Pluim, JPW jan 2019 at Optimal input configuration of dynamic contrast enhanced MRI in convolutional neural networks for liver segmentation
• Convolutional Neural Networks for Segmentation of the Left Atrium from Gadolinium-Enhancement MRI Images
  de Vente, Coen, Veta, Mitko, Razeghi, Orod, Niederer, Steven, Pluim, Josien, Rhode, Kawal, Karim, Rashed jan 2019 in Convolutional Neural Networks for Segmentation of the Left Atrium from Gadolinium-Enhancement MRI Images: Statistical Atlases and Computational Models of the Heart. Atrial Segmentation and LV Quantification Challenges - 9th International Workshop, STACOM 2018, Held in Conjunction with MICCAI 2018, Revised Selected Papers p. 348-356 (; vol. )
• Muti-shell Diffusion MRI Harmonisation and Enhancement Challenge (MUSHAC): Progress and Results
  Ning, Lipeng, Bonet-Carne, Elisenda, Grussu, Francesco, Sepehrband, Farshid, Kaden, Enrico, Veraart, Jelle, Blumberg, Stefano B., Khoo, Can Son, Palombo, Marco, Coll-Font, Jaume, Scherrer, Benoit, Warfield, Simon K., Karayumak, Suheyla Cetin, Rathi, Yogesh, Koppers, Simon, Weninger, Leon, Ebert, Julia, Merhof, Dorit, Moyer, Daniel, Pietsch, Maximilian, Christiaens, Daan, Teixeira, Rui, Tournier, Jacques Donald, Zhylka, Andrey, Pluim, Josien, Parker, Greg, Rudrapatna, Umesh, Evans, John, Charron, Cyril, Jones, Derek K., Tax, Chantal W.M. jan 2019 in Muti-shell Diffusion MRI Harmonisation and Enhancement Challenge (MUSHAC):Progress and Results Computational diffusion MRI p. 217-224 (; vol. )
• Progressively growing convolutional networks for end-to-end deformable image registration
  Eppenhof, Koen A.J., Lafarge, Maxime W., Pluim, Josien P.W. jan 2019 in Progressively growing convolutional networks for end-to-end deformable image registration: Medical Imaging 2019 p. (; vol. )
• Detection of acini in histopathology slides: Towards automated prediction of breast cancer risk
  Wetstein, Suzanne C., Onken, Allison M., Baker, Gabrielle M., Pyle, Michael E., Pluim, Josien P.W., Tamimi, Rulla M., Heng, Yujing J., Veta, Mitko jan 2019 in Detection of acini in histopathology slides:Towards automated prediction of breast cancer risk Medical Imaging 2019 p. (; vol. )
• Learning Domain-Invariant Representations of Histological Images
  Lafarge, Maxime W, Pluim, Josien P W, Eppenhof, Koen A J, Veta, Mitko 2019 in Frontiers in medicine 6
• Selection Strategies for Atlas-Based Mosaicing of Left Atrial 3-D Transesophageal Echocardiography Data
  Mulder, Harriët W., van Stralen, Marijn, Ren, Ben, Haak, Alexander, van Burken, Gerard, Viergever, Max A., Bosch, Johan G., Pluim, Josien P.W. Jul 2018 in Ultrasound in Medicine and Biology 44 (7), p. 1533-1543
• Inferring a third spatial dimension from 2D histological images
  Lafarge, Maxime W., Pluim, Josien P.W., Eppenhof, Koen A.J., Moeskops, Pim, Veta, Mitko may 2018 in Inferring a third spatial dimension from 2D histological images: 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018 p. 586-589 (; vol. )
• Automatic classification of focal liver lesions based on clinical DCE-MR and T2-weighted images: A feasibility study
  Jansen, M. J.A., Kuijf, H. J., Pluim, J. P.W. may 2018 in Automatic classification of focal liver lesions based on clinical DCE-MR and T2-weighted images:A feasibility study 2018 IEEE 15th International Symposium on Biomedical Imaging, ISBI 2018 p. 245-248 (; vol. )
• Reconnection of Interrupted Curvilinear Structures via Cortically Inspired Completion for Ophthalmologic Images
  Zhang, Jiong, Bekkers, Erik, Chen, Da, Berendschot, Tos T.J.M., Schouten, Jan, Pluim, Josien P.W., Shi, Yonggang, Dashtbozorg, Behdad, Romeny, Bart M.Ter Haar May 2018 in IEEE Transactions on Biomedical Engineering 65 (5), p. 1151-1165
• Error estimation of deformable image registration of pulmonary CT scans using convolutional neural networks
  Eppenhof, Koen A.J., Pluim, Josien P.W. Apr 2018 in Journal of Medical Imaging 5 (2),
• Estimating B₁⁺ in the breast at 7T using a generic template
  van Rijssel, Michael J., Pluim, Josien P. W., Luijten, Peter R., Gilhuijs, Kenneth G. A., Raaijmakers, Alexander J. E., Klomp, Dennis W. J. Mar 2018 in NMR in Biomedicine 31 (5),
• Deformable image registration using convolutional neural networks
  Eppenhof, Koen A.J., Lafarge, Maxime W., Moeskops, Pim, Veta, Mitko, Pluim, Josien P.W. jan 2018 in Deformable image registration using convolutional neural networks: Medical Imaging 2018 p. (; vol. )
• Roto-translation covariant convolutional networks for medical image analysis
  Bekkers, Erik J., Lafarge, Maxime W., Veta, Mitko, Eppenhof, Koen A.J., Pluim, Josien P.W., Duits, Remco jan 2018 in Roto-translation covariant convolutional networks for medical image analysis: Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 - 21st International Conference, 2018, Proceedings p. 440-448 (; vol. )
• Crowd disagreement about medical images is informative
  Cheplygina, Veronika, Pluim, Josien P.W. jan 2018 in Crowd disagreement about medical images is informative: Intravascular Imaging and Computer Assisted Stenting and Large-Scale Annotation of Biomedical Data and Expert Label Synthesis - 7th Joint International Workshop, CVII-STENT 2018 and Third International Workshop, LABELS 2018 Held in Conjunction with MICCAI 2018 p. 105-111 (; vol. )
• Evaluation of a deep learning approach for the segmentation of brain tissues and white matter hyperintensities of presumed vascular origin in MRI
  Moeskops, Pim, de Bresser, Jeroen, Kuijf, Hugo J., Mendrik, AM, Biessels, Geert Jan, Pluim, Josien P.W., Išgum, Ivana 2018 in Neuroimage: Clinical [E] 17 p. 251-262
• Automatic detection of cortical microinfarcts on 3T brain MRI using deep convolutional neural networks
  Kuijf, Hugo, Veta, Mitko, Hilal, Saima, van Veluw, Susanne, Viergever, Max A., Pluim, JPW, Chen, Christopher, Biessels, Geert Jan 2018 at Automatic detection of cortical microinfarcts on 3T brain MRI using deep convolutional neural networks
• Evaluation of motion correction for clinical dynamic contrast enhanced MRI of the liver
  Jansen, M. J.A., Kuijf, H. J., Veldhuis, W. B., Wessels, F. J., Van Leeuwen, M. S., Pluim, J. P.W. Sep 2017 in Physics in Medicine and Biology 62 (19), p. 7556-7568
• Atlas-Based Mosaicing of Left Atrial 3-D Transesophageal Echocardiography Images
  Mulder, Harriët W., van Stralen, Marijn, Ren, Ben, Haak, Alexander, Viergever, Max A., Bosch, Johan G., Pluim, JPW Apr 2017 in Ultrasound in Medicine and Biology 3 (4), p. 765-774
• The truth is hard to make: Validation of medical image registration
  Pluim, Josien P.W., Muenzing, Sascha E.A., Eppenhof, Koen A.J., Murphy, Keelin apr 2017 in The truth is hard to make:Validation of medical image registration 2016 23rd International Conference on Pattern Recognition, ICPR 2016 p. 2294-2300 (; vol. )
• Subject-specific liver motion modeling in MRI: A feasibility study on spatiotemporal prediction
  Noorda, Yolanda H., Bartels, Lambertus W., Viergever, Max A., Pluim, JPW Mar 2017 in Physics in Medicine and Biology 62 (7), p. 2581-2597
• Gland segmentation in colon histology images: The glas challenge contest
  Sirinukunwattana, Korsuk, Pluim, JPW, Chen, Hao, Qi, Xiaojuan, Heng, Pheng-Ann, Guo, Yun Bo, Wang, Li Yang, Matuszewski, Bogdan J, Bruni, Elia, Sanchez, Urko, Böhm, Anton, Ronneberger, Olaf, Cheikh, Bassem Ben, Racoceanu, Daniel, Kainz, Philipp, Pfeiffer, Michael, Urschler, Martin, Snead, David R J, Rajpoot, Nasir M Jan 2017 in Medical Image Analysis 35 p. 489-502
• Domain-adversarial neural networks to address the appearance variability of histopathology images
  Lafarge, Maxime W., Pluim, Josien P.W., Eppenhof, Koen A.J., Moeskops, Pim, Veta, Mitko 2017 in Domain-adversarial neural networks to address the appearance variability of histopathology images: Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings p. 83-91 (; vol. )
• Motion correction of dynamic contrast enhanced MRI of the liver
  Jansen, Mariëlle J.A., Veldhuis, Wouter B., Van Leeuwen, Maarten S., Pluim, Josien P.W. 2017 in Motion correction of dynamic contrast enhanced MRI of the liver: Medical Imaging 2017: Image Processing p. (; vol. )
• Adversarial training and dilated convolutions for brain MRI segmentation
  Moeskops, Pim, Veta, Mitko, Lafarge, Maxime W., Eppenhof, Koen A.J., Pluim, Josien P.W. 2017 in Adversarial training and dilated convolutions for brain MRI segmentation: Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings p. 56-64 (; vol. )
• Exploring the Similarity of Medical Imaging Classification Problems
  Cheplygina, Veronika, Moeskops, Pim, Veta, Mitko, Dashtbozorg, Behdad, Pluim, Josien P.W. 2017 in Exploring the Similarity of Medical Imaging Classification Problems: Intravascular Imaging and Computer Assisted Stenting, and Large-Scale Annotation of Biomedical Data and Expert Label Synthesis - 6th Joint International Workshops, CVII-STENT 2017 and 2nd International Workshop, LABELS 2017 Held in Conjunction with MICCAI 2017, Proceedings p. 59-66 (; vol. )
• Automatic segmentation of the intracranial volume in fetal MR images
  Khalili, N., Moeskops, P., Claessens, N. H.P., Scherpenzeel, S., Turk, E., de Heus, R., Benders, M. J.N.L., Viergever, M. A., Pluim, J. P.W., Išgum, I. 2017 in Automatic segmentation of the intracranial volume in fetal MR images: Fetal, Infant and Ophthalmic Medical Image Analysis - International Workshop, FIFI 2017 and 4th International Workshop, OMIA 2017 Held in Conjunction with MICCAI 2017, Proceedings p. 42-51 (; vol. )
• Supervised local error estimation for nonlinear image registration using convolutional neural networks
  Eppenhof, Koen A.J., Pluim, Josien P.W. 2017 in Supervised local error estimation for nonlinear image registration using convolutional neural networks: Medical Imaging 2017: Image Processing p. (; vol. )
• Robust Retinal Vessel Segmentation via Locally Adaptive Derivative Frames in Orientation Scores
  Zhang, Jiong, Dashtbozorg, Behdad, Bekkers, Erik, Pluim, Josien, Duits, Remco, Ter Haar Romeny, Bart Dec 2016 in IEEE Transactions on Medical Imaging 35 (12),
• Automatic segmentation and registration of abdominal aortic aneurysms using 3D ultrasound
  Van Disseldorp, E. M J, Van Dronkelaar, J. J., Pluim, J. P W, Van De Vosse, Frans, Van Sambeek, M. R H M, Lopata, R. G P nov 2016 in Automatic segmentation and registration of abdominal aortic aneurysms using 3D ultrasound: 2016 IEEE International Ultrasonics Symposium, IUS 2016 p. (; vol. )
• Subject-specific four-dimensional liver motion modeling based on registration of dynamic MRI
  Noorda, Yolanda H, Bartels, LW, Viergever, Max A, Pluim, Josien P W Jan 2016 in Journal of Medical Imaging 3 (1),
• A survey of medical image registration - under review
  Viergever, Max A, Maintz, J B Antoine, Klein, Stefan, Murphy, Keelin, Staring, Marius, Pluim, JPW 2016 in Medical Image Analysis 33 p. 140-144
• Mitosis Counting in Breast Cancer: Object-Level Interobserver Agreement and Comparison to an Automatic Method
  Veta, Mitko, van Diest, Paul J, Jiwa, Mehdi, Al-Janabi, Shaimaa, Pluim, JPW 2016 in PLoS ONE [E] 11 (8),
• IMPROVED SEGMENTATION OF MULTIPLE CAVITIES OF THE HEART IN WIDE-VIEW 3-D TRANSESOPHAGEAL ECHOCARDIOGRAMS
  Haak, Alexander, Ren, Ben, Mulder, Harriet W., Vegas-Sanchez-Ferrero, Gonzalo, van Burken, Gerard, van der Steen, Antonius F. W., van Stralen, M, Pluim, JPW, van Walsum, Theo, Bosch, Johannes G. Jul 2015 in Ultrasound in Medicine and Biology 41 (7), p. 1991-2000
• Segmentation of Multiple Heart Cavities in 3-D Transesophageal Ultrasound Images
  Haak, Alexander, Vegas-Sanchez-Ferrero, Gonzalo, Mulder, Harriet W., Ren, Ben, Kirisli, Hortense A., Metz, Coert, van Burken, Gerard, van Stralen, M, Pluim, JPW, van der Steen, Antonius F. W., van Walsum, Theo, Bosch, Johannes G. Jun 2015 in Ieee transactions on ultrasonics ferroelectrics and frequency control 62 (6), p. 1179-1189
• Arterial and portal venous liver perfusion using selective spin labelling MRI
  Schalkx, Hanke J., Petersen, Esben T., Peters, Nicky H. G. M., Veldhuis, WB, van Leeuwen, MS, Pluim, JPW, van den Bosch, Maurice A. A. J., van Stralen, M Jun 2015 in European Radiology 25 (6), p. 1529-1540
• Assessment of algorithms for mitosis detection in breast cancer histopathology images
  Veta, Mitko, van Diest, Paul J., Willems, Stefan M., Madabhushi, Anant, Cruz-Roa, Angel, Gonzalez, Fabio, Larsen, Anders B L, Vestergaard, Jacob S., Dahl, Anders B., Cireşan, Dan C., Schmidhuber, Jürgen, Giusti, Alessandro, Gambardella, Luca M., Tek, F. Boray, Walter, Thomas, Wang, Ching Wei, Kondo, Satoshi, Matuszewski, Bogdan J., Precioso, Frederic, Snell, Violet, Kittler, Josef, de Campos, Teofilo E., Khan, Adnan M., Rajpoot, Nasir M., Arkoumani, Evdokia, Lacle, Miangela M., Viergever, Max A., Pluim, JPW Feb 2015 in Medical Image Analysis 20 (1), p. 237-248
• Evaluation of image-based bias field correction at 7T
  van Rijssel, Mike, Pluim, JPW, van der Velden, Bas, van der Velden, Tijl, Krikken, E, Wijnen, Jannie, Gilhuijs, Kenneth, Klomp, DWJ oct 2015 at Evaluation of image-based bias field correction at 7T
• Improving label fusion in multi-atlas based segmentation by locally combining atlas selection and performance estimation
  Langerak, T. R., van der Heide, U. A., Kotte, A. N. T. J., Berendsen, F. F., Pluim, J. P. W. Jan 2015 in Computer Vision and Image Understanding 130 p. 71-79
• Coregistration of preoperative computed tomography and intraoperative three-dimensional rotational x-ray images for cochlear implant surgical evaluation
  Pearlman, P.C., van Deurzen, M.H.W., Pluim, J.P.W., Grolman, W. Dec 2014 in Otology & Neurotology 35 (10), p. 1759-1764
• Multimodality infarct identification for optimal image-guided intramyocardial cell injections.
  van Slochteren, F.J., van Es, R, Koudstaal, S., van der Spoel, T.I.G., Sluijter, J.P.G., Verbree, J.M., Pruim, R.H., Pluim, J.P.W., Leiner, T., Doevendans, P.A.F.M., Chamuleau, S.A.J. Nov 2014 in Netherlands Heart Journal 22 (11), p. 493-500
• Segmentation of multiple heart cavities in wide-view fused 3D transesophageal echocardiograms
  Haak, Alexander, Mulder, Harriët W., Ren, Ben, Vegas-Sánchez-Ferrero, Gonzalo, Van Burken, Gerard, Van Der Steen, Antonius F.W., Van Stralen, Marijn, Pluim, Josien P.W., Van Walsum, Theo, Bosch, Johannes G. oct 2014 in Segmentation of multiple heart cavities in wide-view fused 3D transesophageal echocardiograms: IEEE International Ultrasonics Symposium, IUS p. 691-694 (; vol. )
• Registration of structurally dissimilar images in MRI-based brachytherapy
  Berendsen, F.F., Kotte, A.N.T.J., de Leeuw, A.A.C., Jurgenliemk-Schulz, I.M., Viergever, M.A., Pluim, J.P.W. 2014 in Physics in Medicine and Biology 59 (15), p. 4033-4045
• Breast cancer histopathology image analysis: a review
  Veta, M., Pluim, J.P.W., van Diest, P.J., Viergever, M.A. 2014 in IEEE Transactions on Biomedical Engineering 61 (5), p. 1400-1411
• DIRBoost-An algorithm for boosting deformable image registration: Application to lung CT intra-subject registration
  Münzing, SEA, van Ginneken, B., Viergever, M.A., Pluim, J.P.W. 2014 in Medical Image Analysis 18 (3), p. 449-459
• Multiframe registration of real-time three-dimensional echocardiography time series
  Mulder, Harriët, van Stralen, M., van der Zwaan, H.B., Leung, K.Y.E., Bosch, J.G., Pluim, J.P.W. 2014 in Journal of Medical Imaging 1 (1), p. 014004-014004
• Registration of CT to pre-treatment MRI for planning of MR-HIFU ablation treatment of painful bone metastases
  Noorda, Y.H., Bartels, L.W., Huisman, M., Nijenhuis, R.J., van den Bosch, M.A.A.J., Pluim, J.P.W. 2014 in Physics in Medicine and Biology 59 (15), p. 4167-4179
• Corrections to "breast cancer histopathology image analysis: a review"
  Veta, M., Pluim, J.P.W., van Diest, P.J., Viergever, M.A. 2014 in IEEE Transactions on Biomedical Engineering 61 (11), p. 2819
• Liver perfusion in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI): comparison of enhancement in Gd-BT-DO3A and Gd-EOB-DTPA in normal liver parenchyma
  Schalkx, H.J., van Stralen, M., Coenegrachts, K., van den Bosch, M.A.A.J., van Kessel, C.S., van Hillegersberg, R., van Erpecum, K.J., Verkooijen, H.M., Pluim, J.P.W., Veldhuis, W.B., van Leeuwen, M.S. 2014 in European Radiology 24 (9), p. 2146-2156
• Implicit surface registration with surface-oriented anisotropic deformation field smoothing
  Pearlman, Paul C., Isgum, Ivana, Kersbergen, Karina J., Benders, Manon J.N.L., Viergever, Max A., Pluim, Josien P.W. aug 2013 in Implicit surface registration with surface-oriented anisotropic deformation field smoothing: ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging p. 480-483 (; vol. )
• Simultaneous pairwise registration for image mosaicing of TEE data
  Mulder, H. W., Van Stralen, M., Ren, B., Berendsen, F. F., Bosch, J. G., Pluim, J. P.W. aug 2013 in Simultaneous pairwise registration for image mosaicing of TEE data: ISBI 2013 - 2013 IEEE 10th International Symposium on Biomedical Imaging p. 242-245 (; vol. )
• A patient specific 4D MRI liver motion model based on sparse imaging and registration
  Noorda, Yolanda H., Bartels, Lambertus W., Van Stralen, Marijn, Pluim, Josien P.W. jun 2013 in A patient specific 4D MRI liver motion model based on sparse imaging and registration: Medical Imaging 2013 p. (; vol. )
• Detecting mitotic figures in breast cancer histopathology images
  Veta, M., Van Diest, P. J., Pluim, J. P W jun 2013 in Detecting mitotic figures in breast cancer histopathology images: Medical Imaging 2013 p. (; vol. )
• Automatic nuclei segmentation in H&E stained breast cancer histopathology images
  Veta, M., van Diest, P.J., Kornegoor, R., Huisman, A., Viergever, M.A., Pluim, J.P.W. 2013 in PLoS ONE [E] 8 (7), p. e70221
• 7T fMRI reveals feasibility of covert visual attention-based brain-computer interfacing with signals obtained solely from cortical grey matter accessible by subdural surface electrodes
  Andersson, J.P., Ramsey, N.F., Viergever, M.A., Pluim, J.P.W. 2013 in Clinical Neurophysiology 124 (11), p. 2191-2197
• Multiatlas-based segmentation with preregistration atlas selection
  Langerak, T.R., Berendsen, F.F., van der Heide, U.A., Kotte, A.N.T.J., Pluim, J.P.W. 2013 in Medical Physics 40 (9), p. 091701
• Free-form image registration regularized by a statistical shape model: application to organ segmentation in cervical MR
  Berendsen, F.F., van der Heide, U.A., Langerak, T.R., Kotte, A.N.T.J., Pluim, J.P.W. 2013 in Computer Vision and Image Understanding 117 (9), p. 1119-1127
• Expert-driven label fusion in multi-atlas-based segmentation of the prostate using weighted atlases
  Langerak, T.R., van der Heide, U.A., Kotte, A.N.T.J., Berendsen, F.F., van Vulpen, M., Pluim, J.P.W. 2013 in International Journal of Computer Assisted Radiology and Surgery 8 (6), p. 929-936
• A transoesophageal echocardiographic image acquisition protocol for wide-view fusion of three-dimensional datasets to support atrial fibrillation catheter ablation
  Ren, B., Mulder, H.W., Haak, A., van Stralen, M., Szili-Torok, T., Pluim, J.P.W., Geleijnse, M.L., Bosch, J.G. 2013 in Journal of Interventional Cardiac Electrophysiology 37 (1), p. 21-26
• Navigation of a telepresence robot via covert visuospatial attention and real-time fMRI
  Andersson, J.P., Pluim, J.P.W., Viergever, M.A., Ramsey, N.F. 2013 in Brain Topography 26 (1), p. 177-185
• Comparison of spatiotemporal interpolators for 4D image reconstruction from 2D transesophageal ultrasound
  Haak, Alexander, Van Stralen, Marijn, Van Burken, Gerard, Klein, Stefan, Pluim, Josien P.W., De Jong, Nico, Van Der Steen, Antonius F.W., Bosch, Johannes G. may 2012 in Comparison of spatiotemporal interpolators for 4D image reconstruction from 2D transesophageal ultrasound: Medical Imaging 2012 p. (; vol. )
• Optimal kernel sizes for 4D image reconstruction using normalized convolution from sparse fast-rotating transesophageal 2D ultrasound images
  Haak, Alexander, Klein, Stefan, Van Burken, Gerard, De Jong, Nico, Van Der Steen, Antonius F.W., Bosch, Johannes G., Van Stralen, Marijn, Pluim, Josien P.W. dec 2012 in Optimal kernel sizes for 4D image reconstruction using normalized convolution from sparse fast-rotating transesophageal 2D ultrasound images: 2012 IEEE International Ultrasonics Symposium, IUS 2012 p. 703-706 (; vol. )
• Elastic demons: Characterizing cortical development in neonates using an implicit surface registration
  Pearlman, Paul C., IÅ¡gum, Ivana, Kersbergen, Karina J., Benders, Manon J.N.L., Viergever, Max A., Pluim, Josien P.W. oct 2012 in Elastic demons:Characterizing cortical development in neonates using an implicit surface registration Spatio-temporal Image Analysis for Longitudinal and Time-Series Image Data - Second International Workshop, STIA 2012, Held in Conjunction with MICCAI 2012, Proceedings p. 38-49 (; vol. )
• Toward automatic regional analysis of pulmonary function using inspiration and expiration thoracic CT
  Murphy, K., Pluim, J.P.W., van Rikxoort, E.M., de Jong, P.A., de Hoop, B.J., Gietema, H.A., Mets, O.M., de Bruijne, M., Lo, P., Prokop, W.M., van Ginneken, B. 2012 in Medical Physics 39 (3), p. 1650-1662
• Real-time decoding of the direction of covert visuospatial attention
  Andersson, J.P., Ramsey, N.F., Raemaekers, M.A.H.L.L., Viergever, M.A., Pluim, J.P.W. 2012 in Journal of Neural Engineering 9 (4), p. 045004
• Patient specific prostate segmentation in 3-d magnetic resonance images
  Chandra, S.S., Dowling, J.A., Shen, K.K., Raniga, P., Pluim, J.P.W., Greer, P.B., Salvador, O., Fripp, J. 2012 in IEEE Transactions on Medical Imaging 31 (10), p. 1955-1964
• Prognostic value of automatically extracted nuclear morphometric features in whole slide images of male breast cancer
  Veta, M., Kornegoor, R., Huisman, A., Verschuur-Maes, A.H.J., Viergever, M.A., Pluim, J.P.W., van Diest, P.J. 2012 in Modern Pathology 25 (12), p. 1559-1565
• Mono- and multimodal registration of optical breast images
  Pearlman, P.C., Adams, A.L.L., Elias, S.G., Mali, W.P.T.M., Viergever, M.A., Pluim, J.P.W. 2012 in Journal of Biomedical Optics 17 (8), p. 080901
• Supervised quality assessment of medical image registration: Application to intra-patient CT lung registration
  Munzing, S.E.A., van Ginneken, B., Murphy, K., Pluim, J.P.W. 2012 in Medical Image Analysis 16 (8), p. 1521-1531
• Determination of a facial nerve safety zone for navigated temporal bone surgery
  Voormolen, E.H.J., van Stralen, M., Woerdeman, P.A., Pluim, J.P.W., Noordmans, H.J., Viergever, M.A., Regli, L.P.E., Berkelbach van der Sprenkel, J.W. 2012 in Neurosurgery 70 (1 suppl operative), p. 50-60 discussion 60
• Registration of multi-view apical 3D echocardiography images
  Mulder, H. W., Van Stralen, M., Van Der Zwaan, H. B., Leung, K. Y.E., Bosch, J. G., Pluim, J. P.W. jun 2011 in Registration of multi-view apical 3D echocardiography images: Medical Imaging 2011 p. (; vol. )
• Spatiotemporal interpolation by normalized convolution for 4D transesophageal echocardiography
  Haak, Alexander, Van Stralen, Marijn, Van Burken, Gerard, Klein, Stefan, Pluim, Josien P.W., De Jong, Nico, Van Der Steen, Antonius F.W., Bosch, Johannes G. dec 2011 in Spatiotemporal interpolation by normalized convolution for 4D transesophageal echocardiography: 2011 IEEE International Ultrasonics Symposium, IUS 2011 p. 152-155 (; vol. )
• Marker-controlled watershed segmentation of nuclei in H&E stained breast cancer biopsy images
  Veta, M., Huisman, A., Viergever, M. A., Van Diest, P. J., Pluim, J. P.W. nov 2011 in Marker-controlled watershed segmentation of nuclei in H&E stained breast cancer biopsy images: 2011 8th IEEE International Symposium on Biomedical Imaging p. 618-621 (; vol. )
• Accelerated cognitive decline in patients with type 2 diabetes: MRI correlates and risk factors
  Reijmer, Y.D., Van den Berg, E., de Bresser, J.H.J.M., Kessels, R.P.C., Kappelle, L.J., Algra, A., Brands, A.M.A., Breedijk, M.A., Brundel, M., van Gijn, J., Gispen, W.H., van Huffelen, A.C., Mali, W.P.T.M., Pluim, J.P.W., Rutten, G.E.H.M., Tiehuis, A.M., de Valk, H.W., Viergever, M.A., Utrecht Diabetic Encephalopathy, x, Biessels, G.J. 2011 in Diabetes/Metabolism Research and Reviews 27 (2), p. 195-202
• Preconditioned stochastic gradient descent optimisation for monomodal image registration
  Klein, S., Staring, M., Andersson, J.P., Pluim, J.P.W. 2011 in Lecture Notes in Computer Science 6892 p. 549-556
• Special Issue on the 2010 Conference on Medical Image Computing and Computer-Assisted Intervention. Editorial
  Viergever, M.A., Jiang, T., Navab, N., Pluim, J.P.W. 2011 in Medical Image Analysis 15 (5), p. 669
• Registration of 2D x-ray images to 3D MRI by generating pseudo-CT data
  van der Bom, M.J., Pluim, J.P.W., Gounis, M.J., van de Kraats, E.B., Sprinkhuizen, S.M., Timmer, J., Homan, R., Bartels, L.W. 2011 in Physics in Medicine and Biology 56 (4), p. 1031-1043
• Real-time decoding of brain responses to visuospatial attention using 7T fMRI
  Andersson, J.P., Pluim, J.P.W., Siero, J.C.W., Klein, S., Viergever, M.A., Ramsey, N.F. 2011 in PLoS ONE [E] 6 (11), p. e27638
• Evaluation of Registration Methods on Thoracic CT: The EMPIRE10 Challenge
  Murphy, K., van Ginneken, B., Münzing, S.E.A., Viergever, M.A., et al., X, Pluim, J.P.W. 2011 in IEEE Transactions on Medical Imaging 30 (11), p. 1901-1920
• Semi-automatic construction of reference standards for evaluation of image registration
  Murphy, K., van Ginneken, B., Klein, S., Staring, M., de Hoop, B.J., Viergever, M.A., Pluim, J.P.W. 2011 in Medical Image Analysis 15 (1), p. 71-84
• Evaluation of Methods for Pulmonary Image Registration: the EMPIRE10 study
  Murphy, K., van Ginneken, B., Reinhardt, J.M., Kabus, S., Ding, K., Deng, X., Pluim, J.P.W. 2010 in Evaluation of Methods for Pulmonary Image Registration: the EMPIRE10 study: Medical Image Analysis for the Clinic - A Grand Challenge p. 11-22 (; vol. )
• Robust initialization of 2D-3D image registration using the projection-slice theorem and phase correlation
  van der Bom, M.J., Bartels, L.W., Gounis, M.J., Homan, R., Timmer, J., Viergever, M.A., Pluim, J.P.W. 2010 in Medical Physics 37 (4), p. 1884-1892
• elastix: a toolbox for intensity-based medical image registration
  Klein, S., Staring, M., Murphy, K., Viergever, M.A., Pluim, J.P.W. 2010 in IEEE Transactions on Medical Imaging 29 (1), p. 196-205
• Microvascular Determinants of Cognitive Decline and Brain Volume Change in Elderly Patients with Type 2 Diabetes.
  de Bresser, J.H.J.M., Reijmer, Y.D., Van den Berg, E., Breedijk, M.A., Kappelle, L.J., Viergever, M.A., Algra, A., Brands, A.M.A., Brundel, M., van Gijn, J., Gispen, W.H., van der Grond, J., De Haan, E.H.F., van Huffelen, A.C., Jongen, C., Kessels, R.P.C., Mali, W.P.T.M., Manschot, S.M., Pluim, J.P.W., Rutten, G.E.H.M., Tiehuis, A.M., de Valk, H.W., Utrecht Diabetic Encephalopathy, x, Biessels, G.J. 2010 in Dementia and Geriatric Cognitive Disorders 30 (5), p. 381-386
• Knowledge driven regularization of the deformation field for PDE based nonrigid registration algorithms
  Münzing, S.E.A., van Ginneken, B., Pluim, J.P.W. 2010 in Knowledge driven regularization of the deformation field for PDE based nonrigid registration algorithms: Medical Image Analysis for the Clinic - A Grand Challenge p. 127-136 (; vol. )
• Arterial spin labeling perfusion MRI at multiple delay times: a correlative study with H(2)(15)O positron emission tomography in patients with symptomatic carotid artery occlusion
  Bokkers, R.P.H., Bremmer, J.P., van Berckel, B.N.M., Lammertsma, A.A., Hendrikse, J., Pluim, J.P.W., Kappelle, L.J., Boellaard, R., Klijn, C.J.M. 2010 in Journal of Cerebral Blood Flow and Metabolism 30 (1), p. 222-229
• Automatic segmentation of pulmonary lobes robust against incomplete fissures
  van Rikxoort, E.M., Prokop, W.M., de Hoop, B.J., Viergever, M.A., Pluim, J.P.W., van Ginneken, B. 2010 in IEEE Transactions on Medical Imaging 29 (6), p. 1286-1296
• Label fusion in atlas-based segmentation using a Selective and Iterative Method for Performance Level Estimation (SIMPLE)
  Langerak, T.R., van der Heide, U.A., Kotte, A.N.T.J., Viergever, M.A., van Vulpen, M., Pluim, J.P.W. 2010 in IEEE Transactions on Medical Imaging 29 (12), p. 2000-2008
• Adaptive local multi-atlas segmentation: application to the heart and the caudate nucleus
  van Rikxoort, E.M., Isgum, I., Arzhaeva, Y., Staring, M., Klein, S., Viergever, M.A., Pluim, J.P.W., van Ginneken, B. 2010 in Medical Image Analysis 14 (1), p. 39-49
• BCI control using 4 direction spatial visual attention and real-time fMRI at 7T
  Andersson, J.P., Ramsey, N.F., Pluim, J.P.W., Viergever, M.A. 2010 in BCI control using 4 direction spatial visual attention and real-time fMRI at 7T: Conference proceedings IEEE Engineering in Medicine and Biology Society p. 4221-4225 (; vol. )
• Automated aortic calcium scoring on low-dose chest computed tomography
  Isgum, I., Rutten, A., Prokop, W.M., Staring, M., Klein, S., Pluim, J.P.W., Viergever, M.A., van Ginneken, B. 2010 in Medical Physics 37 (2), p. 714-723
• Construction of periventricular white matter hyperintensity maps by spatial normalization of the lateral ventricles
  Jongen, C., van der Grond, J., Anbeek, P., Viergever, M.A., Biessels, G.J., van Huffelen, A.C., de Valk, H.W., Algra, A., Gispen, W.H., van Gijn, J., Kappelle, L.J., Manschot, S.M., Brands, A.M.A., De Haan, E.H.F., Kessels, R.P., den Berg, E.V., de Bresser, J.H.J.M., Mali, W.P.T.M., Tiehuis, A.M., on behalf of the, Utrecht Diabetic Encephalopathy Study Group, Pluim, J.P.W. 2009 in Human Brain Mapping 30 (7), p. 2056-2062
• Evaluation of 4D-CT lung registration
  Kabus, S., Klinder, T., Murphy, K., van Ginneken, B., Lorenz, C., Pluim, J.P.W. 2009 in Evaluation of 4D-CT lung registration: Medical Image Computing and Computer-Assisted Intervention p. 747-754 (; vol. )
• Registration of cervical MRI using multifeature mutual information
  Staring, M., van der Heide, U.A., Klein, S., Viergever, M.A., Pluim, J.P.W. 2009 in IEEE Transactions on Medical Imaging 28 (9), p. 1412-1421
• Label fusion using performance estimation with iterative label selection
  Langerak, T.R., van der Heide, U.A., Lips, I.M., Kotte, A.N.T.J., van Vulpen, M., Pluim, J.P.W. 2009 in Label fusion using performance estimation with iterative label selection: Proceedings International Symposium on Biomedical Imaging 2009 p. 1186-1189 (; vol. )
• Image subtraction facilitates assessment of volume and density change in ground-glass opacities in chest CT
  Staring, M., Pluim, J.P.W., de Hoop, B.J., Klein, S., van Ginneken, B., Gietema, H.A., Nossent, G.D., Schaefer-Prokop, C., van de Vorst, S., Prokop, W.M. 2009 in Investigative Radiology 44 (2), p. 61-66
• Adaptive Stochastic Gradient Descent Optimisation for Image Registration
  Klein, S., Pluim, J.P.W., Staring, M., Viergever, M.A. 2009 in International Journal of Computer Vision 81 (3), p. 227-239
• fMRI based BCI control using spatial visual attention at 7T
  Andersson, J.P., Viergever, M.A., Pluim, J.P.W., Ramsey, N.F., Siero, J.C.W. 2009 in fMRI based BCI control using spatial visual attention at 7T: Proceedings IEEE EMBS Conference on Neural Engineering 2009 p. 444-446 (; vol. )
• Automatic detection of registration errors for quality assessment in medical image registration
  Munzing, S.E.A., Murphy, K., van Ginneken, B., Pluim, J.P.W. 2009 in Automatic detection of registration errors for quality assessment in medical image registration: SPIE Medical Imaging: Image Processing p. 72590K-72590K-9 (; vol. )
• A technique for improving 2D X-ray to 3D MRI registration in fluoroscopy-guided orthopedic interventions
  van der Bom, M.J., Pluim, J.P.W., Gounis, M., Bartels, L.W. 2009 in A technique for improving 2D X-ray to 3D MRI registration in fluoroscopy-guided orthopedic interventions: Proceedings International Society Magnetic Resonance in Medicine 2009 p. (; vol. )
• Optimal discrete multi-resolution deformable image registration
  van Stralen, M., Pluim, J.P.W. 2009 in Optimal discrete multi-resolution deformable image registration: Proceedings International Symposium on Biomedical Imaging 2009 p. 947-950 (; vol. )
• Automatic segmentation of the pulmonary lobes from fissures, airways, and lung borders: evaluation of robustness against missing data
  van Rikxoort, E.M., Prokop, W.M., de Hoop, B.J., Viergever, M.A., Pluim, J.P.W., van Ginneken, B. 2009 in Automatic segmentation of the pulmonary lobes from fissures, airways, and lung borders: evaluation of robustness against missing data: Medical Image Computing and Computer-Assisted Intervention p. 263-271 (; vol. )
• Enforcing stochastic inverse consistency in non-rigid image registration and matching
  Yeung, S.-K., Tang, C.-K., Shi, P., Pluim, J.P.W., Viergever, M.A., Chung, C.S. 2008 in Enforcing stochastic inverse consistency in non-rigid image registration and matching: Computer Vision and Pattern Recognition p. (; vol. )
• Automatic segmentation of the prostate in 3D MR images by atlas matching using localized mutual information
  Klein, S., van der Heide, U.A., Lips, I.M., van Vulpen, M., Staring, M., Pluim, J.P.W. 2008 in Medical Physics 35 (4), p. 1407-1417
• Semi-automatic reference standard construction for quantitative evaluation of lung CT registration
  Murphy, K., van Ginneken, B., Pluim, J.P.W., Klein, S., Staring, M. 2008 in Semi-automatic reference standard construction for quantitative evaluation of lung CT registration: Medical Image Computing and Computer-Assisted Intervention p. 1006-1013 (; vol. )
• Quantitative assessment of registration in thoracic CT
  Murphy, K., van Ginneken, B., Pluim, J.P.W., Klein, S., Staring, M. 2008 in Quantitative assessment of registration in thoracic CT: The First International Workshop on Pulmonary Image Analysis p. 203-211 (; vol. )
• Editorial
  Likar, B., Pluim, J.P.W. 2008 in Medical Image Analysis 12 (1), p. 1-2
• Segmentation of the prostate in MR images by atlas matching
  Klein, S., van der Heide, U.A., Raaymakers, B.W., Kotte, A.N.T.J., Staring, M., Pluim, J.P.W. 2007 in Segmentation of the prostate in MR images by atlas matching: International Symposium on Biomedical Imaging 2007 p. 1300-1303 (; vol. )
• A rigidity penalty term for nonrigid registration
  Staring, M., Klein, S., Pluim, J.P.W. 2007 in Medical Physics 34 (11), p. 4098-4108
• Automated measurement of brain and white matter lesion volume in type 2 diabetes mellitus
  Jongen, C., van der Grond, J., Kappelle, L.J., Biessels, G.J., Viergever, M.A., Pluim, J.P.W. 2007 in Diabetologia 50 (7), p. 1509-1516
• Medical Imaging 2007: Image Processing
  Pluim, J.P.W., Reinhardt, J.M. 2007 in Medical Imaging 2007: Image Processing: Proceedings of SPIE p. (; vol. )
• Evaluation of optimization methods for nonrigid medical image registration using mutual information and B-splines
  Klein, S., Staring, M., Pluim, J.P.W. 2007 in IEEE transactions on image processing 16 (12), p. 2879-2890
• Constructing white matter lesion maps for group comparisons
  Jongen, C., van der Grond, J., Biessels, G.J., Pluim, J.P.W. 2007 in Constructing white matter lesion maps for group comparisons: Fifth international congress on Vascular Dementia p. 122-122 (; vol. )
• Segmentation of the prostate in MR images by atlas matching using localised mutual information
  Klein, S., van der Heide, U.A., Staring, M., Kotte, A.N.T.J., Raaymakers, B.W., Pluim, J.P.W. 2007 in Segmentation of the prostate in MR images by atlas matching using localised mutual information: XVth International Conference on the use of Computers in Radiation Therapy p. 585-589 (; vol. )
• Projection-slice theorem based 2D-3D registration
  van der Bom, M.J., Pluim, J.P.W., Homan, R., Timmer, J., Bartels, L.W. 2007 in Projection-slice theorem based 2D-3D registration: SPIE Medical Imaging: Image Processing p. (; vol. )
• Nonrigid registration with tissue-dependent filtering of the deformation field
  Staring, M., Klein, S., Pluim, J.P.W. 2007 in Physics in Medicine and Biology 52 (23), p. 6879-6892
• A comparison of acceleration techniques for nonrigid medical image registration
  Klein, S., Staring, M., Pluim, J.P.W. 2006 in A comparison of acceleration techniques for nonrigid medical image registration: International Workshop on Biomedical Image Registration p. 151-159 (; vol. )
• Normalized mutual information based registration using k-means clustering and shading correction
  Knops, Z.F., Maintz, J.B.A., Viergever, M.A., Pluim, J.P.W. 2006 in Medical Image Analysis 10 (3), p. 432-439
• Evaluation of a Rigidity Penalty Term for Nonrigid Registration
  Staring, M., Klein, S., Pluim, J.P.W. 2006 in Evaluation of a Rigidity Penalty Term for Nonrigid Registration: Deform '06 p. 41-50 (; vol. )
• Nonrigid registration using a rigidity constraint
  Staring, M., Klein, S., Pluim, J.P.W. 2006 in Nonrigid registration using a rigidity constraint: SPIE: Medical Imaging: Image Processing p. 614413-1-614413-10 (; vol. )
• Comparison of gradient approximation techniques for optimisation of mutual information in nonrigid registration
  Klein, S., Staring, M., Pluim, J.P.W. 2005 in Comparison of gradient approximation techniques for optimisation of mutual information in nonrigid registration: Proceedings of SPIE: Medical Imaging: Image Processing p. 192-203 (; vol. )
• A voxel based analysis of white matter lesions in diabetic subjects
  Jongen, C., van der Grond, J., Pluim, J.P.W. 2005 in A voxel based analysis of white matter lesions in diabetic subjects: Neuroimage p. (; vol. )
• Nonrigid registration with adaptive, content-based filtering of the deformation field
  Staring, M., Klein, S., Pluim, J.P.W. 2005 in Nonrigid registration with adaptive, content-based filtering of the deformation field: Proceedings of SPIE Medical Imaging p. 212-221 (; vol. )
• Non-rigid registration based active appearance models for 3D medical image segmentation
  Klemencic, J., Pluim, J.P.W., Viergever, M.A., Schnack, H.G., Valencic, V. 2004 in Journal of Imaging Science and Technology 48 p. 166-171
• Construction and evaluation of an average CT brain image for inter-subject registration.
  Jongen, C., Pluim, J.P.W., Nederkoorn, P.J., Viergever, M.A., Niessen, W.J. 2004 in Computers in Biology and Medicine 34 (8), p. 647-662
• f-information measures in medical image registration.
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 2004 in IEEE Transactions on Medical Imaging 23 p. 1506-1518
• Atlas-based analysis of cerebral infarction pattern in CT images of patients with Internal Carotid Artery stenosis.
  Jongen, C., Nederkoorn, P.J., Niessen, W.J., Pluim, J.P.W. 2004 in Investigative Radiology 39 p. 462-469
• Registration using segment intensity remapping and mutual information
  Knops, Z.F., Maintz, J.B.A., Viergever, M.A., Pluim, J.P.W. 2004 in Registration using segment intensity remapping and mutual information: Lecture notes in computer science. p. 805-812 (; vol. )
• Ventricle registration for inter-subject white matter lesion analysis
  Jongen, C., van der Grond, J., Pluim, J.P.W. 2004 in Ventricle registration for inter-subject white matter lesion analysis: Lecture Notes in Computer Science p. 712-719 (; vol. )
• Image registration (editorial)
  Pluim, J.P.W., Fitzpatrick, J.M. 2003 in IEEE Transactions on Medical Imaging 22 (11), p. 1341-1343
• Mutual-information-based registration of medical images: a survey
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 2003 in IEEE Transactions on Medical Imaging 22 p. 986-1004
• Normalized mutual information based registration using K-means clustering based histogram binning
  Knops, Z.F., Maintz, J.B.A., Viergever, M.A., Pluim, J.P.W. 2003 in Normalized mutual information based registration using K-means clustering based histogram binning: SPIE Medical Imaging, 2003 p. (; vol. )
• Normalized mutual information based PET-MR registration using K-means clustering and shading correction
  Knops, Z.F., Maintz, J.B.A., Pluim, J.P.W. 2003 in Normalized mutual information based PET-MR registration using K-means clustering and shading correction: Lecture Notes in Computer Science p. 31-39 (; vol. )
• 3D Appearance model for hippocampus segmentation from MRI
  Klemencic, J., Pluim, J.P.W., Viergever, M.A., Schnack, H.G., Valencic, V. 2003 in 3D Appearance model for hippocampus segmentation from MRI: SPIE Medical Imaging, 2003 p. (; vol. )
• Improved image registration robustness by an extension of mutual information
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 2002 in Improved image registration robustness by an extension of mutual information: ??? p. (; vol. )
• Medical image computing and computer-assisted intervention
  Pluim, J.P.W., Niessen, W.J., Viergever, M.A. 2002 in Medical Image Analysis 6 p. 181-181
• Construction of an average CT brain image for brain infarct pattern comparison
  Jongen, C., Pluim, J.P.W., Viergever, M.A., Niessen, W.J. 2002 in Construction of an average CT brain image for brain infarct pattern comparison: Computer-Assisted Radiology and Surgery p. 425-429 (; vol. )
• Registration, segmentation and visualization of multimodal brain images.
  Viergever, M.A., Maintz, J.B.A., Niessen, W.J., Noordmans, H.J., Pluim, J.P.W., Stokking, R., Vincken, K.L. 2001 in Computerized Medical Imaging and Graphics 25 (2), p. 147-151
• Two-step registration of subacute to hyperacute stroke MRIs.
  Anbeek, P., Vincken, K.L., van Osch, M.J.P., Pluim, J.P.W., van der Grond, J., Viergever, M.A. 2001 in Two-step registration of subacute to hyperacute stroke MRIs.: Lecture notes in computer science p. 1279-1280 (; vol. )
• f-Information measures in medical image registration
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 2001 in f-Information measures in medical image registration: Proceedings of SPIE: Medical Imaging: Image processing. p. (; vol. )
• Mutual information matching in multiresolution contexts
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 2001 in Image and Vision Computing 19 (1-2), p. 45-52
• Interpolation artefacts in mutual information based image registration
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 2000 in Computer Vision and Image Understanding 77 p. 211-232
• Image registration by maximization of combined mutual information and gradient information
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 2000 in IEEE Transactions on Medical Imaging 19 p. 809-814
• Image registration by maximization of combined mutual information and gradient information
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 2000 in Image registration by maximization of combined mutual information and gradient information: Medical Image Computing and Computer-asssited Intervention p. 452-461 (; vol. )
• Mutual information matching and interpolation artefacts.
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 1999 in Mutual information matching and interpolation artefacts.: Proc.SPIE p. 56-65 (; vol. )
• Quantitative comparison of sinc-approximating kernels for medical image interpolation
  Meijering, H.W., Niessen, W.J., Pluim, J.P.W., Viergever, M.A. 1999 in Quantitative comparison of sinc-approximating kernels for medical image interpolation: Medical Image Computing and Computer-Assisted Intervention p. 210-217 (; vol. )
• Mutual information matching in multiresolution contexts
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 1999 in Mutual information matching in multiresolution contexts: Biomedical image registration p. 46-60 (; vol. )
• Mutual Information and Interpolation Artefacts
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 1999 in Mutual Information and Interpolation Artefacts: Medical Imaging 1999 - Image Processing p. 56-65 (; vol. )
• Mutual information matching in multiresolution contexts
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 1999 in Mutual information matching in multiresolution contexts: Slovenian Pattern Recognition Society p. 46-60 (; vol. )
• A multiscale approach to mutual information matching
  Pluim, J.P.W., Maintz, J.B.A., Viergever, M.A. 1998 in A multiscale approach to mutual information matching: Medical Imaging - Image Processing p. 1334-1344 (; vol. )