1 code implementation • 26 Apr 2023 • Ishaan Bhat, Josien P. W. Pluim, Max A. Viergever, Hugo J. Kuijf
We propose the Generalized Probabilistic U-Net, which extends the Probabilistic U-Net by allowing more general forms of the Gaussian distribution as the latent space distribution that can better approximate the uncertainty in the reference segmentations.
no code implementations • 15 Aug 2022 • Carole H. Sudre, Kimberlin Van Wijnen, Florian Dubost, Hieab Adams, David Atkinson, Frederik Barkhof, Mahlet A. Birhanu, Esther E. Bron, Robin Camarasa, Nish Chaturvedi, Yuan Chen, Zihao Chen, Shuai Chen, Qi Dou, Tavia Evans, Ivan Ezhov, Haojun Gao, Marta Girones Sanguesa, Juan Domingo Gispert, Beatriz Gomez Anson, Alun D. Hughes, M. Arfan Ikram, Silvia Ingala, H. Rolf Jaeger, Florian Kofler, Hugo J. Kuijf, Denis Kutnar, Minho Lee, Bo Li, Luigi Lorenzini, Bjoern Menze, Jose Luis Molinuevo, Yiwei Pan, Elodie Puybareau, Rafael Rehwald, Ruisheng Su, Pengcheng Shi, Lorna Smith, Therese Tillin, Guillaume Tochon, Helene Urien, Bas H. M. van der Velden, Isabelle F. van der Velpen, Benedikt Wiestler, Frank J. Wolters, Pinar Yilmaz, Marius de Groot, Meike W. Vernooij, Marleen de Bruijne
This challenge aimed to promote the development of methods for automated detection and segmentation of small and sparse imaging markers of cerebral small vessel disease, namely enlarged perivascular spaces (EPVS) (Task 1), cerebral microbleeds (Task 2) and lacunes of presumed vascular origin (Task 3) while leveraging weak and noisy labels.
no code implementations • 27 Jul 2022 • Kimberley M. Timmins, Maarten J. Kamphuis, Iris N. Vos, Birgitta K. Velthuis, Irene C. van der Schaaf, Hugo J. Kuijf
The model consisted of a mesh convolutional neural network including additional novel input edge features of shape index and curvedness which describe the surface topology.
1 code implementation • 26 Jul 2022 • Ishaan Bhat, Josien P. W. Pluim, Hugo J. Kuijf
We propose the Generalized Probabilistic U-Net, which extends the Probabilistic U-Net by allowing more general forms of the Gaussian distribution as the latent space distribution that can better approximate the uncertainty in the reference segmentations.
1 code implementation • 22 Jun 2022 • Ishaan Bhat, Josien P. W. Pluim, Max A. Viergever, Hugo J. Kuijf
We study the role played by features computed from neural network uncertainty estimates and shape-based features computed from binary predictions in reducing false positives in liver lesion detection by developing a classification-based post-processing step for different uncertainty estimation methods.
no code implementations • 8 Jun 2022 • Djennifer K. Madzia-Madzou, Hugo J. Kuijf
The method is tested using Fashion MNIST, Medical Out-of-Distribution Analysis Challenge (MOOD), and in-house brain MRI; using patches of sizes 16x16 and 32x32.
1 code implementation • 5 Aug 2021 • Denis Kutnar, Bas H. M. van der Velden, Marta Girones Sanguesa, Mirjam I. Geerlings, J. Matthijs Biesbroek, Hugo J. Kuijf
Lacunes of presumed vascular origin are fluid-filled cavities of between 3 - 15 mm in diameter, visible on T1 and FLAIR brain MRI.
1 code implementation • 5 Aug 2021 • Marta Girones Sanguesa, Denis Kutnar, Bas H. M. van der Velden, Hugo J. Kuijf
Cerebral microbleeds are small, dark, round lesions that can be visualised on T2*-weighted MRI or other sequences sensitive to susceptibility effects.
1 code implementation • 3 Aug 2021 • Hugo J. Kuijf
Final evaluation on the test set of the VALDO challenge is pending.
no code implementations • 22 Jul 2021 • Bas H. M. van der Velden, Hugo J. Kuijf, Kenneth G. A. Gilhuijs, Max A. Viergever
With an increase in deep learning-based methods, the call for explainability of such methods grows, especially in high-stakes decision making areas such as medical image analysis.
no code implementations • 20 Jan 2021 • Kimberley M. Timmins, Irene C. van der Schaaf, Ynte M. Ruigrok, Birgitta K. Velthuis, Hugo J. Kuijf
The L2-optimized VAE outperforms SSIM, with improved reconstruction metrics and DSIs for both datasets.
no code implementations • 12 Jan 2021 • Ishaan Bhat, Hugo J. Kuijf, Veronika Cheplygina, Josien P. W. Pluim
We find that the use of a dropout rate of 0. 5 produces the least number of false positives in the neural network predictions and the trained classifier filters out approximately 90% of these false positives detections in the test-set.
1 code implementation • 15 Oct 2019 • Mariëlle J. A. Jansen, Hugo J. Kuijf, Maarten Niekel, Wouter B. Veldhuis, Frank J. Wessels, Max A. Viergever, Josien P. W. Pluim
Primary tumors have a high likelihood of developing metastases in the liver and early detection of these metastases is crucial for patient outcome.
1 code implementation • 22 Aug 2019 • Mariëlle J. A. Jansen, Hugo J. Kuijf, Josien P. W. Pluim
In this study, the optimal input configuration of DCE MR images for convolutional neural networks (CNNs) is studied.
1 code implementation • 1 Apr 2019 • Hugo J. Kuijf, J. Matthijs Biesbroek, Jeroen de Bresser, Rutger Heinen, Simon Andermatt, Mariana Bento, Matt Berseth, Mikhail Belyaev, M. Jorge Cardoso, Adrià Casamitjana, D. Louis Collins, Mahsa Dadar, Achilleas Georgiou, Mohsen Ghafoorian, Dakai Jin, April Khademi, Jesse Knight, Hongwei Li, Xavier Lladó, Miguel Luna, Qaiser Mahmood, Richard McKinley, Alireza Mehrtash, Sébastien Ourselin, Bo-yong Park, HyunJin Park, Sang Hyun Park, Simon Pezold, Elodie Puybareau, Leticia Rittner, Carole H. Sudre, Sergi Valverde, Verónica Vilaplana, Roland Wiest, Yongchao Xu, Ziyue Xu, Guodong Zeng, Jian-Guo Zhang, Guoyan Zheng, Christopher Chen, Wiesje van der Flier, Frederik Barkhof, Max A. Viergever, Geert Jan Biessels
Segmentation methods had to be containerized and submitted to the challenge organizers.
no code implementations • 22 Nov 2018 • Bas H. M. van der Velden, Bob D. de Vos, Claudette E. Loo, Hugo J. Kuijf, Ivana Isgum, Kenneth G. A. Gilhuijs
A constrained volume growing method uses these manually placed seed points as input and generates a tumor segmentation.