Medical Image Analysis

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• 3D Camera Monitoring of Rodent Irradiation Geometry for High Precision Shielding

  Author: Slegt, V. J., 29 Sept 2022

  Supervisor: Raaijmakers, A. J. E. (Supervisor 1), Pluim, J. P. W. (Supervisor 2), Schwab, H. (Supervisor 2), Staut, N. (External person) (External coach) & Verhaegen, F. J. W. (External person) (External coach)

  Student thesis: Master

• 3D medical image segmentation with labeled and unlabeled data using autoencoders

  Author: Sital, C. K., 28 Nov 2019

  Supervisor: Raaijmakers, A. (Supervisor 1), Weese, J. (External person) (External coach) & Brosch, T. (External person) (External coach)

  Student thesis: Master

• A computational biology framework: a data analysis tool to support biomedical engineers in their research

  Author: Beishuizen, T. P. A., 29 Nov 2018

  Supervisor: Bosnacki, D. (Supervisor 1), Cheplygina, V. (Supervisor 2), Hilbers, P. A. J. (Supervisor 2), Fletcher, G. (Supervisor 2) & Vanschoren, J. (Supervisor 2)

  Student thesis: Master

• A Functionalized Anatomical Model for Transcutaneous Electrical Stimulation of the Spinal Cord to Improve Upper Extremity Motor Function

  Author: de Graaf, M. A. F. A., 13 Sept 2021

  Supervisor: Raaijmakers, A. J. E. (Supervisor 1), Pluim, J. P. W. (Supervisor 2), Lopata, R. G. P. (Supervisor 2) & Paoles, E. (External coach)

  Student thesis: Master

• Altered Global Organization of Structural Covariance Networks Relate to Childhood Absence Epilepsy

  Author: Eussen, M. J. A., 2022

  Supervisor: Breeuwer, M. (Supervisor 1), Drenthen, G. S. (External coach), Bosnacki, D. (Supervisor 2) & Scannell, C. (Supervisor 2)

  Student thesis: Master

• Analysis of Automated Segmentation of Stomach Contents in Longitudinal Magnetic Resonance Images using a 2D and 3D Deep Learning Approach

  Author: Wolf, H. N. A., 25 Aug 2022

  Supervisor: Veta, M. (Supervisor 1), Pluim, J. P. W. (Supervisor 2), Schwab, H. (Supervisor 2), Smeets, P. A. M. (External person) (External coach), Camps, G. (External person) (External coach) & Witteman, B. (External person) (External coach)

  Student thesis: Master

• Analyzing the relation between brain lesions and short association fibers using diffusion MRI

  Author: Kamps, J. J. W., Jun 2017

  Supervisor: Sepasian, N. (Supervisor 1), Fuster, A. (Supervisor 2) & Pluim, J. P. W. (Supervisor 2)

  Student thesis: Master

• Assessment of paired and unpaired learning to improve the image quality of onboard CBCT for radiotherapy of prostate cancer

  Author: Kerckhaert, C. E. M., 31 Mar 2022

  Supervisor: Pluim, J. P. W. (Supervisor 1), van Eijnatten, M. (Supervisor 2), Tijssen, H. N. (External coach) & Markvoort, A. J. (Supervisor 2)

  Student thesis: Master

• Automated B-Line Detection and Localization in Lung Ultrasound

  Author: Lucassen, R. T., 25 Aug 2022

  Supervisor: Veta, M. (Supervisor 1), Pluim, J. P. W. (Supervisor 2) & Lopata, R. G. P. (Supervisor 2)

  Student thesis: Master

• Automated Cardiac MR Scar Quantification with an Optimized Cascaded Pipeline and GAN-Based Data Augmentation

  Author: Lustermans, D. R. P. R. M., 19 May 2022

  Supervisor: Breeuwer, M. (Supervisor 1), Scannell, C. (External coach) & Veta, M. (Supervisor 2)

  Student thesis: Master

• Automated spinous process segmentation in X-ray images using convolutional neural networks

  Author: Roodhorst, S., 17 Dec 2018

  Supervisor: Pluim, J. (Supervisor 1) & van Walsum, T. (External person) (External coach)

  Student thesis: Master

• Automatic Cerebrovascular Segmentation of TOF-MRAs Using Deep Learning to Aid in Intracranial Aneurysm Detection

  Author: de Vos, V., 14 Jun 2021

  Supervisor: Pluim, J. P. W. (Supervisor 1), Cheplygina, V. (Supervisor 2), Wu, M. (Supervisor 2), Kuijf, H. J. (External coach) & Timmins, K. M. (External person) (External coach)

  Student thesis: Master

• Automatic myocardial scar segmentation and quantification in LGE CMR images

  Author: Borleh, A., 27 Aug 2020

  Supervisor: Pluim, J. P. W. (Supervisor 1), Breeuwer, M. (Supervisor 2) & Hilbers, P. A. J. (Supervisor 2)

  Student thesis: Master

• Autonomous Patient-Specific Magnetic Resonance Imaging Sequence Design via Real-Time Deep Reinforcement Learning

  Author: Verschuren, S. H. A., 31 Oct 2022

  Supervisor: Raaijmakers, A. J. E. (Supervisor 1), Scannell, C. (Supervisor 2), Schwab, H. (Supervisor 2), van den Berg, C. A. T. (External person) (External coach) & Terpstra, M. (External person) (External coach)

  Student thesis: Master

• Auto-segmentation of the Pituitary Adenoma and Normal Pituitary Tissue in Patients with Acromegaly

  Author: Vromans, J., Oct 2022

  Supervisor: Breeuwer, M. (Supervisor 1), Klein, S. S. (External person) (External coach), Raaijmakers, A. J. E. (Supervisor 2) & Neggers, S. J. C. M. M. (External person) (External coach)

  Student thesis: Master

• Benchmarking of Activity Inference Methods against Total Count Variation in Single-Cell RNA Sequencing and Incorporation in Trajectory Inference

  Author: de Rooij, M., 2022

  Supervisor: Hilbers, P. A. J. (Supervisor 1), Eduati, F. (Supervisor 2), Finotello, F. (External person) (External coach), Raaijmakers, A. J. E. (Supervisor 2) & Pellegatta, S. (External person) (External coach)

  Student thesis: Master

• Biomechanical model-based deformable image registration for CT-guided percutaneous liver tumor ablation interventions

  Author: Cruts, J. M. H., 14 Jun 2021

  Supervisor: van de Vosse, F. N. (Supervisor 1), Pluim, J. P. W. (Supervisor 2), Baragona, M. (External person) (External coach), Isfort, P. (External person) (External coach) & van Walsum, T. (External person) (External coach)

  Student thesis: Master

• Brain blood perfusion and white matter integrity in accelerated cognitive ageing patiens with epilepsy

  Author: Stevens, J. C. J. M., 31 Oct 2019

  Supervisor: Breeuwer, M. (Supervisor 1), Pluim, J. (Supervisor 2), Aldenkamp, A. (Supervisor 2), Zinger, S. (Supervisor 2), Mestrom, R. (Supervisor 2) & Bernas, A. (Supervisor 2)

  Student thesis: Master

• Canonical correlation analysis on microbial and metabolite data of individuals with metabolic syndrome

  Author: van der Stam, J., 19 Jan 2019

  Supervisor: Hilbers, P. A. J. (Supervisor 1), van Riel, N. (Supervisor 2), Veta, M. (Supervisor 2), Levin, E. (External person) (External coach) & Nieuwdorp, M. (External person) (External coach)

  Student thesis: Master

• Causal candidate genes identification for familial hypercholesterolemia family based on whole-genome sequencing

  Author: Wang, Q., 31 Aug 2017

  Supervisor: Hilbers, P. A. J. (Supervisor 1), van Riel, N. A. W. (Supervisor 2), Hovingh, K. (External person) (External coach), Bosnacki, D. (Supervisor 2) & Veta, M. (Supervisor 2)

  Student thesis: Master

• Challenges for Accelerated Partial Breast Irradiation on an MR-Linac: Electron streaming effect, synthetic CT for dose calculations and plan adaptation to daily MRI

  Author: de Hond, Y. J. M., 19 Apr 2021

  Supervisor: Raaijmakers, A. J. E. (Supervisor 1), Hackett, S. L. (External person) (External coach), Houweling, A. C. (External person) (External coach), van Eijnatten, M. (Supervisor 2) & Lopata, R. G. P. (Supervisor 2)

  Student thesis: Master

• Clustered tumor phenotypes and resectability prediction for PDA using radiomic feature analysis

  Author: Janse, M. H. A., 27 Sept 2018

  Supervisor: de With, P. H. N. (Supervisor 1), Pluim, J. P. W. (Supervisor 2), Zinger, S. (Supervisor 2) & Hermans, J. J. (External person) (External coach)

  Student thesis: Master

• Content based CT retrieval for pulmonary nodules: deep metric learning based feature extraction

  Author: Aerts, T. G., 28 Feb 2019

  Supervisor: Menkovski, V. (Supervisor 1), Holenderski, M. (Supervisor 2) & Veta, M. (Supervisor 2)

  Student thesis: Master

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• Continuous arterial blood pressure estimations with the use of Photoplethysmography: A machine learning and arterial modelling approach

  Author: van Waesberge, K., 11 Oct 2021

  Supervisor: van de Vosse, F. N. (Supervisor 1), Serrarens, A. (External coach), Veta, M. (Supervisor 2), Huberts, W. (Supervisor 2) & Wijntjes, P. (Supervisor 2)

  Student thesis: Master

• Convolutional neural networks for detection of metastases in patients diagnosed with breast cancer

  Author: Nijhof, T. G., 25 Jan 2018

  Supervisor: Pluim, J. (Supervisor 1)

  Student thesis: Master

• Corneal endothelial cell segmentation and biomarker extraction in specular microscopy images using deep learning

  Author: Timmers, D. F. M., 13 Sept 2021

  Supervisor: Veta, M. (Supervisor 1), van Eijnatten, M. (Supervisor 2) & Bosnacki, D. (Supervisor 2)

  Student thesis: Master

• Counterfactual Inference on Retina Fundus Images using Deep Structural Causal Models

  Author: Liao, S., 12 Dec 2022

  Supervisor: Menkovski, V. (Supervisor 1), Veta, M. (Supervisor 2) & Minartz, K. (Supervisor 2)

  Student thesis: Master

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• CycleGAN for coronay vessel segmentation

  Author: van den Bosch, P. C. J., 29 Aug 2019

  Supervisor: Pluim, J. (Supervisor 1), Bovendeerd, P. (Supervisor 2), Veta, M. (Supervisor 2) & Oliván Bescós, J. (External person) (External coach)

  Student thesis: Master

• Deep Gray Matter Segmentation in Multiple Sclerosis: a Deep Learning Approach

  Author: Koopman, K., 13 Dec 2021

  Supervisor: Breeuwer, M. (Supervisor 1), Brouwer, I. (External person) (External coach) & Vrenken, H. (External person) (External coach)

  Student thesis: Master

• Deep learning approaches for prostate cancer detection and grading in Bi-parametric MRI

  Author: de Vente, C. W., 29 Aug 2019

  Supervisor: Veta, M. (Supervisor 1), Vos, P. (External person) (External coach), van Riel, N. (Supervisor 2) & Pluim, J. (Supervisor 2)

  Student thesis: Master

• Deep learning-based analysis of bone marrow histopathology images

  Author: van Eekelen, L., 19 Apr 2021

  Supervisor: Veta, M. (Supervisor 1), Pinckaers, H. (External person) (External coach), Hebeda, K. (External person) (External coach) & Litjens, G. J. S. (External coach)

  Student thesis: Master

• Deep learning-based anatomy recognition for robot-assisted minimally invasive esophagectomy

  Author: Jaspers, T. J. M., 31 Oct 2022

  Supervisor: van Eijnatten, M. (Supervisor 1), Ruurda, J. P. (External person) (External coach), Raaijmakers, A. J. E. (Supervisor 2), Bosnacki, D. (Supervisor 2), van der Sommen, F. (Supervisor 2), de Jongh, C. (External person) (External coach) & den Boer, R. B. (External person) (External coach)

  Student thesis: Master

• Deep learning based classification of spitzoid lesions on H&E stained histopathology whole slide images

  Author: van Kerkvoorde, J. A. J. P., 27 Aug 2020

  Supervisor: Veta, M. (Supervisor 1), van Eijnatten, M. (Supervisor 2), Bosnacki, D. (Supervisor 2), Blokx, W. A. M. (External person) (External coach) & Stathonikos, N. (External person) (External coach)

  Student thesis: Master

• Deep Learning Based Deformable Image Registration of Abdominal CT scans during CT-Guided RF Ablation of Liver Tumours

  Author: van den Berg, M. A., 25 Aug 2022

  Supervisor: van Eijnatten, M. (Supervisor 1), Raaijmakers, A. J. E. (Supervisor 2), Grisoni, F. (Supervisor 2), van Walsum, T. (External person) (External coach) & Moelker, A. (External person) (External coach)

  Student thesis: Master

• Deep Learning-based Hyperspectral Imaging: an intraoperative margin assessment technique for improving breast cancer surgery

  Author: de Kruif, N., 11 Oct 2021

  Supervisor: Pluim, J. P. W. (Supervisor 1), van Eijnatten, M. (Supervisor 2) & Bosnacki, D. (Supervisor 2)

  Student thesis: Master

• Deep learning based image enhancement in limited-view ultrasound tomography

  Author: van Pagee, L. J., 29 Sept 2022

  Supervisor: Schwab, H. (Supervisor 1), Awasthi, N. (Supervisor 2) & Brunsveld, L. (Supervisor 2)

  Student thesis: Master

• Deep learning-based synthetic CT generation for brain MR-only radiotherapy: a multi-view approach on heterogeneous MRI of pediatric patients

  Author: Bentvelzen, L. G., 27 Aug 2020

  Supervisor: Breeuwer, M. (Supervisor 1), Maspero, M. (External person) (External coach) & Philippens, M. E. P. (External person) (External coach)

  Student thesis: Master

• Deep learning for the detection of cerebral microinfarcts in MR images

  Author: Volmer, L. F., 31 Oct 2019

  Supervisor: Pluim, J. (Supervisor 1), Veta, M. (Supervisor 2) & van Riel, N. (Supervisor 2)

  Student thesis: Master

• Deep Learning for Ultrasound Beamforming in the Radon Domain

  Author: Jansen, G. E., 13 Sept 2021

  Supervisor: Lopata, R. G. P. (Supervisor 1), Schwab, H. (Supervisor 2), Awasthi, N. (Supervisor 2), van Eijnatten, M. (Supervisor 2) & van Sambeek, M. R. H. M. (Supervisor 2)

  Student thesis: Master

• Deep Learning on Computed Tomography Scans to Predict Immunotherapy Response of Patients with Metastatic Melanoma

  Author: de Mooij, R. A. J., 24 Nov 2022

  Supervisor: Veta, M. (Supervisor 1), Scannell, C. (Supervisor 2), Tel, J. (Supervisor 2) & ter Maat, R. (External coach)

  Student thesis: Master

• Detection of Ductal Carcinoma in Situ in Whole-Slide Images Using Deep Learning

  Author: Janssen, D. W. H., 13 Dec 2021

  Supervisor: Veta, M. (Supervisor 1), Breeuwer, M. (Supervisor 2) & Bosnacki, D. (Supervisor 2)

  Student thesis: Master

• Developing a fluid-structure interaction model to study intraluminal thrombus in abdominal aorta aneurysms

  Author: Fonken, J. H. C., 27 Aug 2020

  Supervisor: Lopata, R. G. P. (Supervisor 1), van de Vosse, F. N. (Supervisor 2), van Sambeek, M. R. H. M. (Supervisor 2), Raaijmakers, A. J. E. (Supervisor 2) & Nievergeld, A. H. M. (Supervisor 2)

  Student thesis: Master

• Development and evaluation of radiation therapy dose distribution prediction models for breast cancer

  Author: Bakx, N. L. M., 27 Aug 2020

  Supervisor: Pluim, J. P. W. (Supervisor 1), Hurkmans, C. (External coach), Bluemink, H. (External coach) & Hagelaar, E. (External person) (External coach)

  Student thesis: Master

• Development of Image Registration Workflow for Matching of Adolescent to Child Anatomy

  Author: Husić, A., 25 Aug 2022

  Supervisor: Breeuwer, M. (Supervisor 1), Zachiu, C. (External person) (External coach) & Seravalli, E. (External person) (External coach)

  Student thesis: Master

• Diffusion tensor residuals as a potential biomarker for brain tissue damage

  Author: van Rijn, A. P., 23 Apr 2020

  Supervisor: Pluim, J. P. W. (Supervisor 1), Leemans, A. L. G. (External person) (External coach) & de Luca, A. (External person) (External coach)

  Student thesis: Master

• Dosimetric Evaluation of Central Lung SBRT on the MR-linac: a Case Series

  Author: van den Dobbelsteen, M., 22 Feb 2021

  Supervisor: Raaijmakers, A. J. E. (Supervisor 1), van Eijnatten, M. (Supervisor 2), Foolen, J. (Supervisor 2), Hackett, S. L. (External person) (External coach) & Fast, M. F. (External person) (External coach)

  Student thesis: Master

• Evaluation of the daily dose based on CBCT for locoregional breast cancer radiotherapy

  Author: Broeckaert, F. V. A. M., 31 Oct 2022

  Supervisor: Raaijmakers, A. J. E. (Supervisor 1), Breeuwer, M. (Supervisor 2) & Lopata, R. G. P. (Supervisor 2)

  Student thesis: Master

• Exploring Brain Connectivity in Ageing Using Explainable Deep Learning

  Author: van Asch, T. G., 28 Feb 2022

  Supervisor: Breeuwer, M. (Supervisor 1), Jansen, J. F. A. (External coach) & de Jong, N. (External person) (External coach)

  Student thesis: Master

• Effect of SNR and user-defined tractography parameters on group analyses of diffusion tensor metrics

  Author: Vos, I. N., 27 Feb 2020

  Supervisor: Breeuwer, M. (Supervisor 1), Leemans, A. L. G. (External person) (External coach) & de Luca, A. (External person) (External coach)

  Student thesis: Master

• Feasibility of MRI-guided Radiotherapy for Head-and-Neck Cancer on a 1.5T MR-Linac: MR-Linac treatment plan evaluation, robustness of MR-Linac planning and the electron return effect

  Author: Massop, S., 19 Apr 2021

  Supervisor: Pluim, J. P. W. (Supervisor 1), Philippens, M. E. P. (External person) (External coach), Raaijmakers, A. J. E. (Supervisor 2) & van Rietbergen, B. (Supervisor 2)

  Student thesis: Master