[FG] Center for medical Image Analysis & Navigation

Karnam, Murali et al. (2025) ‘User-specified inverse kinematics taught in virtual reality reduce time and effort to hand-guide redundant surgical robots’, Communications Engineering, 4(1). Available at: https://doi.org/10.1038/s44172-025-00357-x.

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Corbaz, H. et al. (2025) ‘A Comparative Study of CT Perfusion Postprocessing Tools in Medium/Distal Vessel Occlusion Stroke’, American Journal of Neuroradiology [Preprint]. Available at: https://doi.org/10.3174/ajnr.a8616.

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Schicklin, C. et al. (2025) ‘Correction: Schicklin et al. Method to Generate Chlorine Dioxide Gas In Situ for Sterilization of Automated Incubators. Pathogens 2024, 13, 1024’, Pathogens, 14(4), p. 368. Available at: https://doi.org/10.3390/pathogens14040368.

Sinues, Pablo et al. (2025) ‘Pain induces a rapid characteristic metabolic signature detectable in breath’. Research Square. Available at: https://doi.org/10.21203/rs.3.rs-6048423/v1.

Schwartz, R. et al. (2025) ‘Genetic Distinctions Between Reticular Pseudodrusen and Drusen: A Genome-Wide Association Study’, American Journal of Ophthalmology [Preprint]. Available at: https://doi.org/10.1016/j.ajo.2025.03.007.

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Prétot, Dominique et al. (2025) ‘Retinal oxygen metabolic function in choroideremia and retinitis pigmentosa’, Graefe’s Archive for Clinical and Experimental Ophthalmology, 263(2), pp. 379–385. Available at: https://doi.org/10.1007/s00417-024-06659-8.

Basler, S. et al. (2025) ‘Molecular breath profile of acute COPD exacerbations’, Journal of Breath Research, 19(1). Available at: https://doi.org/10.1088/1752-7163/ad9ac4.

Bieder, Florentin et al. (2025) ‘Modeling the Neonatal Brain Development Using Implicit Neural Representations’, in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 1–11. Available at: https://doi.org/10.1007/978-3-031-74561-4_1.

Birrer, Mathias et al. (2025) ‘Radiofrequency ablation (RFA) in unresectable pancreatic adenocarcinoma: meta-analysis & systematic review’, Surgical Endoscopy . 10.12.2024, 39(1), pp. 141–152. Available at: https://doi.org/10.1007/s00464-024-11450-1.

Durrer, Alicia et al. (2025) ‘Denoising Diffusion Models for 3D Healthy Brain Tissue Inpainting’, in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) . Marrakesh, Morocco: Springer Science and Business Media Deutschland GmbH (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) ), pp. 87–97. Available at: https://doi.org/10.1007/978-3-031-72744-3_9.

Friedrich, P., Frisch, Y. and Cattin, P.C. (2025) ‘Deep Generative Models for 3D Medical Image Synthesis’, in Generative Machine Learning Models in Medical Image Computing. Cham: Springer Nature Switzerland (Generative Machine Learning Models in Medical Image Computing), pp. 255–278. Available at: https://doi.org/10.1007/978-3-031-80965-1_13.

Friedrich, Paul et al. (2025) ‘WDM: 3D Wavelet Diffusion Models for High-Resolution Medical Image Synthesis’, in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 11–21. Available at: https://doi.org/10.1007/978-3-031-72744-3_2.

Terheyden, J.H. et al. (2025) ‘Validating candidate endpoints for intermediate age-related macular degeneration trials in a multi-centre setting—lessons from the MACUSTAR study’, Eye (Basingstoke) [Preprint]. Available at: https://doi.org/10.1038/s41433-024-03568-2.

Wehrli, Michael et al. (2025) ‘Generating 3D pseudo-healthy knee MR images to support trochleoplasty planning’, International Journal of Computer Assisted Radiology and Surgery [Preprint]. Available at: https://doi.org/10.1007/s11548-025-03343-y.

Zeng, J. et al. (2024) ‘Pharmacometabolomics via real-time breath analysis captures metabotypes of asthmatic children associated with salbutamol responsiveness’, iScience, 27(12), p. 111446. Available at: https://doi.org/10.1016/j.isci.2024.111446.

Cathomas, Marionna et al. (2024) ‘Safety and effectivity of Kono-S anastomosis in Crohn’s patients: a systematic review and Meta-analysis’, Langenbeck’s Archives of Surgery, 409(1). Available at: https://doi.org/10.1007/s00423-024-03412-x.

Manavi Roodsari, Samaneh et al. (2024) ‘Deep learning-based approach for high spatial resolution fibre shape sensing’, Communications Engineering, 3(1). Available at: https://doi.org/10.1038/s44172-024-00166-8.

Ochs, Vincent et al. (2024) ‘Development of predictive model for predicting postoperative BMI and optimize bariatric surgery: a single center pilot study’, Surgery for Obesity and Related Diseases, 20(12), pp. 1234–1243. Available at: https://doi.org/10.1016/j.soard.2024.06.012.

Cathomas, Marionna et al. (2024) ‘Adherence to enhanced recovery after surgery (ERAS) in older adults following colorectal resection’, Journal of Geriatric Oncology. 12.09.2024, 15(8). Available at: https://doi.org/10.1016/j.jgo.2024.102062.

Schicklin, C. et al. (2024) ‘Method to Generate Chlorine Dioxide Gas In Situ for Sterilization of Automated Incubators’, Pathogens, 13(11), p. 1024. Available at: https://doi.org/10.3390/pathogens13111024.

Paul Friedrich, Yannik Frisch and Philippe C. Cattin (2024) ‘Deep Generative Models for 3D Medical Image Synthesis’. Available at: https://doi.org/10.48550/ARXIV.2410.17664.

Schwartz, R. et al. (2024) ‘Genetic Distinctions Between Reticular Pseudodrusen and Drusen: Insights from a Genome-Wide Association Study’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.09.18.24313862.

de Vente, Coen et al. (2024) ‘Generalizable Deep Learning for the Detection of Incomplete and Complete Retinal Pigment Epithelium and Outer Retinal Atrophy: A MACUSTAR Report’, Translational Vision Science and Technology, 13(9). Available at: https://doi.org/10.1167/tvst.13.9.11.

Kunz, Julia Madlaina et al. (2024) ‘Assessment of resectability of pancreatic cancer using novel immersive high-performance virtual reality rendering of abdominal computed tomography and magnetic resonance imaging’, International Journal of Computer Assisted Radiology and Surgery, 19(9), pp. 1677–1687. Available at: https://doi.org/10.1007/s11548-023-03048-0.

Stritt, Kevin et al. (2024) ‘Risk Factors of Asymptomatic Kidney Stone Passage in Adults with Recurrent Kidney Stones’, Clinical Journal of the American Society of Nephrology, 19(9), pp. 1130–1137. Available at: https://doi.org/10.2215/CJN.0000000000000496.

Taha-Mehlitz, Stephanie et al. (2024) ‘Machine learning-based preoperative analytics for the prediction of anastomotic leakage in colorectal surgery: a swiss pilot study’, Surgical Endoscopy, 38(7), pp. 3672–3683. Available at: https://doi.org/10.1007/s00464-024-10926-4.

Taha-Mehlitz, Stephanie et al. (2024) ‘Machine learning-based preoperative analytics for the prediction of anastomotic leakage in colorectal surgery: a swiss pilot study’, Surgical Endoscopy, 38(7), pp. 3672–3683. Available at: https://doi.org/10.1007/s00464-024-10926-4.

Nahhas, M.K. et al. (2024) ‘Reviewing the potential of hearables for the assessment of bruxism Litareturrecherche zur Eignung von Hearables für die Erkennung von Bruxismus’, At-Automatisierungstechnik, 72(5), pp. 389–398. Available at: https://doi.org/10.1515/auto-2024-0029.

Valmaggia, Philippe (2024) Eye and heart synchronisation: development of time-resolved optical coherence tomography with electrocardiographic coupling. Doctoral Thesis. Universität Basel.

Taha, Anas et al. (2024) ‘Analysis of artificial intelligence in thyroid diagnostics and surgery: A scoping review’, American Journal of Surgery, 229, pp. 57–64. Available at: https://doi.org/10.1016/j.amjsurg.2023.11.019.

Maloca, Peter M. et al. (2024) ‘Human selection bias drives the linear nature of the more ground truth effect in explainable deep learning optical coherence tomography image segmentation’, Journal of Biophotonics, 17(2). Available at: https://doi.org/10.1002/jbio.202300274.

Ochs, Vincent et al. (2024) ‘An analysis of virtual reality in abdominal surgery—A scoping review’, International Journal of Medical Robotics and Computer Assisted Surgery, 20(1). Available at: https://doi.org/10.1002/rcs.2623.

Ochs, Vincent et al. (2024) ‘An analysis of virtual reality in abdominal surgery—A scoping review’, International Journal of Medical Robotics and Computer Assisted Surgery, 20(1). Available at: https://doi.org/10.1002/rcs.2623.

Taha-Mehlitz, Stephanie et al. (2024) ‘Is pain control for chronic neuropathic pain after inguinal hernia repair using endoscopic retroperitoneal neurectomy effective? A meta-analysis of 142 patients from 1995 to 2022’, Langenbeck’s Archives of Surgery, 408(1). Available at: https://doi.org/10.1007/s00423-022-02748-6.

Cagol, Alessandro et al. (2024) ‘Association of Spinal Cord Atrophy and Brain Paramagnetic Rim Lesions With Progression Independent of Relapse Activity in People With MS’, Neurology, 102(1). Available at: https://doi.org/10.1212/wnl.0000000000207768.

Cagol, Alessandro et al. (2024) ‘Association of Spinal Cord Atrophy and Brain Paramagnetic Rim Lesions With Progression Independent of Relapse Activity in People With MS’, Neurology, 102(1). Available at: https://doi.org/10.1212/wnl.0000000000207768.

Awchi, Mo et al. (2024) ‘Metabolic trajectories of diabetic ketoacidosis onset described by breath analysis’, Frontiers in Endocrinology, 15. Available at: https://doi.org/10.3389/fendo.2024.1360989.

Durrer, Alicia, Cattin, Philippe C. and Wolleb, Julia (2024) ‘Denoising Diffusion Models for Inpainting of Healthy Brain Tissue’, in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 35–45. Available at: https://doi.org/10.1007/978-3-031-76163-8_4.

Durrer, Alicia et al. (2024) ‘Denoising diffusion models for 3D healthy brain tissue inpainting’, in Medical Image Computing and Computer Assisted Interventions. Marrakesh (Medical Image Computing and Computer Assisted Interventions).

Filipozzi, M. et al. (2024) ‘Ultra Miniaturized Absolute Rotary Encoder Integrated into Hinge Joint’, in Proceedings of IEEE Sensors. Institute of Electrical and Electronics Engineers Inc. (Proceedings of IEEE Sensors). Available at: https://doi.org/10.1109/SENSORS60989.2024.10784533.

Orso Pusterla et al. (2024) ‘An automated pipeline for computation and analysis of functional ventilation and perfusion lung MRI with matrix pencil decomposition: TrueLung’, Zeitschrift fur Medizinische Physik [Preprint]. Available at: https://doi.org/10.1016/j.zemedi.2024.08.001.

Seppi, Carlo and Cattin, C. Cattin (2024) Deep-Learning Approach for Tissue Classification using Acoustic Waves during Ablation with an Er:YAG Laser (Updated). arXiv.org. Available at: https://doi.org/https://arxiv.org/abs/2406.14570v2.

Sola-Martínez, R.A. et al. (2024) ‘Preservation of exhaled breath samples for analysis by off-line SESI-HRMS: proof-of-concept study’, Journal of Breath Research, 18(1). Available at: https://doi.org/10.1088/1752-7163/ad10e1.

von Niederhäusern, Peter A. et al. (2024) ‘Augmented reality for sentinel lymph node biopsy’, International Journal of Computer Assisted Radiology and Surgery, 19(1), pp. 171–180. Available at: https://doi.org/10.1007/s11548-023-03014-w.

von Niederhäusern, P.A. et al. (2024) ‘Augmented reality for sentinel lymph node biopsy’, International Journal of Computer Assisted Radiology and Surgery, 19(1), pp. 171–180. Available at: https://doi.org/10.1007/s11548-023-03014-w.

Wolleb, Julia et al. (2024) ‘Binary Noise for Binary Tasks: Masked Bernoulli Diffusion for Unsupervised Anomaly Detection’, in Lecture Notes in Computer Science. Cham: Springer Nature Switzerland (Lecture Notes in Computer Science), pp. 135–145. Available at: https://doi.org/10.1007/978-3-031-72120-5_13.

Denk, Nora et al. (2023) ‘Cynomolgus monkey’s retina volume reference database based on hybrid deep learning optical coherence tomography segmentation’, Scientific Reports, 13(1). Available at: https://doi.org/10.1038/s41598-023-32739-6.

Hamidi, Arsham et al. (2023) ‘Towards phase-sensitive optical coherence tomography in smart laser osteotomy: temperature feedback’, Lasers in Medical Science, 38(1). Available at: https://doi.org/10.1007/s10103-023-03886-z.

Hamidi, A. et al. (2023) ‘Multimodal feedback systems for smart laser osteotomy: Depth control and tissue differentiation’, Lasers in Surgery and Medicine, 55(10), pp. 900–911. Available at: https://doi.org/10.1002/lsm.23732.

Maloca, Peter M. et al. (2023) ‘Validation of collaborative cyberspace virtual reality oculometry enhanced with near real-time spatial audio’, Scientific Reports, 13(1). Available at: https://doi.org/10.1038/s41598-023-37267-x.

Ansari, Georg et al. (2023) ‘The Optical Coherence Tomography and Microperimetry Biomarker Evaluation in Patients with Geographic Atrophy (OMEGA) Study: Design and Baseline Characteristics - OMEGA Report 1’, Ophthalmic Research, 66(1), pp. 1392–1401. Available at: https://doi.org/10.1159/000535375.

Ochs, Vincent et al. (2023) ‘Development and validation of a predictive model of the hospital cost associated with bariatric surgery’, Obesity Research and Clinical Practice, 17(6), pp. 529–535. Available at: https://doi.org/10.1016/j.orcp.2023.10.003.

Schnider, Eva et al. (2023) ‘Improved distinct bone segmentation in upper-body CT through multi-resolution networks’, International Journal of Computer Assisted Radiology and Surgery, 18(11), pp. 2091–2099. Available at: https://doi.org/10.1007/s11548-023-02957-4.

Żelechowski, M. et al. (2023) ‘Automatic patient positioning based on robot rotational workspace for extended reality’, International Journal of Computer Assisted Radiology and Surgery, 18(11), pp. 1951–1959. Available at: https://doi.org/10.1007/s11548-023-02967-2.

Awchi, M. et al. (2023) ‘Prediction of systemic free and total valproic acid by off-line analysis of exhaled breath in epileptic children and adolescents’, Journal of Breath Research, 17(4). Available at: https://doi.org/10.1088/1752-7163/acf782.

Saad, Baraa et al. (2023) ‘Safety and efficacy of LA-ERCP procedure following Roux-en-Y gastric bypass: a systematic review and meta-analysis’, Surgical Endoscopy, 37(9), pp. 6682–6694. Available at: https://doi.org/10.1007/s00464-023-10276-7.

Taha, Anas et al. (2023) ‘Second Primary Cancer among Patients with Papillary Thyroid Carcinoma Following the Chernobyl Disaster’, JAMA Network Open. 17.08.2023, 6(8). Available at: https://doi.org/10.1001/jamanetworkopen.2023.29559.

Maintz, Michaela et al. (2023) ‘Parameter optimization in a finite element mandibular fracture fixation model using the design of experiments approach’, Journal of the Mechanical Behavior of Biomedical Materials, 144. Available at: https://doi.org/10.1016/j.jmbbm.2023.105948.

Arnold, Kim et al. (2023) ‘Real-Time Volatile Metabolomics Analysis of Dendritic Cells’, Analytical Chemistry, 95(25), pp. 9415–9421. Available at: https://doi.org/10.1021/acs.analchem.3c00516.

Roodsari, S.M. et al. (2023) Deep-learning-based high spatial resolution fiber shape sensing. Research Square Platform LLC. Available at: https://doi.org/10.21203/rs.3.rs-2573095/v1.

Bayhaqi, Y.A. et al. (2023) ‘Real-time closed-loop tissue-specific laser osteotomy using deep-learning-assisted optical coherence tomography’, Biomedical Optics Express, 14(6), pp. 2986–3002. Available at: https://doi.org/10.1364/BOE.486660.

Manavi Roodsari, Samaneh et al. (2023) ‘Shape sensing of optical fiber Bragg gratings based on deep learning’, Machine Learning: Science and Technology, 4(2). Available at: https://doi.org/10.1088/2632-2153/acda10.

Tsagkas, Charidimos et al. (2023) ‘Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis’, Multiple Sclerosis Journal, 29(6), pp. 702–718. Available at: https://doi.org/10.1177/13524585221139152.

Tsagkas, Charidimos et al. (2023) ‘Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis’, Multiple Sclerosis Journal, 29(6), pp. 702–718. Available at: https://doi.org/10.1177/13524585221139152.

Awchi M et al. (2023) ‘UHPLC-MS/MS-Based Identity Confirmation of Amino Acids Involved in Response to and Side Effects from Antiseizure Medications’, Journal of Proteome Research, 22(3), pp. 990–995. Available at: https://doi.org/10.1021/acs.jproteome.2c00835.

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Tsagkas C et al. (2023) ‘Fully Automatic Method for Reliable Spinal Cord Compartment Segmentation in Multiple Sclerosis’, American Journal of Neuroradiology, 44(2), pp. 218–227. Available at: https://doi.org/10.3174/ajnr.A7756.

Tsagkas, C. et al. (2023) ‘Fully Automatic Method for Reliable Spinal Cord Compartment Segmentation in Multiple Sclerosis’, American Journal of Neuroradiology, 44(2), pp. 218–227. Available at: https://doi.org/10.3174/ajnr.a7756.

Bieder, Florentin et al. (2023) ‘Memory-Efficient 3D Denoising Diffusion Models for Medical Image Processing’, in Ipek Oguz, Jack Noble, Xiaoxiao Li, Martin Styner, Christian Baumgartner, Mirabela Rusu, Tobias Heinmann, Despina Kontos, Bennett Landman, Benoit Dawant (ed.) Medical Imaging with Deep Learning. Nashville, TN (Medical Imaging with Deep Learning). Available at: https://proceedings.mlr.press/v227/bieder24a.html.

Bieder, Florentin et al. (2023) ‘Memory-Efficient 3D Denoising Diffusion Models for Medical Image Processing’, in Proceedings of machine learning research. Nashville, TN, USA: MLResearchPress (Medical Imaging with Deep Learning), pp. 552–567.

Cetin, Cigdem et al. (2023) ‘Bone ablation performance of a Tm-Cr-Ho:YAG Laser’, in Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE (Progress in Biomedical Optics and Imaging - Proceedings of SPIE). Available at: https://doi.org/10.1117/12.2647703.

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Durrer, Alicia et al. (2023) ‘Diffusion Models for Contrast Harmonization of Magnetic Resonance Images’, in Proceedings of Machine Learning Research, pp. 526–551.

Enodien, Bassey et al. (2023) ‘The development of machine learning in bariatric surgery’, Frontiers in Surgery, 10, p. 1102711. Available at: https://doi.org/10.3389/fsurg.2023.1102711.

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Friedrich, P. et al. (2023) ‘Point Cloud Diffusion Models for Automatic Implant Generation’, in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vancouver, Canada: Springer Science and Business Media Deutschland GmbH (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)), pp. 112–122. Available at: https://doi.org/10.1007/978-3-031-43996-4_11.

Hamidi, A. et al. (2023) ‘Towards miniaturized OCT-guided laser osteotomy: integration of fiber-coupled Er:YAG laser with OCT’, Optics Continuum, 2(10), pp. 2106–2115. Available at: https://doi.org/10.1364/OPTCON.497483.

Karnam, Murali et al. (2023) ‘Qualitative and quantitative assessment of admittance controllers for hand-guiding surgical robots’, At-Automatisierungstechnik, 71, pp. 515–527. Available at: https://doi.org/10.1515/auto-2023-0063.

Karnam, Murali et al. (2023) ‘Workspace-aware Planning of a Surgical Robot Mounting in Virtual Reality’, in Mechanisms and Machine Science. Springer Science and Business Media B.V. (Mechanisms and Machine Science), pp. 13–19. Available at: https://doi.org/10.1007/978-3-031-32446-8_2.

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Taha, Anas et al. (2023) ‘Machine learning in pancreas surgery, what is new? literature review’, Frontiers in Surgery, 10. Available at: https://doi.org/10.3389/fsurg.2023.1142585.

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Maloca PM et al. (2022) ‘Reference database of total retinal vessel surface area derived from volume-rendered optical coherence tomography angiography’, Scientific Reports, 12(1), p. 3695. Available at: https://doi.org/10.1038/s41598-022-07439-2.

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Valmaggia, Philippe et al. (2022) ‘Iris Color Matters—A Contractility Analysis With Dynamic Volume-Rendered Optical Coherence Tomography Pupillometry’, Translational Vision Science and Technology, 11(11). Available at: https://doi.org/10.1167/tvst.11.11.6.

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Bayhaqi Y.A. et al. (2022) ‘Deep-Learning-Based Fast Optical Coherence Tomography (OCT) Image Denoising for Smart Laser Osteotomy’, IEEE Transactions on Medical Imaging, 41(10), pp. 2615–2628. Available at: https://doi.org/10.1109/TMI.2022.3168793.

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Taha A et al. (2022) ‘The development of machine learning in lung surgery: A narrative review’, Frontiers in Surgery, 9, p. 914903. Available at: https://doi.org/10.3389/fsurg.2022.914903.