[FG] Center for medical Image Analysis & Navigation

Feczko, Eric et al. (2025) ‘Baby Open Brains: An open-source dataset of infant brain segmentations’, Scientific Data, 12. Available at: https://doi.org/10.1038/s41597-025-05404-y.

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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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Valmaggia, Philippe et al. (2025) ‘Heart-retina time analysis using electrocardiogram-coupled time-resolved dynamic optical coherence tomography’, Scientific Reports. 02.01.2025, 15(1). Available at: https://doi.org/10.1038/s41598-024-84417-w.

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Ansari, Georg et al. (2025) ‘Evaluating the Progression of Retinal Sensitivity Loss in Geographic Atrophy Using Machine-Learning-Based Structure-Function Correlation (OMEGA 2)’, Investigative Ophthalmology and Visual Science, 66. Available at: https://doi.org/10.1167/iovs.66.11.34.

Zeng, J. et al. (2025) ‘Breath Analysis of Propofol and Associated Metabolic Signatures: A Pilot Study Using Secondary Electrospray Ionization-High-resolution Mass Spectrometry’, Anesthesiology, 143(2), pp. 345–356. Available at: https://doi.org/10.1097/ALN.0000000000005531.

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Schwartz, R. et al. (2025) ‘Genetic Distinctions Between Reticular Pseudodrusen and Drusen: A Genome-Wide Association Study’, American Journal of Ophthalmology, 274, pp. 286–295. Available at: https://doi.org/10.1016/j.ajo.2025.03.007.

Wehrli, Michael et al. (2025) ‘Generating 3D pseudo-healthy knee MR images to support trochleoplasty planning’, International Journal of Computer Assisted Radiology and Surgery , 20(6), pp. 1059–1066. Available at: https://doi.org/10.1007/s11548-025-03343-y.

Goncalves, M. et al. (2025) ‘fMRIPrep Lifespan: Extending A Robust Pipeline for Functional MRI Preprocessing to Developmental Neuroimaging’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2025.05.14.654069.

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Schicklin, C. et al. (2025) ‘Correction to: Method to Generate Chlorine Dioxide Gas In Situ for Sterilization of Automated Incubators (Pathogens, (2024), 13, 11, (1024), 10.3390/pathogens13111024)’, Pathogens, 14(4), p. 368. Available at: https://doi.org/10.3390/pathogens14040368.

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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.

Azrak, O. et al. (2025) ‘Early White Matter Microstructure Alterations in Infants with Down Syndrome’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2025.02.26.25322913.

Li, J. et al. (2025) ‘MedShapeNet - a large-scale dataset of 3D medical shapes for computer vision’, Biomedizinische Technik, 70(1), pp. 71–90. Available at: https://doi.org/10.1515/bmt-2024-0396.

Oliveira, M.L. et al. (2025) ‘Development and evaluation of a deep learning model to reduce exomass-related metal artefacts in cone-beam CT: an ex vivo study using porcine mandibles’, Dentomaxillofacial Radiology, 54(2), pp. 109–117. Available at: https://doi.org/10.1093/dmfr/twae062.

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.

Grobshäuser, Ellen et al. (2025) ‘Investigation of Endothelial Cell Density after PreserFlo Implantation Compared to Contralateral Eyes without PreserFlo Implantation-A Retrospective Analysis’, Klinische Monatsblatter fur Augenheilkunde, 242, pp. 392–397. Available at: https://doi.org/10.1055/a-2495-8580.

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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) . 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. 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.

Davaux, F. et al. (2025) ‘Attention Rings for Shape Analysis and Application to MRI Quality Control’, 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/10.1117/12.3047233.

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.

Duverney, Cédric (2025) Robot-assisted systems for manipulation and machining of small-sized objects. Doctoral Thesis. University of Basel.

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) . 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. 11–21. Available at: https://doi.org/10.1007/978-3-031-72744-3_2.

Hong, Y. et al. (2025) ‘Structural Connectome Gradients and Their Relationship to IQ in Early Childhood’. Elsevier BV. Available at: https://doi.org/10.2139/ssrn.5125937.

Luo, X. et al. (2025) ‘Practical Applications of Secondary/Extractive Electrospray Ionization (SESI): A Versatile Tool for Real-Time Chemical Analysis’, Mass Spectrometry Reviews [Preprint]. Available at: https://doi.org/10.1002/mas.21938.

Michaela Valerie Maintz (2025) Simulation-driven methods for the next generation of patient-specific osteosynthesis plates. Doctoral Thesis. University of Basel.

Valladon, L. et al. (2025) ‘Static and Dynamic Edge Convolution for PointNet based White Matter Fiber Segmentation’, 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/10.1117/12.3047338.

Valmaggia, Philippe (2025) Eye and Heart Synchronisation: Development of Time-Resolved Optical Coherence Tomography with Electrocardiographic Coupling. Doctoral Thesis. Universität Basel.

Yin, W. et al. (2025) ‘Charting brain functional development from birth to 6 years of age’. Available at: https://doi.org/10.1038/s41562-025-02160-2.

Zeng, Jiafa et al. (2024) ‘Pharmacometabolomics via real-time breath analysis captures metabotypes of asthmatic children associated with salbutamol responsiveness’, iScience. 20.12.2024, 27(12). 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.

Künstle, Noëmi et al. (2024) ‘Differences in autophagy marker levels at birth in preterm vs. term infants’, Pediatric Research. 29.05.2024, 96(5), pp. 1299–1305. Available at: https://doi.org/10.1038/s41390-024-03273-6.

Saemann, Attill et al. (2024) ‘Assessment of Interrater Reliability and Accuracy of Cerebral Aneurysm Morphometry Using 3D Virtual Reality, 2D Digital Subtraction Angiography, and 3D Reconstruction: A Randomized Comparative Study’, Brain Sciences. 26.09.2024, 14(10). Available at: https://doi.org/10.3390/brainsci14100968.

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.

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) . 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. 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 Science and Business Media Deutschland GmbH (Lecture Notes in Computer Science), pp. 135–145. Available at: https://doi.org/10.1007/978-3-031-72120-5_13.

Zeng, J. (2024) Therapeutic monitoring in a pediatric clinical setting via breath analysis by high resolution mass spectrometry. Doctoral Thesis.

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, Arsham 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.

Adisa, Adewale et al. (2023) ‘Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries’, British Journal of Surgery, 110(7), pp. 804–817. Available at: https://doi.org/10.1093/bjs/znad092.

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, Yakub 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.

Cédric Schicklin, Manuela Eugster and Georg Rauter (2023) ‘Kinematic analysis of a parallel mechanism for automated imaging of an Organ-on-a-Chip culture system’, in Neunte IFToMM D-A-CH Konferenz 2023. Basel (Neunte IFToMM D-A-CH Konferenz 2023). Available at: https://doi.org/10.17185/DUEPUBLICO/77403.

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.

Enodien B et al. (2023) ‘Gastrointestinal Stromal Tumor (GIST): A Remarkable Case Report and Literature Review.’, 15(3). Available at: https://doi.org/10.7759/cureus.35931.

Tsagkas C et al. (2023) ‘Longitudinal assessment of cervical spinal cord compartments in multiple sclerosis’, Multiple Sclerosis and Related Disorders, 71, p. 104545. Available at: https://doi.org/10.1016/j.msard.2023.104545.