Peer-Reviewed Publication
Biomed Tech (Berl)2025;70(1):71-90.February 25, 2025Journal Article
MedShapeNet - a large-scale dataset of 3D medical shapes for computer vision.
Jianning Li1,2,3, Zongwei Zhou4, Jiancheng Yang5, Antonio Pepe2,3, Christina Gsaxner2,3,6, Gijs Luijten1,2,3,7, Chongyu Qu4, Tiezheng Zhang4, Xiaoxi Chen8, Wenxuan Li4, Marek Wodzinski9,10, Paul Friedrich11, Kangxian Xie12, Yuan Jin2,3,13, Narmada Ambigapathy1, Enrico Nasca1, Naida Solak2,3, Gian Marco Melito14, Viet Duc Vu15, Afaque R Memon16,17, Christopher Schlachta18, Sandrine De Ribaupierre18, Rajnikant Patel18, Roy Eagleson18, Xiaojun Chen19,17, Heinrich Mächler20, Jan Stefan Kirschke21, Ezequiel de la Rosa22,23, Patrick Ferdinand Christ24, Hongwei Bran Li24, David G Ellis25, Michele R Aizenberg25, Sergios Gatidis26, Thomas Küstner26, Nadya Shusharina27, Nicholas Heller28, Vincent Andrearczyk29, Adrien Depeursinge29,30, Mathieu Hatt31, Anjany Sekuboyina23, Maximilian T Löffler32, Hans Liebl32, Reuben Dorent33,34, Tom Vercauteren33, Jonathan Shapey33, Aaron Kujawa33, Stefan Cornelissen35,36, Patrick Langenhuizen35,36, Achraf Ben-Hamadou37,38, Ahmed Rekik37,38, Sergi Pujades39, Edmond Boyer39, Federico Bolelli40, Costantino Grana40, Luca Lumetti40, Hamidreza Salehi41, Jun Ma42,43,44, Yao Zhang45, Ramtin Gharleghi46, Susann Beier46, Arcot Sowmya47, Eduardo A Garza-Villarreal48, Thania Balducci48, Diego Angeles-Valdez48,49, Roberto Souza50, Leticia Rittner51, Richard Frayne52,53, Yuanfeng Ji54, Vincenzo Ferrari55,56, Soumick Chatterjee57,58, Florian Dubost59, Stefanie Schreiber60,61,62, Hendrik Mattern60,61,63, Oliver Speck60,61,63, Daniel Haehn64, Christoph John65, Andreas Nürnberger61,57, João Pedrosa66,67, Carlos Ferreira66,67, Guilherme Aresta68, António Cunha66,69, Aurélio Campilho66,67, Yannick Suter70, Jose Garcia71, Alain Lalande72,73, Vicky Vandenbossche74, Aline Van Oevelen74, Kate Duquesne74, Hamza Mekhzoum75, Jef Vandemeulebroucke75, Emmanuel Audenaert74, Claudia Krebs76, Timo van Leeuwen77, Evie Vereecke77, Hauke Heidemeyer78, Rainer Röhrig78, Frank Hölzle6, Vahid Badeli79, Kathrin Krieger80, Matthias Gunzer80,81, Jianxu Chen80, Timo van Meegdenburg1,82, Amin Dada1, Miriam Balzer1, Jana Fragemann1, Frederic Jonske1, Moritz Rempe1, Stanislav Malorodov1, Fin H Bahnsen1, Constantin Seibold1, Alexander Jaus83, Zdravko Marinov83, Paul F Jaeger84,85, Rainer Stiefelhagen83, Ana Sofia Santos1,86, Mariana Lindo1,86, André Ferreira1,86, Victor Alves86, Michael Kamp1,87,88,89, Amr Abourayya1,88, Felix Nensa1,90, Fabian Hörst1,87, Alexander Brehmer1, Lukas Heine1,87, Yannik Hanusrichter91,92, Martin Weßling91,92, Marcel Dudda93,94, Lars E Podleska95, Matthias A Fink96, Julius Keyl1, Konstantinos Tserpes97, Moon-Sung Kim1,90,87, Shireen Elhabian98, Hans Lamecker99, Dženan Zukić100, Beatriz Paniagua100, Christian Wachinger101, Martin Urschler102, Luc Duong103, Jakob Wasserthal104, Peter F Hoyer105, Oliver Basu106,7, Thomas Maal107, Max J H Witjes108, Gregor Schiele109, Ti-Chiun Chang110, Seyed-Ahmad Ahmadi111, Ping Luo54, Bjoern Menze24, Mauricio Reyes70,112, Thomas M Deserno113, Christos Davatzikos114, Behrus Puladi6,78, Pascal Fua5, Alan L Yuille4, Jens Kleesiek1,115,116,87, Jan Egger1,2,3,87,7
1Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen (AöR), Essen, Germany.
2Institute of Computer Graphics and Vision (ICG), Graz University of Technology, Graz, Austria.
3Computer Algorithms for Medicine Laboratory (Cafe), Graz, Austria.
4Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
5Computer Vision Laboratory, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
6Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Aachen, Germany.
7Center for Virtual and Extended Reality in Medicine (ZvRM), University Hospital Essen, University Medicine Essen, Essen, Germany.
8Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
9Department of Measurement and Electronics, AGH University of Science and Technology, Krakow, Poland.
10Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO Valais), Sierre, Switzerland.
11Center for Medical Image Analysis & Navigation (CIAN), Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.
12Department of Computer Science and Engineering, University at Buffalo, SUNY, NY, 14260, USA.
13Research Center for Connected Healthcare Big Data, ZhejiangLab, Hangzhou, Zhejiang, China.
14Institute of Mechanics, Graz University of Technology, Graz, Austria.
15Department of Diagnostic and Interventional Radiology, University Hospital Giessen, Justus-Liebig-University Giessen, Giessen, Germany.
16Department of Mechanical Engineering, Mehran University of Engineering and Technology, Jamshoro, Sindh, Pakistan.
17Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
18Canadian Surgical Technologies & Advanced Robotics (CSTAR), University Hospital, London, Canada.
19State Key Laboratory of Mechanical System and Vibration, School of Mechanical Engineering, Institute of Biomedical Manufacturing and Life Quality Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
20Department of Cardiac Surgery, Medical University Graz, Graz, Austria.
21Geschäftsführender Oberarzt Abteilung für Interventionelle und Diagnostische Neuroradiologie, Universitätsklinikum der Technischen Universität München, München, Germany.
22icometrix, Leuven, Belgium.
23Department of Informatics, Technical University of Munich, Garching bei München, Germany.
24Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
25Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, USA.
26University Hospital of Tuebingen Diagnostic and Interventional Radiology Medical Image and Data Analysis (MIDAS.lab), Tuebingen, Germany.
27Division of Radiation Biophysics, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
28University of Minnesota, Minneapolis, MN, USA.
29Institute of Informatics, HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland, Sierre, Switzerland.
30Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Lausanne, Switzerland.
31LaTIM, INSERM UMR 1101, Univ Brest, Brest, France.
32Department of Neuroradiology, Klinikum Rechts der Isar, Munich, Germany.
33King's College London, Strand, London, UK.
34Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
35Elisabeth-TweeSteden Hospital, Tilburg, Netherlands.
36Video Coding & Architectures Research Group, Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands.
37Centre de Recherche en Numérique de Sfax, Laboratory of Signals, Systems, Artificial Intelligence and Networks, Sfax, Tunisia.
38Udini, Aix-en-Provence, France.
39Inria, Université Grenoble Alpes, CNRS, Grenoble, France.
40"Enzo Ferrari" Department of Engineering, University of Modena and Reggio Emilia, Modena, Italy.
41Department of Artificial Intelligence in Medical Sciences, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
42Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
43Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada.
44Vector Institute, Toronto, ON, Canada.
45Shanghai AI Laboratory, Shanghai, People's Republic of China.
46School of Mechanical and Manufacturing Engineering, UNSW, Sydney, NSW, Australia.
47School of Computer Science and Engineering, UNSW, Sydney, NSW, Australia.
48Institute of Neurobiology, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro, Mexico.
49Department of Biomedical Sciences of Cells and Systems, Cognitive Neuroscience Center, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.
50Advanced Imaging and Artificial Intelligence Lab, Electrical and Software Engineering Department, The Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
51Medical Image Computing Lab, School of Electrical and Computer Engineering (FEEC), University of Campinas, Campinas, Brazil.
52Radiology and Clinical Neurosciences Departments, The Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
53Seaman Family MR Research Centre, Foothills Medical Center, Calgary, Canada.
54University of Hongkong, Pok Fu Lam, Hong Kong, People's Republic of China.
55Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy.
56EndoCAS Center, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy.
57Data and Knowledge Engineering Group, Faculty of Computer Science, Otto von Guericke University Magdeburg, Magdeburg, Germany.
58Genomics Research Centre, Human Technopole, Milan, Italy.
59Stanford University, Stanford, CA, USA.
60German Centre for Neurodegenerative Disease, Magdeburg, Germany.
61Centre for Behavioural Brain Sciences, Magdeburg, Germany.
62Department of Neurology, Medical Faculty, University Hospital of Magdeburg, Magdeburg, Germany.
63Department of Biomedical Magnetic Resonance, Otto von Guericke University Magdeburg, Magdeburg, Germany.
64University of Massachusetts Boston, Boston, MA, USA.
65Ecubed Solutions, Bensheim, Germany.
66Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal.
67Faculty of Engineering, University of Porto (FEUP), Porto, Portugal.
68Christian Doppler Lab for Artificial Intelligence in Retina, Department of Ophthalmology and Optometry, Medical University of Vienna, Vienna, Austria.
69Universidade of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
70ARTORG Center for Biomedical Engineering Research, University of Bern, Bern, Switzerland.
71Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
72ICMUB Laboratory, Faculty of Medicine, CNRS UMR 6302, University of Burgundy, Dijon, France.
73Medical Imaging Department, University Hospital of Dijon, Dijon, France.
74Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
75Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel, Brussels, Belgium.
76Department of Cellular and Physiological Sciences, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada.
77Department of Development & Regeneration, KU Leuven Campus Kulak, Kortrijk, Belgium.
78Institute of Medical Informatics, University Hospital RWTH Aachen, Aachen, Germany.
79Institute of Fundamentals and Theory in Electrical Engineering, Graz University of Technology, Graz, Austria.
80Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
81Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany.
82Faculty of Statistics, Technical University Dortmund, Dortmund, Germany.
83Computer Vision for Human-Computer Interaction Lab, Department of Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.
84German Cancer Research Center (DKFZ) Heidelberg, Interactive Machine Learning Group, Heidelberg, Germany.
85Helmholtz Imaging, DKFZ Heidelberg, Heidelberg, Germany.
86Center Algoritmi, LASI, University of Minho, Braga, Portugal.
87Cancer Research Center Cologne Essen (CCCE), University Medicine Essen (AöR), Essen, Germany.
88Institute for Neuroinformatics, Ruhr University Bochum, Bochum, Germany.
89Department of Data Science & AI, Monash University, Clayton, VIC, Australia.
90Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen (AöR), Essen, Germany.
91Department of Tumour Orthopaedics and Revision Arthroplasty, Orthopaedic Hospital Volmarstein, Wetter, Germany.
92Center for Musculoskeletal Surgery, University Hospital of Essen, Essen, Germany.
93Department of Trauma, Hand and Reconstructive Surgery, University Hospital Essen, Essen, Germany.
94Department of Orthopaedics and Trauma Surgery, BG-Klinikum Duisburg, University of Duisburg-Essen, Essen , Germany.
95Department of Tumor Orthopedics and Sarcoma Surgery, University Hospital Essen (AöR), Essen, Germany.
96Clinic for Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany.
97Department of Informatics and Telematics, Harokopio University of Athens, Tavros, Greece.
98Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, USA.
99Stryker Berlin GmbH, Germany.
100Medical Computing, Kitware Inc., Carrboro, NC, USA.
101Lab for Artificial Intelligence in Medical Imaging, Department of Radiology, Technical University Munich, Munich, Germany.
102Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Graz, Austria.
103Department of Software and IT Engineering, Ecole de Technologie Superieure, Montreal, Quebec, Canada.
104Clinic of Radiology & Nuclear Medicine, University Hospital Basel, Basel, Switzerland.
105Pediatric Clinic II, University Children's Hospital Essen, University Duisburg-Essen, Essen, Germany.
106Pediatric Clinic III, University Children's Hospital Essen, University Duisburg-Essen, Essen, Germany.
107Radboudumc 3D-Lab , Department of Oral and Maxillofacial Surgery , Radboud University Nijmegen Medical Centre, Nijmegen , The Netherlands.
1083D Lab, Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, Groningen, the Netherlands.
109Intelligent Embedded Systems Lab, University of Duisburg-Essen, Bismarckstraße 90, 47057 Duisburg, Germany.
110MRL, Merck & Co., Inc., Rahway, NJ 07065, USA.
111NVIDIA GmbH, Bavaria Towers - Blue Tower, Munich, Germany.
112Department of Radiation Oncology, University Hospital Bern, University of Bern, Bern, Switzerland.
113Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany.
114Center for Biomedical Image Computing and Analytics , Penn Neurodegeneration Genomics Center , University of Pennsylvania, Philadelphia , PA , USA ; and Center for AI and Data Science for Integrated Diagnostics, University of Pennsylvania, Philadelphia, PA, USA.
115German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany.
116Department of Physics, TU Dortmund University, Dortmund, Germany.
Abstract
OBJECTIVES: The shape is commonly used to describe the objects. State-of-the-art algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from the growing popularity of ShapeNet (51,300 models) and Princeton ModelNet (127,915 models). However, a large collection of anatomical shapes (…
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