MedShapeNet - a large-scale dataset of 3D medical shapes for computer vision

Jianning Li^{1

2

3}, Zongwei Zhou⁴, Jiancheng Yang⁵, Antonio Pepe^{2

3}, Christina Gsaxner^{2

3

6}, Gijs Luijten^{1

2

3

7}, Chongyu Qu⁴, Tiezheng Zhang⁴, Xiaoxi Chen⁸, Wenxuan Li⁴, Marek Wodzinski^{9

10}, Paul Friedrich¹¹, Kangxian Xie¹², Yuan Jin^{2

3

13}, Narmada Ambigapathy¹, Enrico Nasca¹, Naida Solak^{2

3}, Gian Marco Melito¹⁴, Viet Duc Vu¹⁵, Afaque R Memon^{16

17}, Christopher Schlachta¹⁸, Sandrine De Ribaupierre¹⁸, Rajnikant Patel¹⁸, Roy Eagleson¹⁸, Xiaojun Chen^{19

17}, Heinrich Mächler²⁰, Jan Stefan Kirschke²¹, Ezequiel de la Rosa^{22

23}, Patrick Ferdinand Christ²⁴, Hongwei Bran Li²⁴, David G Ellis²⁵, Michele R Aizenberg²⁵, Sergios Gatidis²⁶, Thomas Küstner²⁶, Nadya Shusharina²⁷, Nicholas Heller²⁸, Vincent Andrearczyk²⁹, Adrien Depeursinge^{29

30}, Mathieu Hatt³¹, Anjany Sekuboyina²³, Maximilian T Löffler³², Hans Liebl³², Reuben Dorent^{33

34}, Tom Vercauteren³³, Jonathan Shapey³³, Aaron Kujawa³³, Stefan Cornelissen^{35

36}, Patrick Langenhuizen^{35

36}, Achraf Ben-Hamadou^{37

38}, Ahmed Rekik^{37

38}, Sergi Pujades³⁹, Edmond Boyer³⁹, Federico Bolelli⁴⁰, Costantino Grana⁴⁰, Luca Lumetti⁴⁰, Hamidreza Salehi⁴¹, Jun Ma^{42

43

44}, Yao Zhang⁴⁵, Ramtin Gharleghi⁴⁶, Susann Beier⁴⁶, Arcot Sowmya⁴⁷, Eduardo A Garza-Villarreal⁴⁸, Thania Balducci⁴⁸, Diego Angeles-Valdez^{48

49}, Roberto Souza⁵⁰, Leticia Rittner⁵¹, Richard Frayne^{52

53}, Yuanfeng Ji⁵⁴, Vincenzo Ferrari^{55

56}, Soumick Chatterjee^{57

58}, Florian Dubost⁵⁹, Stefanie Schreiber^{60

61

62}, Hendrik Mattern^{60

61

63}, Oliver Speck^{60

61

63}, Daniel Haehn⁶⁴, Christoph John⁶⁵, Andreas Nürnberger^{61

57}, João Pedrosa^{66

67}, Carlos Ferreira^{66

67}, Guilherme Aresta⁶⁸, António Cunha^{66

69}, Aurélio Campilho^{66

67}, Yannick Suter⁷⁰, Jose Garcia⁷¹, Alain Lalande^{72

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 Gunzer^{80

81}, Jianxu Chen⁸⁰, Timo van Meegdenburg^{1

82}, Amin Dada¹, Miriam Balzer¹, Jana Fragemann¹, Frederic Jonske¹, Moritz Rempe¹, Stanislav Malorodov¹, Fin H Bahnsen¹, Constantin Seibold¹, Alexander Jaus⁸³, Zdravko Marinov⁸³, Paul F Jaeger^{84

85}, Rainer Stiefelhagen⁸³, Ana Sofia Santos^{1

86}, Mariana Lindo^{1

86}, André Ferreira^{1

86}, Victor Alves⁸⁶, Michael Kamp^{1

87

88

89}, Amr Abourayya^{1

88}, Felix Nensa^{1

90}, Fabian Hörst^{1

87}, Alexander Brehmer¹, Lukas Heine^{1

87}, Yannik Hanusrichter^{91

92}, Martin Weßling^{91

92}, Marcel Dudda^{93

94}, Lars E Podleska⁹⁵, Matthias A Fink⁹⁶, Julius Keyl¹, Konstantinos Tserpes⁹⁷, Moon-Sung Kim^{1

90

87}, Shireen Elhabian⁹⁸, Hans Lamecker⁹⁹, Dženan Zukić¹⁰⁰, Beatriz Paniagua¹⁰⁰, Christian Wachinger¹⁰¹, Martin Urschler¹⁰², Luc Duong¹⁰³, Jakob Wasserthal¹⁰⁴, Peter F Hoyer¹⁰⁵, Oliver Basu^{106

7}, Thomas Maal¹⁰⁷, Max J H Witjes¹⁰⁸, Gregor Schiele¹⁰⁹, Ti-Chiun Chang¹¹⁰, Seyed-Ahmad Ahmadi¹¹¹, Ping Luo⁵⁴, Bjoern Menze²⁴, Mauricio Reyes^{70

112}, Thomas M Deserno¹¹³, Christos Davatzikos¹¹⁴, Behrus Puladi^{6

78}, Pascal Fua⁵, Alan L Yuille⁴, Jens Kleesiek^{1

115

116

87}, Jan Egger^{1

2

3

87

7}

Affiliations

¹ Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen (AöR), Essen, Germany.
² Institute of Computer Graphics and Vision (ICG), Graz University of Technology, Graz, Austria.
³ Computer Algorithms for Medicine Laboratory (Cafe), Graz, Austria.
⁴ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁵ Computer Vision Laboratory, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
⁶ Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Aachen, Germany.
⁷ Center for Virtual and Extended Reality in Medicine (ZvRM), University Hospital Essen, University Medicine Essen, Essen, Germany.
⁸ Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
⁹ Department of Measurement and Electronics, AGH University of Science and Technology, Krakow, Poland.
¹⁰ Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO Valais), Sierre, Switzerland.
¹¹ Center for Medical Image Analysis & Navigation (CIAN), Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.
¹² Department of Computer Science and Engineering, University at Buffalo, SUNY, NY, 14260, USA.
¹³ Research Center for Connected Healthcare Big Data, ZhejiangLab, Hangzhou, Zhejiang, China.
¹⁴ Institute of Mechanics, Graz University of Technology, Graz, Austria.
¹⁵ Department of Diagnostic and Interventional Radiology, University Hospital Giessen, Justus-Liebig-University Giessen, Giessen, Germany.
¹⁶ Department of Mechanical Engineering, Mehran University of Engineering and Technology, Jamshoro, Sindh, Pakistan.
¹⁷ Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
¹⁸ Canadian Surgical Technologies & Advanced Robotics (CSTAR), University Hospital, London, Canada.
¹⁹ State 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.
²⁰ Department of Cardiac Surgery, Medical University Graz, Graz, Austria.
²¹ Geschäftsführender Oberarzt Abteilung für Interventionelle und Diagnostische Neuroradiologie, Universitätsklinikum der Technischen Universität München, München, Germany.
²² icometrix, Leuven, Belgium.
²³ Department of Informatics, Technical University of Munich, Garching bei München, Germany.
²⁴ Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
²⁵ Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, USA.
²⁶ University Hospital of Tuebingen Diagnostic and Interventional Radiology Medical Image and Data Analysis (MIDAS.lab), Tuebingen, Germany.
²⁷ Division of Radiation Biophysics, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
²⁸ University of Minnesota, Minneapolis, MN, USA.
²⁹ Institute of Informatics, HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland, Sierre, Switzerland.
³⁰ Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Lausanne, Switzerland.
³¹ LaTIM, INSERM UMR 1101, Univ Brest, Brest, France.
³² Department of Neuroradiology, Klinikum Rechts der Isar, Munich, Germany.
³³ King's College London, Strand, London, UK.
³⁴ Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
³⁵ Elisabeth-TweeSteden Hospital, Tilburg, Netherlands.
³⁶ Video Coding & Architectures Research Group, Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands.
³⁷ Centre de Recherche en Numérique de Sfax, Laboratory of Signals, Systems, Artificial Intelligence and Networks, Sfax, Tunisia.
³⁸ Udini, Aix-en-Provence, France.
³⁹ Inria, Université Grenoble Alpes, CNRS, Grenoble, France.
⁴⁰ "Enzo Ferrari" Department of Engineering, University of Modena and Reggio Emilia, Modena, Italy.
⁴¹ Department of Artificial Intelligence in Medical Sciences, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
⁴² Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
⁴³ Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada.
⁴⁴ Vector Institute, Toronto, ON, Canada.
⁴⁵ Shanghai AI Laboratory, Shanghai, People's Republic of China.
⁴⁶ School of Mechanical and Manufacturing Engineering, UNSW, Sydney, NSW, Australia.
⁴⁷ School of Computer Science and Engineering, UNSW, Sydney, NSW, Australia.
⁴⁸ Institute of Neurobiology, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro, Mexico.
⁴⁹ Department of Biomedical Sciences of Cells and Systems, Cognitive Neuroscience Center, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.
⁵⁰ Advanced Imaging and Artificial Intelligence Lab, Electrical and Software Engineering Department, The Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
⁵¹ Medical Image Computing Lab, School of Electrical and Computer Engineering (FEEC), University of Campinas, Campinas, Brazil.
⁵² Radiology and Clinical Neurosciences Departments, The Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
⁵³ Seaman Family MR Research Centre, Foothills Medical Center, Calgary, Canada.
⁵⁴ University of Hongkong, Pok Fu Lam, Hong Kong, People's Republic of China.
⁵⁵ Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy.
⁵⁶ EndoCAS Center, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy.
⁵⁷ Data and Knowledge Engineering Group, Faculty of Computer Science, Otto von Guericke University Magdeburg, Magdeburg, Germany.
⁵⁸ Genomics Research Centre, Human Technopole, Milan, Italy.
⁵⁹ Stanford University, Stanford, CA, USA.
⁶⁰ German Centre for Neurodegenerative Disease, Magdeburg, Germany.
⁶¹ Centre for Behavioural Brain Sciences, Magdeburg, Germany.
⁶² Department of Neurology, Medical Faculty, University Hospital of Magdeburg, Magdeburg, Germany.
⁶³ Department of Biomedical Magnetic Resonance, Otto von Guericke University Magdeburg, Magdeburg, Germany.
⁶⁴ University of Massachusetts Boston, Boston, MA, USA.
⁶⁵ Ecubed Solutions, Bensheim, Germany.
⁶⁶ Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal.
⁶⁷ Faculty of Engineering, University of Porto (FEUP), Porto, Portugal.
⁶⁸ Christian Doppler Lab for Artificial Intelligence in Retina, Department of Ophthalmology and Optometry, Medical University of Vienna, Vienna, Austria.
⁶⁹ Universidade of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
⁷⁰ ARTORG Center for Biomedical Engineering Research, University of Bern, Bern, Switzerland.
⁷¹ Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
⁷² ICMUB Laboratory, Faculty of Medicine, CNRS UMR 6302, University of Burgundy, Dijon, France.
⁷³ Medical Imaging Department, University Hospital of Dijon, Dijon, France.
⁷⁴ Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
⁷⁵ Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel, Brussels, Belgium.
⁷⁶ Department of Cellular and Physiological Sciences, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada.
⁷⁷ Department of Development & Regeneration, KU Leuven Campus Kulak, Kortrijk, Belgium.
⁷⁸ Institute of Medical Informatics, University Hospital RWTH Aachen, Aachen, Germany.
⁷⁹ Institute of Fundamentals and Theory in Electrical Engineering, Graz University of Technology, Graz, Austria.
⁸⁰ Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
⁸¹ Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany.
⁸² Faculty of Statistics, Technical University Dortmund, Dortmund, Germany.
⁸³ Computer Vision for Human-Computer Interaction Lab, Department of Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.
⁸⁴ German Cancer Research Center (DKFZ) Heidelberg, Interactive Machine Learning Group, Heidelberg, Germany.
⁸⁵ Helmholtz Imaging, DKFZ Heidelberg, Heidelberg, Germany.
⁸⁶ Center Algoritmi, LASI, University of Minho, Braga, Portugal.
⁸⁷ Cancer Research Center Cologne Essen (CCCE), University Medicine Essen (AöR), Essen, Germany.
⁸⁸ Institute for Neuroinformatics, Ruhr University Bochum, Bochum, Germany.
⁸⁹ Department of Data Science & AI, Monash University, Clayton, VIC, Australia.
⁹⁰ Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen (AöR), Essen, Germany.
⁹¹ Department of Tumour Orthopaedics and Revision Arthroplasty, Orthopaedic Hospital Volmarstein, Wetter, Germany.
⁹² Center for Musculoskeletal Surgery, University Hospital of Essen, Essen, Germany.
⁹³ Department of Trauma, Hand and Reconstructive Surgery, University Hospital Essen, Essen, Germany.
⁹⁴ Department of Orthopaedics and Trauma Surgery, BG-Klinikum Duisburg, University of Duisburg-Essen, Essen , Germany.
⁹⁵ Department of Tumor Orthopedics and Sarcoma Surgery, University Hospital Essen (AöR), Essen, Germany.
⁹⁶ Clinic for Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany.
⁹⁷ Department of Informatics and Telematics, Harokopio University of Athens, Tavros, Greece.
⁹⁸ Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, USA.
⁹⁹ Stryker Berlin GmbH, Germany.
¹⁰⁰ Medical Computing, Kitware Inc., Carrboro, NC, USA.
¹⁰¹ Lab for Artificial Intelligence in Medical Imaging, Department of Radiology, Technical University Munich, Munich, Germany.
¹⁰² Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Graz, Austria.
¹⁰³ Department of Software and IT Engineering, Ecole de Technologie Superieure, Montreal, Quebec, Canada.
¹⁰⁴ Clinic of Radiology & Nuclear Medicine, University Hospital Basel, Basel, Switzerland.
¹⁰⁵ Pediatric Clinic II, University Children's Hospital Essen, University Duisburg-Essen, Essen, Germany.
¹⁰⁶ Pediatric Clinic III, University Children's Hospital Essen, University Duisburg-Essen, Essen, Germany.
¹⁰⁷ Radboudumc 3D-Lab , Department of Oral and Maxillofacial Surgery , Radboud University Nijmegen Medical Centre, Nijmegen , The Netherlands.
¹⁰⁸ 3D Lab, Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, Groningen, the Netherlands.
¹⁰⁹ Intelligent Embedded Systems Lab, University of Duisburg-Essen, Bismarckstraße 90, 47057 Duisburg, Germany.
¹¹⁰ MRL, Merck & Co., Inc., Rahway, NJ 07065, USA.
¹¹¹ NVIDIA GmbH, Bavaria Towers - Blue Tower, Munich, Germany.
¹¹² Department of Radiation Oncology, University Hospital Bern, University of Bern, Bern, Switzerland.
¹¹³ Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany.
¹¹⁴ Center 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.
¹¹⁵ German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany.
¹¹⁶ Department of Physics, TU Dortmund University, Dortmund, Germany.

PMID: 39733351
DOI: 10.1515/bmt-2024-0396

Free article

MedShapeNet - a large-scale dataset of 3D medical shapes for computer vision

Jianning Li et al. Biomed Tech (Berl). 2024.

Free article

. 2024 Dec 30;70(1):71-90.

doi: 10.1515/bmt-2024-0396. Print 2025 Feb 25.

Authors

Affiliations

¹ Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen (AöR), Essen, Germany.
² Institute of Computer Graphics and Vision (ICG), Graz University of Technology, Graz, Austria.
³ Computer Algorithms for Medicine Laboratory (Cafe), Graz, Austria.
⁴ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁵ Computer Vision Laboratory, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
⁶ Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Aachen, Germany.
⁷ Center for Virtual and Extended Reality in Medicine (ZvRM), University Hospital Essen, University Medicine Essen, Essen, Germany.
⁸ Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
⁹ Department of Measurement and Electronics, AGH University of Science and Technology, Krakow, Poland.
¹⁰ Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO Valais), Sierre, Switzerland.
¹¹ Center for Medical Image Analysis & Navigation (CIAN), Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.
¹² Department of Computer Science and Engineering, University at Buffalo, SUNY, NY, 14260, USA.
¹³ Research Center for Connected Healthcare Big Data, ZhejiangLab, Hangzhou, Zhejiang, China.
¹⁴ Institute of Mechanics, Graz University of Technology, Graz, Austria.
¹⁵ Department of Diagnostic and Interventional Radiology, University Hospital Giessen, Justus-Liebig-University Giessen, Giessen, Germany.
¹⁶ Department of Mechanical Engineering, Mehran University of Engineering and Technology, Jamshoro, Sindh, Pakistan.
¹⁷ Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
¹⁸ Canadian Surgical Technologies & Advanced Robotics (CSTAR), University Hospital, London, Canada.
¹⁹ State 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.
²⁰ Department of Cardiac Surgery, Medical University Graz, Graz, Austria.
²¹ Geschäftsführender Oberarzt Abteilung für Interventionelle und Diagnostische Neuroradiologie, Universitätsklinikum der Technischen Universität München, München, Germany.
²² icometrix, Leuven, Belgium.
²³ Department of Informatics, Technical University of Munich, Garching bei München, Germany.
²⁴ Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
²⁵ Department of Neurosurgery, University of Nebraska Medical Center, Omaha, NE, USA.
²⁶ University Hospital of Tuebingen Diagnostic and Interventional Radiology Medical Image and Data Analysis (MIDAS.lab), Tuebingen, Germany.
²⁷ Division of Radiation Biophysics, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
²⁸ University of Minnesota, Minneapolis, MN, USA.
²⁹ Institute of Informatics, HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland, Sierre, Switzerland.
³⁰ Department of Nuclear Medicine and Molecular Imaging, Lausanne University Hospital (CHUV), Lausanne, Switzerland.
³¹ LaTIM, INSERM UMR 1101, Univ Brest, Brest, France.
³² Department of Neuroradiology, Klinikum Rechts der Isar, Munich, Germany.
³³ King's College London, Strand, London, UK.
³⁴ Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
³⁵ Elisabeth-TweeSteden Hospital, Tilburg, Netherlands.
³⁶ Video Coding & Architectures Research Group, Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands.
³⁷ Centre de Recherche en Numérique de Sfax, Laboratory of Signals, Systems, Artificial Intelligence and Networks, Sfax, Tunisia.
³⁸ Udini, Aix-en-Provence, France.
³⁹ Inria, Université Grenoble Alpes, CNRS, Grenoble, France.
⁴⁰ "Enzo Ferrari" Department of Engineering, University of Modena and Reggio Emilia, Modena, Italy.
⁴¹ Department of Artificial Intelligence in Medical Sciences, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
⁴² Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
⁴³ Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada.
⁴⁴ Vector Institute, Toronto, ON, Canada.
⁴⁵ Shanghai AI Laboratory, Shanghai, People's Republic of China.
⁴⁶ School of Mechanical and Manufacturing Engineering, UNSW, Sydney, NSW, Australia.
⁴⁷ School of Computer Science and Engineering, UNSW, Sydney, NSW, Australia.
⁴⁸ Institute of Neurobiology, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro, Mexico.
⁴⁹ Department of Biomedical Sciences of Cells and Systems, Cognitive Neuroscience Center, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.
⁵⁰ Advanced Imaging and Artificial Intelligence Lab, Electrical and Software Engineering Department, The Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
⁵¹ Medical Image Computing Lab, School of Electrical and Computer Engineering (FEEC), University of Campinas, Campinas, Brazil.
⁵² Radiology and Clinical Neurosciences Departments, The Hotchkiss Brain Institute, University of Calgary, Calgary, Canada.
⁵³ Seaman Family MR Research Centre, Foothills Medical Center, Calgary, Canada.
⁵⁴ University of Hongkong, Pok Fu Lam, Hong Kong, People's Republic of China.
⁵⁵ Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy.
⁵⁶ EndoCAS Center, Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy.
⁵⁷ Data and Knowledge Engineering Group, Faculty of Computer Science, Otto von Guericke University Magdeburg, Magdeburg, Germany.
⁵⁸ Genomics Research Centre, Human Technopole, Milan, Italy.
⁵⁹ Stanford University, Stanford, CA, USA.
⁶⁰ German Centre for Neurodegenerative Disease, Magdeburg, Germany.
⁶¹ Centre for Behavioural Brain Sciences, Magdeburg, Germany.
⁶² Department of Neurology, Medical Faculty, University Hospital of Magdeburg, Magdeburg, Germany.
⁶³ Department of Biomedical Magnetic Resonance, Otto von Guericke University Magdeburg, Magdeburg, Germany.
⁶⁴ University of Massachusetts Boston, Boston, MA, USA.
⁶⁵ Ecubed Solutions, Bensheim, Germany.
⁶⁶ Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal.
⁶⁷ Faculty of Engineering, University of Porto (FEUP), Porto, Portugal.
⁶⁸ Christian Doppler Lab for Artificial Intelligence in Retina, Department of Ophthalmology and Optometry, Medical University of Vienna, Vienna, Austria.
⁶⁹ Universidade of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal.
⁷⁰ ARTORG Center for Biomedical Engineering Research, University of Bern, Bern, Switzerland.
⁷¹ Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
⁷² ICMUB Laboratory, Faculty of Medicine, CNRS UMR 6302, University of Burgundy, Dijon, France.
⁷³ Medical Imaging Department, University Hospital of Dijon, Dijon, France.
⁷⁴ Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
⁷⁵ Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel, Brussels, Belgium.
⁷⁶ Department of Cellular and Physiological Sciences, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada.
⁷⁷ Department of Development & Regeneration, KU Leuven Campus Kulak, Kortrijk, Belgium.
⁷⁸ Institute of Medical Informatics, University Hospital RWTH Aachen, Aachen, Germany.
⁷⁹ Institute of Fundamentals and Theory in Electrical Engineering, Graz University of Technology, Graz, Austria.
⁸⁰ Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.
⁸¹ Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, Germany.
⁸² Faculty of Statistics, Technical University Dortmund, Dortmund, Germany.
⁸³ Computer Vision for Human-Computer Interaction Lab, Department of Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.
⁸⁴ German Cancer Research Center (DKFZ) Heidelberg, Interactive Machine Learning Group, Heidelberg, Germany.
⁸⁵ Helmholtz Imaging, DKFZ Heidelberg, Heidelberg, Germany.
⁸⁶ Center Algoritmi, LASI, University of Minho, Braga, Portugal.
⁸⁷ Cancer Research Center Cologne Essen (CCCE), University Medicine Essen (AöR), Essen, Germany.
⁸⁸ Institute for Neuroinformatics, Ruhr University Bochum, Bochum, Germany.
⁸⁹ Department of Data Science & AI, Monash University, Clayton, VIC, Australia.
⁹⁰ Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen (AöR), Essen, Germany.
⁹¹ Department of Tumour Orthopaedics and Revision Arthroplasty, Orthopaedic Hospital Volmarstein, Wetter, Germany.
⁹² Center for Musculoskeletal Surgery, University Hospital of Essen, Essen, Germany.
⁹³ Department of Trauma, Hand and Reconstructive Surgery, University Hospital Essen, Essen, Germany.
⁹⁴ Department of Orthopaedics and Trauma Surgery, BG-Klinikum Duisburg, University of Duisburg-Essen, Essen , Germany.
⁹⁵ Department of Tumor Orthopedics and Sarcoma Surgery, University Hospital Essen (AöR), Essen, Germany.
⁹⁶ Clinic for Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany.
⁹⁷ Department of Informatics and Telematics, Harokopio University of Athens, Tavros, Greece.
⁹⁸ Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, USA.
⁹⁹ Stryker Berlin GmbH, Germany.
¹⁰⁰ Medical Computing, Kitware Inc., Carrboro, NC, USA.
¹⁰¹ Lab for Artificial Intelligence in Medical Imaging, Department of Radiology, Technical University Munich, Munich, Germany.
¹⁰² Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Graz, Austria.
¹⁰³ Department of Software and IT Engineering, Ecole de Technologie Superieure, Montreal, Quebec, Canada.
¹⁰⁴ Clinic of Radiology & Nuclear Medicine, University Hospital Basel, Basel, Switzerland.
¹⁰⁵ Pediatric Clinic II, University Children's Hospital Essen, University Duisburg-Essen, Essen, Germany.
¹⁰⁶ Pediatric Clinic III, University Children's Hospital Essen, University Duisburg-Essen, Essen, Germany.
¹⁰⁷ Radboudumc 3D-Lab , Department of Oral and Maxillofacial Surgery , Radboud University Nijmegen Medical Centre, Nijmegen , The Netherlands.
¹⁰⁸ 3D Lab, Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, Groningen, the Netherlands.
¹⁰⁹ Intelligent Embedded Systems Lab, University of Duisburg-Essen, Bismarckstraße 90, 47057 Duisburg, Germany.
¹¹⁰ MRL, Merck & Co., Inc., Rahway, NJ 07065, USA.
¹¹¹ NVIDIA GmbH, Bavaria Towers - Blue Tower, Munich, Germany.
¹¹² Department of Radiation Oncology, University Hospital Bern, University of Bern, Bern, Switzerland.
¹¹³ Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany.
¹¹⁴ Center 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.
¹¹⁵ German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany.
¹¹⁶ Department of Physics, TU Dortmund University, Dortmund, Germany.

PMID: 39733351
DOI: 10.1515/bmt-2024-0396

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 (e.g., bones, organs, vessels) and 3D models of surgical instruments is missing.

Methods: We present MedShapeNet to translate data-driven vision algorithms to medical applications and to adapt state-of-the-art vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. We present use cases in classifying brain tumors, skull reconstructions, multi-class anatomy completion, education, and 3D printing.

Results: By now, MedShapeNet includes 23 datasets with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing.

Conclusions: MedShapeNet contains medical shapes from anatomy and surgical instruments and will continue to collect data for benchmarks and applications. The project page is: https://medshapenet.ikim.nrw/.

Keywords: 3D medical shapes; anatomy education; augmented reality; benchmark; shapeomics; virtual reality.

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References

1. Esteva, A, Chou, K, Yeung, S, Naik, N, Madani, A, Mottaghi, A, et al.. Deep learning-enabled medical computer vision. npk Digital Med 2021;4:1–9. https://doi.org/10.1038/s41746-020-00376-2 . - DOI
1. Young, T, Hazarika, D, Poria, S, Cambria, E. Recent trends in deep learning based natural language processing. IEEE Comput Intell Mag 2018;13:55–75. https://doi.org/10.1109/mci.2018.2840738 . - DOI
1. Latif, S, Rana, R, Khalifa, S, Jurdak, R, Qadir, J, Schuller, BW. Deep representation learning in speech processing: challenges, recent advances, and future trends. arXiv preprint arXiv:2001.00378. 2020.
1. Sun, C, Shrivastava, A, Singh, S, Gupta, A. Revisiting unreasonable effectiveness of data in deep learning era. In: Proceedings of the IEEE international conference on computer vision ; 2017:843–52 pp.
1. Egger, J, Gsaxner, C, Pepe, A, Pomykala, KL, Jonske, F, Kurz, M, et al.. Medical deep learning—a systematic meta-review. Comput Methods Progr Biomed 2022;221:106874. https://doi.org/10.1016/j.cmpb.2022.106874 . - DOI

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MedShapeNet - a large-scale dataset of 3D medical shapes for computer vision

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MedShapeNet - a large-scale dataset of 3D medical shapes for computer vision

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Abstract

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MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Research Materials