Publication Details
Overview
 
 
Jianning Li, Jianning Li, Zongwei Zhou, Zongwei Zhou, Jiancheng Yang, Jiancheng Yang, Antonio Pepe, Antonio Pepe, Christina Gsaxner, Christina Gsaxner, Gijs Luijten, Gijs Luijten, Chongyu Qu, Chongyu Qu, Tiezheng Zhang, Tiezheng Zhang, Xiaoxi Chen, Xiaoxi Chen, Wenxuan Li, Wenxuan Li, Marek Wodzinski, Marek Wodzinski, Paul Friedrich, Paul Friedrich, Kangxian Xie, Kangxian Xie, Yuan Jin, Yuan Jin, Narmada Ambigapathy, Narmada Ambigapathy, Enrico Nasca, Enrico Nasca, Naida Solak, Naida Solak, Gian Marco Melito, Gian Marco Melito, Viet Duc Vu, Viet Duc Vu, Afaque R. Memon, Afaque R. Memon, Christopher Schlachta, Christopher Schlachta, Sandrine De Ribaupierre, Sandrine De Ribaupierre, Rajnikant Patel, Rajnikant Patel, Roy Eagleson, Roy Eagleson, Xiaojun Chen, Xiaojun Chen, Heinrich Mächler, Heinrich Mächler, Jan Stefan Kirschke, Jan Stefan Kirschke, Ezequiel de la Rosa, Ezequiel de la Rosa, Patrick Ferdinand Christ, Patrick Ferdinand Christ, Hongwei Bran Li, Hongwei Bran Li, David G. Ellis, David G. Ellis, Michele R. Aizenberg, Michele R. Aizenberg, Sergios Gatidis, Sergios Gatidis, Thomas Küstner, Thomas Küstner, Nadya Shusharina, Nadya Shusharina, Nicholas Heller, Nicholas Heller, Vincent Andrearczyk, Vincent Andrearczyk, Adrien Depeursinge, Adrien Depeursinge, Mathieu Hatt, Mathieu Hatt, Anjany Sekuboyina, Anjany Sekuboyina, Maximilian T. Löffler, Maximilian T. Löffler, Hans Liebl, Hans Liebl, Reuben Dorent, Reuben Dorent, Tom Vercauteren, Tom Vercauteren, Jonathan Shapey, Jonathan Shapey, Aaron Kujawa, Aaron Kujawa, Stefan Cornelissen, Stefan Cornelissen, Patrick Langenhuizen, Patrick Langenhuizen, Achraf Ben-Hamadou, Achraf Ben-Hamadou, Ahmed Rekik, Ahmed Rekik, Sergi Pujades, Sergi Pujades, Edmond Boyer, Edmond Boyer, Federico Bolelli, Federico Bolelli, Costantino Grana, Costantino Grana, Luca Lumetti, Luca Lumetti, Hamidreza Salehi, Hamidreza Salehi, Jun Ma, Jun Ma, Yao Zhang, Yao Zhang, Ramtin Gharleghi, Ramtin Gharleghi, Susann Beier, Susann Beier, Arcot Sowmya, Arcot Sowmya, Eduardo A. Garza-Villarreal, Eduardo A. Garza-Villarreal, Thania Balducci, Thania Balducci, Diego Angeles-Valdez, Diego Angeles-Valdez, Roberto Souza, Roberto Souza, Leticia Rittner, Leticia Rittner, Richard Frayne, Richard Frayne, Yuanfeng Ji, Yuanfeng Ji, Vincenzo Ferrari, Vincenzo Ferrari, Soumick Chatterjee, Soumick Chatterjee, Florian Dubost, Florian Dubost, Stefanie Schreiber, Stefanie Schreiber, Hendrik Mattern, Hendrik Mattern, Oliver Speck, Oliver Speck, Daniel Haehn, Daniel Haehn, Christoph John, Christoph John, Andreas Nürnberger, Andreas Nürnberger, João Pedrosa, João Pedrosa, Carlos Ferreira, Carlos Ferreira, Guilherme Aresta, Guilherme Aresta, António Cunha, António Cunha, Aurélio Campilho, Aurélio Campilho, Yannick Suter, Yannick Suter, Jose Garcia, Jose Garcia, Alain Lalande, Alain Lalande, Vicky Vandenbossche, Vicky Vandenbossche, Aline Van Oevelen, Aline Van Oevelen, Kate Duquesne, Kate Duquesne, Hamza Mekhzoum, Hamza Mekhzoum, Jef Vandemeulebroucke, Jef Vandemeulebroucke, Emmanuel Audenaert, Emmanuel Audenaert, Claudia Krebs, Claudia Krebs, Timo van Leeuwen, Timo van Leeuwen, Evie Vereecke, Evie Vereecke, Hauke Heidemeyer, Hauke Heidemeyer, Rainer Röhrig, Rainer Röhrig, Frank Hölzle, Frank Hölzle, Vahid Badeli, Vahid Badeli, Kathrin Krieger, Kathrin Krieger, Matthias Gunzer, Matthias Gunzer, Jianxu Chen, Jianxu Chen, Timo van Meegdenburg, Timo van Meegdenburg, Amin Dada, Amin Dada, Miriam Balzer, Miriam Balzer, Jana Fragemann, Jana Fragemann, Frederic Jonske, Frederic Jonske, Moritz Rempe, Moritz Rempe, Stanislav Malorodov, Stanislav Malorodov, Fin H. Bahnsen, Fin H. Bahnsen, Constantin Seibold, Constantin Seibold, Alexander Jaus, Alexander Jaus, Zdravko Marinov, Zdravko Marinov, Paul F. Jaeger, Paul F. Jaeger, Rainer Stiefelhagen, Rainer Stiefelhagen, Ana Sofia Santos, Ana Sofia Santos, Mariana Lindo, Mariana Lindo, André Ferreira, André Ferreira, Victor Alves, Victor Alves, Michael Kamp, Michael Kamp, Amr Abourayya, Amr Abourayya, Felix Nensa, Felix Nensa, Fabian Hörst, Fabian Hörst, Alexander Brehmer, Alexander Brehmer, Lukas Heine, Lukas Heine, Yannik Hanusrichter, Yannik Hanusrichter, Martin Weßling, Martin Weßling, Marcel Dudda, Marcel Dudda, Lars E. Podleska, Lars E. Podleska, Matthias A. Fink, Matthias A. Fink, Julius Keyl, Julius Keyl, Konstantinos Tserpes, Konstantinos Tserpes, Moon-Sung Kim, Moon-Sung Kim, Shireen Elhabian, Shireen Elhabian, Hans Lamecker, Hans Lamecker, Dženan Zukić, Dženan Zukić, Beatriz Paniagua, Beatriz Paniagua, Christian Wachinger, Christian Wachinger, Martin Urschler, Martin Urschler, Luc Duong, Luc Duong, Jakob Wasserthal, Jakob Wasserthal, Peter F. Hoyer, Peter F. Hoyer, Oliver Basu, Oliver Basu, Thomas Maal, Thomas Maal, Max J. H. Witjes, Max J. H. Witjes, Gregor Schiele, Gregor Schiele, Ti-chiun Chang, Ti-chiun Chang, Seyed-Ahmad Ahmadi, Seyed-Ahmad Ahmadi, Ping Luo, Ping Luo, Bjoern Menze, Bjoern Menze, Mauricio Reyes, Mauricio Reyes, Thomas M. Deserno, Thomas M. Deserno, Christos Davatzikos, Christos Davatzikos, Behrus Puladi, Behrus Puladi, Pascal Fua, Pascal Fua, Alan L. Yuille, Alan L. Yuille, Jens Kleesiek, Jens Kleesiek, Jan Egger, Jan Egger
 

Contribution to journal

Abstract ■

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. 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. 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. MedShapeNet contains medical shapes from anatomy and surgical instruments and will continue to collect data for benchmarks and applications.

Reference ■
 
Li, J, Zhou, Z, Yang, J, Pepe, A, Gsaxner, C, Luijten, G, Qu, C, Zhang, T, Chen, X, Li, W, Wodzinski, M, Friedrich, P, Xie, K, Jin, Y, Ambigapathy, N, Nasca, E, Solak, N, Melito, GM, Vu, VD, Memon, AR, Schlachta, C, Ribaupierre, SD, Patel, R, Eagleson, R, Chen, X, Mächler, H, Kirschke, JS, de la Rosa, E, Christ, PF, Li, HB, Ellis, DG, Aizenberg, MR, Gatidis, S, Küstner, T, Shusharina, N, Heller, N, Andrearczyk, V, Depeursinge, A, Hatt, M, Sekuboyina, A, T. Löffler, M, Liebl, H, Dorent, R, Vercauteren, T, Shapey, J, Kujawa, A, Cornelissen, S, Langenhuizen, P, Ben-Hamadou, A, Rekik, A, Pujades, S, Boyer, E, Bolelli, F, Grana, C, Lumetti, L, Salehi, H, Ma, J, Zhang, Y, Gharleghi, R, Beier, S, Sowmya, A, A. Garza-Villarreal, E, Balducci, T, Angeles-Valdez, D, Souza, R, Rittner, L, Frayne, R, Ji, Y, Ferrari, V, Chatterjee, S, Dubost, F, Schreiber, S, Mattern, H, Speck, O, Haehn, D, John, C, Nürnberger, A, Pedrosa, J, Ferreira, C, Aresta, G, Cunha, A, Campilho, A, Suter, Y, Garcia, J, Lalande, A, Vandenbossche, V, Van Oevelen, A, Duquesne, K, Mekhzoum, H, Vandemeulebroucke, J, Audenaert, E, Krebs, C, van Leeuwen, T, Vereecke, E, Heidemeyer, H, Röhrig, R, Hölzle, F, Badeli, V, Krieger, K, Gunzer, M, Chen, J, van Meegdenburg, T, Dada, A, Balzer, M, Fragemann, J, Jonske, F, Rempe, M, Malorodov, S, H. Bahnsen, F, Seibold, C, Jaus, A, Marinov, Z, F. Jaeger, P, Stiefelhagen, R, Sofia Santos, A, Lindo, M, Ferreira, A, Alves, V, Kamp, M, Abourayya, A, Nensa, F, Hörst, F, Brehmer, A, Heine, L, Hanusrichter, Y, Weßling, M, Dudda, M, E. Podleska, L, A. Fink, M, Keyl, J, Tserpes, K, Kim, M-S, Elhabian, S, Lamecker, H, Zukić, D, Paniagua, B, Wachinger, C, Urschler, M, Duong, L, Wasserthal, J, F. Hoyer, P, Basu, O, Maal, T, J. H. Witjes, M, Schiele, G, Chang, T, Ahmadi, S-A, Luo, P, Menze, B, Reyes, M, M. Deserno, T, Davatzikos, C, Puladi, B, Fua, P, L. Yuille, A, Kleesiek, J & Egger, J 2025, 'MedShapeNet – a large-scale dataset of 3D medical shapes for computer vision', Biomedical Engineering / Biomedizinische Technik, vol. 70, no. 1, pp. 71-90. https://doi.org/10.1515/bmt-2024-0396
Li, J., Zhou, Z., Yang, J., Pepe, A., Gsaxner, C., Luijten, G., Qu, C., Zhang, T., Chen, X., Li, W., Wodzinski, M., Friedrich, P., Xie, K., Jin, Y., Ambigapathy, N., Nasca, E., Solak, N., Melito, G. M., Vu, V. D., ... Egger, J. (2025). MedShapeNet – a large-scale dataset of 3D medical shapes for computer vision. Biomedical Engineering / Biomedizinische Technik, 70(1), 71-90. https://doi.org/10.1515/bmt-2024-0396
@article{65464c90bcda479488cb08a5fc66ec39,
title = "MedShapeNet – a large-scale dataset of 3D medical shapes for computer vision",
abstract = "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. 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. 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. MedShapeNet contains medical shapes from anatomy and surgical instruments and will continue to collect data for benchmarks and applications.",
author = "Jianning Li and Zongwei Zhou and Jiancheng Yang and Antonio Pepe and Christina Gsaxner and Gijs Luijten and Chongyu Qu and Tiezheng Zhang and Xiaoxi Chen and Wenxuan Li and Marek Wodzinski and Paul Friedrich and Kangxian Xie and Yuan Jin and Narmada Ambigapathy and Enrico Nasca and Naida Solak and Melito, \{Gian Marco\} and Vu, \{Viet Duc\} and Memon, \{Afaque R.\} and Christopher Schlachta and Ribaupierre, \{Sandrine De\} and Rajnikant Patel and Roy Eagleson and Xiaojun Chen and Heinrich M{\"a}chler and Kirschke, \{Jan Stefan\} and \{de la Rosa\}, Ezequiel and Christ, \{Patrick Ferdinand\} and Li, \{Hongwei Bran\} and Ellis, \{David G.\} and Aizenberg, \{Michele R.\} and Sergios Gatidis and Thomas K{\"u}stner and Nadya Shusharina and Nicholas Heller and Vincent Andrearczyk and Adrien Depeursinge and Mathieu Hatt and Anjany Sekuboyina and \{T. L{\"o}ffler\}, Maximilian and Hans Liebl and Reuben Dorent and Tom Vercauteren and Jonathan Shapey and Aaron Kujawa and Stefan Cornelissen and Patrick Langenhuizen and Achraf Ben-Hamadou and Ahmed Rekik and Sergi Pujades and Edmond Boyer and Federico Bolelli and Costantino Grana and Luca Lumetti and Hamidreza Salehi and Jun Ma and Yao Zhang and Ramtin Gharleghi and Susann Beier and Arcot Sowmya and \{A. Garza-Villarreal\}, Eduardo and Thania Balducci and Diego Angeles-Valdez and Roberto Souza and Leticia Rittner and Richard Frayne and Yuanfeng Ji and Vincenzo Ferrari and Soumick Chatterjee and Florian Dubost and Stefanie Schreiber and Hendrik Mattern and Oliver Speck and Daniel Haehn and Christoph John and Andreas N{\"u}rnberger and Jo{\~a}o Pedrosa and Carlos Ferreira and Guilherme Aresta and Ant{\'o}nio Cunha and Aur{\'e}lio Campilho and Yannick Suter and Jose Garcia and Alain Lalande and Vicky Vandenbossche and \{Van Oevelen\}, Aline and Kate Duquesne and Hamza Mekhzoum and Jef Vandemeulebroucke and Emmanuel Audenaert and Claudia Krebs and \{van Leeuwen\}, Timo and Evie Vereecke and Hauke Heidemeyer and Rainer R{\"o}hrig and Frank H{\"o}lzle and Vahid Badeli and Kathrin Krieger and Matthias Gunzer and Jianxu Chen and \{van Meegdenburg\}, Timo and Amin Dada and Miriam Balzer and Jana Fragemann and Frederic Jonske and Moritz Rempe and Stanislav Malorodov and \{H. Bahnsen\}, Fin and Constantin Seibold and Alexander Jaus and Zdravko Marinov and \{F. Jaeger\}, Paul and Rainer Stiefelhagen and \{Sofia Santos\}, Ana and Mariana Lindo and Andr{\'e} Ferreira and Victor Alves and Michael Kamp and Amr Abourayya and Felix Nensa and Fabian H{\"o}rst and Alexander Brehmer and Lukas Heine and Yannik Hanusrichter and Martin We{\ss}ling and Marcel Dudda and \{E. Podleska\}, Lars and \{A. Fink\}, Matthias and Julius Keyl and Konstantinos Tserpes and Moon-Sung Kim and Shireen Elhabian and Hans Lamecker and D{\v z}enan Zuki{\'c} and Beatriz Paniagua and Christian Wachinger and Martin Urschler and Luc Duong and Jakob Wasserthal and \{F. Hoyer\}, Peter and Oliver Basu and Thomas Maal and \{J. H. Witjes\}, Max and Gregor Schiele and Ti-chiun Chang and Seyed-Ahmad Ahmadi and Ping Luo and Bjoern Menze and Mauricio Reyes and \{M. Deserno\}, Thomas and Christos Davatzikos and Behrus Puladi and Pascal Fua and \{L. Yuille\}, Alan and Jens Kleesiek and Jan Egger",
note = "Publisher Copyright: {\textcopyright} 2024 Walter de Gruyter GmbH, Berlin/Boston.",
year = "2025",
month = feb,
day = "1",
doi = "10.1515/bmt-2024-0396",
language = "English",
volume = "70",
pages = "71--90",
journal = "Biomedical Engineering / Biomedizinische Technik",
issn = "1862-278X",
publisher = "De Gruyter",
number = "1",
}