Jianning Li, Zongwei Zhou, Jiancheng Yang, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Chongyu Qu, Tiezheng Zhang, Xiaoxi Chen, Wenxuan Li, Et al., Marek Wodzinski, Paul Friedrich, Kangxian Xie, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Viet Duc Vu, Afaque R. Memon, ne_list"Christopher Schlachta, Sandrine De Ribaupierre, Rajnikant Patel, Roy Eagleson, Xiaojun Chen, Heinrich Mächler, Jan Stefan Kirschke, Ezequiel De La Rosa, Patrick Ferdinand Christ, Hongwei Bran Li, David G. Ellis, Michele R. Aizenberg, Sergios Gatidis, Thomas Küstner, Nadya Shusharina, Nicholas Heller, Vincent Andrearczyk, Adrien Depeursinge, Mathieu Hatt, Anjany Sekuboyina, Maximilian T. Löffler, Hans Liebl, Reuben Dorent, Tom Vercauteren, Jonathan Shapey, Aaron Kujawa, Stefan Cornelissen, Patrick Langenhuizen, Achraf Ben-Hamadou, Ahmed Rekik, Sergi Pujades, Edmond Boyer, Federico Bolelli, Costantino Grana, Luca Lumetti, Hamidreza Salehi, Jun Ma, Yao Zhang, Ramtin Gharleghi, Susann Beier, Arcot Sowmya, Eduardo A. Garza-Villarreal, Thania Balducci, Diego Angeles-Valdez, Roberto Souza, Leticia Rittner, Richard Frayne, Yuanfeng Ji, Vincenzo Ferrari, Soumick Chatterjee, Florian Dubost, Stefanie Schreiber, Hendrik Mattern, Oliver Speck, Daniel Haehn, Christoph John, Andreas Nürnberger, João Pedrosa, Carlos Ferreira, Guilherme Aresta, António Cunha, Aurélio Campilho, Yannick Suter, Jose Garcia, Alain Lalande, Vicky Vandenbossche, Aline Van Oevelen, Kate Duquesne,
Hamza Mekhzoum,
Jef Vandemeulebroucke, Emmanuel Audenaert, Claudia Krebs, Timo van Leeuwen, Evie Vereecke, Hauke Heidemeyer, Rainer Röhrig, Frank Hölzle, Vahid Badeli, Kathrin Krieger, Matthias Gunzer, Jianxu Chen, Timo van Meegdenburg, Amin Dada, Miriam Balzer, Jana Fragemann, Frederic Jonske, Moritz Rempe, Stanislav Malorodov, Fin H. Bahnsen, Constantin Seibold, Alexander Jaus, Zdravko Marinov, Paul F. Jaeger, Rainer Stiefelhagen, Ana Sofia Santos, Mariana Lindo, André Ferreira, Victor Alves, Michael Kamp, Amr Abourayya, Felix Nensa, Fabian Hörst, Alexander Brehmer, Lukas Heine, Yannik Hanusrichter, Martin Weßling, Marcel Dudda, Lars E. Podleska, Matthias A. Fink, Julius Keyl, Konstantinos Tserpes, Moon-Sung Kim, Shireen Elhabian, Hans Lamecker, Dženan Zukic, Beatriz Paniagua, Christian Wachinger, Martin Urschler, Luc Duong, Jakob Wasserthal, Peter F. Hoyer, Oliver Basu, Thomas Maal, Max J. H. Witjes, Gregor Schiele, Ti-chiun Chang, Seyed-Ahmad Ahmadi, Ping Luo, Bjoern Menze, Mauricio Reyes, Thomas M. Deserno, Christos Davatzikos, Behrus Puladi, Pascal Fua, Alan L. Yuille, Jens Kleesiek, Jan Egger
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.
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, Zukic, 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 2024, ' MedShapeNet – a large-scale dataset of 3D medical shapes for computer vision ', Biomedical Engineering / Biomedizinische Technik .
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. (2024). MedShapeNet – a large-scale dataset of 3D medical shapes for computer vision . Biomedical Engineering / Biomedizinische Technik .
@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: { extcopyright} 2024 Walter de Gruyter GmbH, Berlin/Boston. " ,
year = " 2024 " ,
month = dec,
day = " 30 " ,
doi = " 10.1515/bmt-2024-0396 " ,
language = " English " ,
journal = " Biomedical Engineering / Biomedizinische Technik " ,
issn = " 1862-278X " ,
publisher = " De Gruyter " ,
}