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arXiv · 2308.16139

MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

Jianning Li·Zongwei Zhou·Jiancheng Yang·Antonio Pepe·Christina Gsaxner·Gijs Luijten·Chongyu Qu·Tiezheng Zhang·Xiaoxi Chen·Wenxuan Li·Marek Wodzinski·Paul Friedrich·Kangxian Xie·Yuan Jin·Narmada Ambigapathy·Enrico Nasca·Naida Solak·Gian Marco Melito·Viet Duc Vu·Afaque R. Memon·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 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
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Abstract

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) 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 numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset 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 (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

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Jianning Li, Zongwei Zhou, Jiancheng Yang, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Chongyu Qu, Tiezheng Zhang, Xiaoxi Chen, Wenxuan Li, Marek Wodzinski, Paul Friedrich, Kangxian Xie, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Viet Duc Vu, Afaque R. Memon, 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 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. 2023-08-30. MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision. https://doi.org/10.1515/bmt-2024-0396

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