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; 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 Zukić; 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

doi:10.48550/arXiv.2308.16139

Preprints, Working Papers, ... Year : 2023

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

(1) , (2) , (3) , (1) , (1) , (1) , (2) , (2) , (4) , (2) , (5) , (6) , (7) , (1) , (8) , (8) , (1) , (1) , (9) , (10) , (11) , (11) , (11) , (11) , (4) , (12) , (13) , (14) , (15) , (15) , (16) , (16) , (17) , (17) , (18) , (19) , (20) , (20) , (21) , (14) , (14) , (22) , (23) , (23) , (23) , (23) , (24) , (24) , (25, 26) , (25, 26) , (27) , (27) , (28) , (28) , (28) , (29) , (30) , (31) , (32) , (32) , (33) , (34) , (34) , (34) , (35) , (36) , (35) , (37) , (38) , (39) , (40) , (41) , (41) , (41) , (42) , (43) , (43) , (44) , (44) , (45) , (44) , (44) , (46) , (47) , (48) , (49) , (49) , (49) , (49) , (49) , (49) , (50) , (51) , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51

Jianning Li

Function : Author

Graz University of Technology [Graz]

Zongwei Zhou

Function : Author

Johns Hopkins University

Jiancheng Yang

Function : Author

Ecole Polytechnique Fédérale de Lausanne

Antonio Pepe

Function : Author

Graz University of Technology [Graz]

Christina Gsaxner

Function : Author

Graz University of Technology [Graz]

Gijs Luijten

Function : Author

Graz University of Technology [Graz]

Chongyu Qu

Function : Author

Johns Hopkins University

Tiezheng Zhang

Function : Author

Johns Hopkins University

Xiaoxi Chen

Function : Author

Shanghai Jiao Tong University [Shanghai]

Wenxuan Li

Function : Author

Johns Hopkins University

Marek Wodzinski

Function : Author

University of Applied Sciences of Western Switzerland

Paul Friedrich

Function : Author

Université de Bâle = University of Basel = Basel Universität

Kangxian Xie

Function : Author

Khoury College of Computer Sciences [Boston]

Yuan Jin

Function : Author

Graz University of Technology [Graz]

Narmada Ambigapathy

Function : Author

University Hospital Essen

Enrico Nasca

Function : Author

University Hospital Essen

Naida Solak

Function : Author

Graz University of Technology [Graz]

Gian Marco Melito

Function : Author

Graz University of Technology [Graz]

Viet Duc Vu

Function : Author

Justus-Liebig-Universität Gießen = Justus Liebig University

Afaque R. Memon

Function : Author

Mehran University of Engineering and Technology [Jamshoro]

Christopher Schlachta

Function : Author

Canadian Surgical Technologies & Advanced Robotics

Sandrine de Ribaupierre

Function : Author

Canadian Surgical Technologies & Advanced Robotics

Rajnikant Patel

Function : Author

Canadian Surgical Technologies & Advanced Robotics

Roy Eagleson

Function : Author

Canadian Surgical Technologies & Advanced Robotics

Xiaojun Chen

Function : Author

Shanghai Jiao Tong University [Shanghai]

Heinrich Mächler

Function : Author

Medical University Graz

Jan Stefan Kirschke

Function : Author

Technische Universität Munchen - Technical University Munich - Université Technique de Munich

Ezequiel de la Rosa

Function : Author

University of Applied Sciences [Munich]

Patrick Ferdinand Christ

Function : Author

Universität Zürich [Zürich] = University of Zurich

Hongwei Bran Li

Function : Author

Universität Zürich [Zürich] = University of Zurich

David G. Ellis

Function : Author

University of Nebraska Medical Center

Michele R. Aizenberg

Function : Author

University of Nebraska Medical Center

Sergios Gatidis

Function : Author

Universitätsklinikum Tübingen - University Hospital of Tübingen

Thomas Küstner

Function : Author

Universitätsklinikum Tübingen - University Hospital of Tübingen

Nadya Shusharina

Function : Author

Harvard Medical School [Boston]

Nicholas Heller

Function : Author

University of Minnesota [Twin Cities]

Vincent Andrearczyk

Function : Author

University of Applied Sciences and Arts of Western Switzerland

Adrien Depeursinge

Function : Author

University of Applied Sciences and Arts of Western Switzerland

Mathieu Hatt

Function : Author

Laboratoire de Traitement de l'Information Medicale

Anjany Sekuboyina

Function : Author

University of Applied Sciences [Munich]

Maximilian Löffler

Function : Author

University of Applied Sciences [Munich]

Hans Liebl

Function : Author

Klinikum rechts der Isar

Reuben Dorent

Function : Author

King‘s College London

Tom Vercauteren

Function : Author

King‘s College London

Jonathan Shapey

Function : Author

King‘s College London

Aaron Kujawa

Function : Author

King‘s College London

Stefan Cornelissen

Function : Author

St. Elisabeth-TweeSteden Hospital

Patrick Langenhuizen

Function : Author

St. Elisabeth-TweeSteden Hospital

Achraf Ben-Hamadou

Function : Author

Centre de Recherche en Numérique de Sfax

Udini [Aix-En-Provence]

Ahmed Rekik

Function : Author

Centre de Recherche en Numérique de Sfax

Udini [Aix-En-Provence]

Sergi Pujades

Function : Author
PersonId : 738926
IdHAL : sergi-pujades
ORCID : 0000-0002-9604-7721
IdRef : 191615536

Capture and Analysis of Shapes in Motion

Edmond Boyer

Function : Author
PersonId : 752316
IdHAL : edmond-boyer
ORCID : 0000-0002-1182-3729
IdRef : 108147797

Capture and Analysis of Shapes in Motion

Federico Bolelli

Function : Author

Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia

Costantino Grana

Function : Author

Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia

Luca Lumetti

Function : Author

Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia

Hamidreza Salehi

Function : Author

Iran University of Medical Sciences [Tehran, Iran]

Jun Ma

Function : Author

University of Toronto

Yao Zhang

Function : Author

Shanghai University

Ramtin Gharleghi

Function : Author

School of Mechanical and Manufacturing Engineering [Sydney]

Susann Beier

Function : Author

School of Mechanical and Manufacturing Engineering [Sydney]

Arcot Sowmya

Function : Author

School of Computer Science and Software Engineering [Australia]

Eduardo A. Garza-Villarreal

Function : Author

Universidad Nacional Autónoma de México = National Autonomous University of Mexico

Thania Balducci

Function : Author

Universidad Nacional Autónoma de México = National Autonomous University of Mexico

Diego Angeles-Valdez

Function : Author

Universidad Nacional Autónoma de México = National Autonomous University of Mexico

Roberto Souza

Function : Author

University of Calgary

Leticia Rittner

Function : Author

Universidade Estadual de Campinas = University of Campinas

Richard Frayne

Function : Author

University of Calgary

Yuanfeng Ji

Function : Author

The University of Hong Kong

Vincenzo Ferrari

Function : Author

University of Pisa - Università di Pisa

Soumick Chatterjee

Function : Author

Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg]

Florian Dubost

Function : Author

Google LLC

Stefanie Schreiber

Function : Author

Center for Behavioral Brain Sciences [Magdeburg]

Hendrik Mattern

Function : Author

Center for Behavioral Brain Sciences [Magdeburg]

Oliver Speck

Function : Author

Center for Behavioral Brain Sciences [Magdeburg]

Daniel Haehn

Function : Author

University of Massachusetts System

Christoph John

Function : Author

Ecubed Solutions [Bensheim]

Andreas Nürnberger

Function : Author

Ecubed Solutions [Bensheim]

João Pedrosa

Function : Author

Universidade do Porto = University of Porto

Carlos Ferreira

Function : Author

Universidade do Porto = University of Porto

Guilherme Aresta

Function : Author

Medizinische Universität Wien = Medical University of Vienna

António Cunha

Function : Author

Universidade do Porto = University of Porto

Aurélio Campilho

Function : Author

Universidade do Porto = University of Porto

Yannick Suter

Function : Author

Center for Biomedical Engineering Research

Jose Garcia

Function : Author

Center for Biomedical Image Computing & Analytics [Philadelphia]

Alain Lalande

Function : Author

Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon]

Vicky Vandenbossche

Function : Author

Universiteit Gent = Ghent University

Aline van Oevelen

Function : Author

Universiteit Gent = Ghent University

Kate Duquesne

Function : Author

Universiteit Gent = Ghent University

Hamza Mekhzoum

Function : Author

Universiteit Gent = Ghent University

Jef Vandemeulebroucke

Function : Author

Universiteit Gent = Ghent University

Emmanuel Audenaert

Function : Author

Universiteit Gent = Ghent University

Claudia Krebs

Function : Author

University of British Columbia [Vancouver]

Timo van Leeuwen

Function : Author

Technologie campus Gent - KU Leuven

Evie Vereecke

Function : Author

Hauke Heidemeyer

Function : Author

Rainer Röhrig

Function : Author

Frank Hölzle

Function : Author

Vahid Badeli

Function : Author

Kathrin Krieger

Function : Author

Matthias Gunzer

Function : Author

Jianxu Chen

Function : Author

Timo van Meegdenburg

Function : Author

Amin Dada

Function : Author

Miriam Balzer

Function : Author

Jana Fragemann

Function : Author

Frederic Jonske

Function : Author

Moritz Rempe

Function : Author

Stanislav Malorodov

Function : Author

Fin H. Bahnsen

Function : Author

Constantin Seibold

Function : Author

Alexander Jaus

Function : Author

Zdravko Marinov

Function : Author

Paul F. Jaeger

Function : Author

Rainer Stiefelhagen

Function : Author

Ana Sofia Santos

Function : Author

Mariana Lindo

Function : Author

André Ferreira

Function : Author

Victor Alves

Function : Author

Michael Kamp

Function : Author

Amr Abourayya

Function : Author

Felix Nensa

Function : Author

Fabian Hörst

Function : Author

Alexander Brehmer

Function : Author

Lukas Heine

Function : Author

Yannik Hanusrichter

Function : Author

Martin Weßling

Function : Author

Marcel Dudda

Function : Author

Lars E. Podleska

Function : Author

Matthias A. Fink

Function : Author

Julius Keyl

Function : Author

Konstantinos Tserpes

Function : Author

Moon-Sung Kim

Function : Author

Shireen Elhabian

Function : Author

Hans Lamecker

Function : Author

Dženan Zukić

Function : Author

Beatriz Paniagua

Function : Author

Christian Wachinger

Function : Author

Martin Urschler

Function : Author

Luc Duong

Function : Author

Jakob Wasserthal

Function : Author

Peter F. Hoyer

Function : Author

Oliver Basu

Function : Author

Thomas Maal

Function : Author

Max J. H. Witjes

Function : Author

Gregor Schiele

Function : Author

Ti-Chiun Chang

Function : Author

Seyed-Ahmad Ahmadi

Function : Author

Ping Luo

Function : Author

Bjoern Menze

Function : Author

Mauricio Reyes

Function : Author

Thomas M. Deserno

Function : Author

Christos Davatzikos

Function : Author

Behrus Puladi

Function : Author

Pascal Fua

Function : Author

Alan L. Yuille

Function : Author

Jens Kleesiek

Function : Author

Jan Egger

Function : Author

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

Domains

Computer Vision and Pattern Recognition [cs.CV] Medical Imaging

Sergi Pujades : Connect in order to contact the contributor

https://inria.hal.science/hal-04397470

Submitted on : Tuesday, January 16, 2024-1:28:56 PM

Last modification on : Saturday, April 27, 2024-3:12:26 AM

Dates and versions

hal-04397470 , version 1 (16-01-2024)

Licence

Attribution - NonCommercial - ShareAlike

Identifiers

HAL Id : hal-04397470 , version 1
ARXIV : 2308.16139
DOI : 10.48550/arXiv.2308.16139

Cite

Jianning Li, Zongwei Zhou, Jiancheng Yang, Antonio Pepe, Christina Gsaxner, et al.. MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision. 2023. ⟨hal-04397470⟩

Export

BibTeX XML-TEI Dublin Core DC Terms EndNote DataCite

Collections

UNIV-BREST INSTITUT-TELECOM UNIV-BOURGOGNE UGA CNRS INRIA INSMI ICMUB LJK LJK_GI LJK_GI_MORPHEO INRIA2 INRIA-EPFL INC-CNRS LATIM IBSAM INRIA-BRASIL

48 View

0 Download

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

Abstract

Domains

Dates and versions

Licence

Identifiers

Cite

Export

Collections

Altmetric

Share