Publications
2025
Aortic Vessel Tree Segmentation for Cardiovascular Diseases Treatment: Status Quo
Yuan Jin, Antonio Pepe, Jianning Li, Christina Gsaxner, Yuxuan Chen, Behrus Puladi, Fen-hua Zhao, Kelsey L. Pomykala, Jens Kleesiek, Alejandro F. Frangi, Jan Egger
ACM Comput. Surv.
MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision
Jianning Li, Antonio Pepe, Christina Gsaxner, Gijs Luijten, Yuan Jin, Narmada Ambigapathy, Enrico Nasca, Naida Solak, Gian Marco Melito, Afaque Rafique Memon, Xiaojun Chen, Jan Stefan Kirschke, Ezequiel de la Rosa, Patrick Ferdinand Christ, Hongwei Bran Li, David G. Ellis, Michele R. Aizenberg, Sergios Gatidis, Thomas Kuestner, Nadya Shusharina, Nicholas Heller, Vincent Andrearczyk, Adrien Depeursinge, Mathieu Hatt, Anjany Sekuboyina, Maximilian Loeffler, 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, Eduardo A. Garza-Villarreal, Thania Balducci, Diego Angeles-Valdez, Roberto Souza, Leticia Rittner, Richard Frayne, Yuanfeng Ji, Soumick Chatterjee, Andreas Nuernberger, Joao Pedrosa, Carlos Ferreira, Guilherme Aresta, Antonio Cunha, Aurelio Campilho, Yannick Suter, Jose Garcia, Alain Lalande, Emmanuel Audenaert, Claudia Krebs, Timo Van Leeuwen, Evie Vereecke, Rainer Roehrig, Frank Hoelzle, Vahid Badeli, Kathrin Krieger, Matthias Gunzer, Jianxu Chen, Amin Dada, Miriam Balzer, Jana Fragemann, Frederic Jonske, Moritz Rempe, Stanislav Malorodov, Fin Hendrik Bahnsen, Constantin Seibold, Alexander Jaus, Ana Sofia Ferreira Santos, Mariana Lindo, André Ferreira, Victor Alves, Michael Kamp, Amr Abourayya, Felix Nensa, Fabian Hoerst, Alexander Brehmer, Lukas Heine, Lars E. Podleska, Matthias A. Fink, Julius Keyl, Konstantinos Tserpes, Moon-Sung Kim, Shireen Elhabian, Hans Lamecker, Dzenan Zukic, Beatriz Paniagua, Christian Wachinger, Martin Urschler, Luc Duong, Jakob Wasserthal, Peter F. Hoyer, Oliver Basu, Thomas Maal, Max J. H. Witjes, Ping Luo, Björn Menze, Mauricio Reyes, Christos Davatzikos, Behrus Puladi, Jens Kleesiek, Jan Egger, Zongwei Zhou, Jiancheng Yang, Chongyu Qu, Tiezheng Zhang, Xiaoxi Chen, Wenxuan Li, Marek Wodzinski, Paul Friedrich, Kangxian Xie, Viet Duc Vu, Christopher Schlachta, Sandrine De Ribaupierre, Rajnikant Patel, Roy Eagleson, Heinrich Mächler, Thomas Küstner, Arcot Sowmya, Vincenzo Ferrari, Florian Dubost, Stefanie Schreiber, Hendrik Mattern, Oliver Speck, Daniel Haehn, Christoph John, Vicky Vandenbossche, Aline Van Oevelen, Kate Duquesne, Hamza Mekhzoum, Jef Vandemeulebroucke, Hauke Heidemeyer, Rainer Röhrig, Frank Hölzle, Timo van Meegdenburg, Zdravko Marinov, Paul F. Jäger, Rainer Stiefelhagen, Fabian Hörst, Yannik Hanusrichter, Martin Weßling, Marcel Dudda, Gregor Schiele, Ti-chiun Chang, Seyed-Ahmad Ahmadi, Thomas M. Deserno, Pascal Fua, Alan L. Yuille
Biomedical Engineering / Biomedizinische Technik 2024
Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images
Johannes Raufeisen, Kunpeng Xie, Fabian Hörst, Till Braunschweig, Jianning Li, Jens Kleesiek, Rainer Röhrig, Jan Egger, Bastian Leibe, Frank Hölzle, Alexander Hermans, Behrus Puladi
Computer Methods and Programs in Biomedicine
How we won BraTS 2023 Adult Glioma challenge? Just faking it! Enhanced Synthetic Data Augmentation and Model Ensemble for brain tumour segmentation
André Ferreira, Naida Solak, Jianning Li, Philipp Dammann, Jens Kleesiek, Victor Alves, Jan Egger
arXiv
GAN-based generation of realistic 3D volumetric data: A systematic review and taxonomy
André Ferreira, Jianning Li, Kelsey L. Pomykala, Jens Kleesiek, Victor Alves, Jan Egger
Medical Image Analysis
A Semi-automatic Cranial Implant Design Tool Based on Rigid ICP Template Alignment and Voxel Space Reconstruction
Michael Lackner, Behrus Puladi, Jens Kleesiek, Jan Egger, Jianning Li
arXiv
Advancing Healthcare Through Open Science: StudierFenster and MedShapeNet
Christina Gsaxner, Gijs Luijten, Jianning Li, Jens Kleesiek, Behrus Puladi, Jan Egger
ChatGPT in healthcare: A taxonomy and systematic review
Jianning Li, Amin Dada, Behrus Puladi, Jens Kleesiek, Jan Egger
Computer Methods and Programs in Biomedicine
CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images
Johannes Raufeisen, Kunpeng Xie, Fabian Hörst, Till Braunschweig, Jianning Li, Jens Kleesiek, Rainer Röhrig, Jan Egger, Bastian Leibe, Frank Hölzle, Alexander Hermans, Behrus Puladi
Zenodo
Multilingual Natural Language Processing Model for Radiology Reports -- The Summary is all you need!
Mariana Lindo, Ana Sofia Ferreira Santos, André Ferreira, Jianning Li, Gijs Luijten, Gustavo Correia, Moon-Sung Kim, Benedikt Michael Schaarschmidt, Cornelius Deuschl, Johannes Haubold, Jens Kleesiek, Jan Egger, Victor Alves
arXiv 2023
3D surgical instrument collection for computer vision and extended reality
Gijs Luijten, Christina Gsaxner, Jianning Li, Antonio Pepe, Narmada Ambigapathy, Moon-Sung Kim, Xiaojun Chen, Jens Kleesiek, Frank Hölzle, Behrus Puladi, Jan Egger
Scientific Data
3D-COSI ~ 3D Collection of Surgical Instruments
Gijs Luijten, Christina Gsaxner, Jianning Li, Antonio Pepe, Narmada Ambigapathy, Moon-Sung Kim, Xiaojun Chen, Jens Kleesiek, Frank Hölzle, Behrus Puladi, Jan Egger
Anatomy Completor: A Multi-class Completion Framework for 3D Anatomy Reconstruction
Jianning Li, Antonio Pepe, Gijs Luijten, Christina Schwarz-Gsaxner, Jens Kleesiek, Jan Egger
arXiv
Open-source skull reconstruction with MONAI
Jianning Li, André Ferreira, Behrus Puladi, Victor Alves, Michael Kamp, Moon-Sung Kim, Felix Nensa, Jens Kleesiek, Seyed-Ahmad Ahmadi, Jan Egger
SoftwareX
Towards clinical applicability and computational efficiency in automatic cranial implant design: An overview of the AutoImplant 2021 cranial implant design challenge
Jianning Li, David G. Ellis, Oldřich Kodym, Laurèl Rauschenbach, Christoph Rieß, Ulrich Sure, Karsten H. Wrede, Carlos M. Alvarez, Marek Wodzinski, Mateusz Daniol, Daria Hemmerling, Hamza Mahdi, Allison Clement, Evan Kim, Zachary Fishman, Cari M. Whyne, James G. Mainprize, Michael R. Hardisty, Shashwat Pathak, Chitimireddy Sindhura, Rama Krishna Sai S. Gorthi, Degala Venkata Kiran, Subrahmanyam Gorthi, Bokai Yang, Ke Fang, Xingyu Li, Artem Kroviakov, Lei Yu, Yuan Jin, Antonio Pepe, Christina Gsaxner, Adam Herout, Victor Alves, Michal Španěl, Michele R. Aizenberg, Jens Kleesiek, Jan Egger
Medical Image Analysis
ChatGPT in Healthcare: A Taxonomy and Systematic Review
Jianning Li, Amin Dada, Jens Kleesiek, Jan Egger
medRxiv
A web-based radiomics module for image feature extraction for tumor characterization
Theresa Huebner, Aaron Berger, Daniel Wild, Jianning Li, Antonio Pepe, Christina Gsaxner, Yuan Jin, Gijs Luijten, Jens Kleesiek, Jan Egger
Medical Imaging 2023: Imaging Informatics for Healthcare, Research, and Applications
FAM: Relative Flatness Aware Minimization
Linara Adilova, Amr Abourayya, Jianning Li, Amin Dada, Henning Petzka, Jan Egger, Jens Kleesiek, Michael Kamp
Topological, Algebraic and Geometric Learning Workshops 2023
On the Impact of Cross-Domain Data on German Language Models
Amin Dada, Aokun Chen, Cheng Peng, Kaleb Smith, Ahmad Idrissi-Yaghir, Constantin Seibold, Jianning Li, Lars Heiliger, Christoph M. Friedrich, Daniel Truhn, Jan Egger, Jiang Bian, Jens Kleesiek, Yonghui Wu
The HoloLens in medicine: A systematic review and taxonomy
Christina Gsaxner, Jianning Li, Antonio Pepe, Yuan Jin, Jens Kleesiek, Dieter Schmalstieg, Jan Egger
Medical Image Analysis 2022
Open-Source Skull Reconstruction with MONAI
Jianning Li, André Ferreira, Behrus Puladi, Victor Alves, Michael Kamp, Moon-Sung Kim, Felix Nensa, Jens Kleesiek, Seyed-Ahmad Ahmadi, Jan Egger
arXiv
The HoloLens in Medicine: A systematic Review and Taxonomy
Christina Gsaxner, Jianning Li, Antonio Pepe, Yuan Jin, Jens Kleesiek, Dieter Schmalstieg, Jan Egger
arXiv
Training beta-VAE by Aggregating a Learned Gaussian Posterior with a Decoupled Decoder
Jianning Li, Jana Fragemann, Seyed-Ahmad Ahmadi, Jens Kleesiek, Jan Egger
arXiv
GAN-based generation of realistic 3D data: A systematic review and taxonomy
André Ferreira, Jianning Li, Kelsey L. Pomykala, Jens Kleesiek, Victor Alves, Jan Egger
arXiv
Medical Deep Learning – A systematic Meta-Review
Jan Egger, Christina Gsaxner, Antonio Pepe, Kelsey L. Pomykala, Frederic Jonske, Manuel Kurz, Jianning Li, Jens Kleesiek
Computer Methods and Programs in Biomedicine
Sparse Convolutional Neural Networks for Medical Image Analysis
Jianning Li, Christina Gsaxner, Antonio Pepe, Dieter Schmalstieg, Jens Kleesiek, Jan Egger
AVT: Multicenter aortic vessel tree CTA dataset collection with ground truth segmentation masks
Lukas Radl, Yuan Jin, Antonio Pepe, Jianning Li, Christina Gsaxner, Fen-hua Zhao, Jan Egger
Radiomics in Head and Neck Cancer Outcome Predictions
Maria Gonçalves, Christina Gsaxner, André Ferreira, Jianning Li, Behrus Puladi, Jens Kleesiek, Jan Egger, Victor Alves
Diagnostics 2021
A web client-based online DICOM browser and NRRD converter for Studierfenster
Christopher A. Ramirez Bedoya, Daniel Wild, Antonio Pepe, Christina Gsaxner, Jianning Li, Jan Egger
Medical Imaging 2021: Imaging Informatics for Healthcare, Research, and Applications
A cloud-based centerline algorithm for Studierfenster
Christina Dionysio, Daniel Wild, Antonio Pepe, Christina Gsaxner, Jianning Li, Luis Alvarez, Jan Egger
Medical Imaging 2021: Imaging Informatics for Healthcare, Research, and Applications
A review on patient-specific facial and cranial implant design using Artificial Intelligence (AI) techniques
Afaque Rafique Memon, Jianning Li, Jan Egger, Xiaojun Chen
Ai-based aortic vessel tree segmentation for cardiovascular diseases treatment: status quo
Yuan Jin, Antonio Pepe, Jianning Li, Christina Gsaxner, Fen-hua Zhao, Jens Kleesiek, Alejandro F. Frangi, Jan Egger
An online platform for automatic skull defect restoration and cranial implant design
Jianning Li, Antonio Pepe, Christina Gsaxner, Jan Egger
Medical Imaging 2021: Image-Guided Procedures, Robotic Interventions, and Modeling
AutoImplant 2020-first MICCAI challenge on automatic cranial implant design
Jianning Li, Pedro Pimentel, Angelika Szengel, Moritz Ehlke, Hans Lamecker, Stefan Zachow, Laura Estacio, Christian Doenitz, Heiko Ramm, Haochen Shi
Automated cross-sectional view selection in CT angiography of aortic dissections with uncertainty awareness and retrospective clinical annotations
Antonio Pepe, Jan Egger, Marina Codari, Martin J. Willemink, Christina Gsaxner, Jianning Li, Peter M. Roth, Gabriel Mistelbauer, Dieter Schmalstieg, Dominik Fleischmann
Automatic skull defect restoration and cranial implant generation for cranioplasty
Jianning Li, Gord von Campe, Antonio Pepe, Christina Gsaxner, Enpeng Wang, Xiaojun Chen, Ulrike Zefferer, Martin Tödtling, Marcell Krall, Hannes Deutschmann
Deep learning and particle filter-based aortic dissection vessel tree segmentation
Yuan Jin, Antonio Pepe, Jianning Li, Christina Gsaxner, Jan Egger
Medical Imaging 2021: Biomedical Applications in Molecular, Structural, and Functional Imaging
Deep learning—a first meta-survey of selected reviews across scientific disciplines, their commonalities, challenges and research impact
Jan Egger, Antonio Pepe, Christina Gsaxner, Yuan Jin, Jianning Li, Roman Kern
Inside-out instrument tracking for surgical navigation in augmented reality
Christina Gsaxner, Jianning Li, Antonio Pepe, Dieter Schmalstieg, Jan Egger
Proceedings of the 27th ACM Symposium on Virtual Reality Software and Technology
Learning to rearrange voxels in binary segmentation masks for smooth manifold triangulation
Jianning Li, Antonio Pepe, Christina Gsaxner, Yuan Jin, Jan Egger
Cranial Implant Design Challenge
Medical image segmentation in oral-maxillofacial surgery
Jianning Li, Marius Erdt, Firdaus Janoos, Ti-chiun Chang, Jan Egger
MUG500+: Database of 500 high-resolution healthy human skulls and 29 craniotomy skulls and implants
Jianning Li, Marcell Krall, Florian Trummer, Afaque Rafique Memon, Antonio Pepe, Christina Gsaxner, Yuan Jin, Xiaojun Chen, Hannes Deutschmann, Ulrike Zefferer
PCA-Skull: 3D Skull Shape Modelling Using Principal Component Analysis
Lei Yu, Jianning Li, Jan Egger
Cranial Implant Design Challenge
SkullBreak/SkullFix–Dataset for automatic cranial implant design and a benchmark for volumetric shape learning tasks
Oldřich Kodym, Jianning Li, Antonio Pepe, Christina Gsaxner, Sasank Chilamkurthy, Jan Egger, Michal Španěl
Sparse Convolutional Neural Network for Skull Reconstruction
Artem Kroviakov, Jianning Li, Jan Egger
Cranial Implant Design Challenge
Synthetic skull bone defects for automatic patient-specific craniofacial implant design
Jianning Li, Christina Gsaxner, Antonio Pepe, Ana Morais, Victor Alves, Gord von Campe, Jürgen Wallner, Jan Egger
Towards the Automatization of Cranial Implant Design in Cranioplasty II
Jianning Li, Jan Egger
Springer International Publishing 
