Jan Egger

Jan Egger

Team Lead AI-guided Therapies

Institute for AI in Medicine, Germany

Jan has over 10 years of experience in developing algorithms in medical image analysis and image-guided therapies, including 5 years of postdoctoral research and development in the healthcare industry. Until now, he has published over 150 peer-reviewed papers, edited several books and won numerous awards for the theses and publications. He is also the PI of the open science client/server-based medical platform StudierFenster and is mentoring the transition of the medical Augmented Reality FWF-project “enFaced” into the Start-up “Augmentomy”. During his career, he supervised and co-supervised around 100 student theses and projects, and was involved in the acquisition of over 14 million euros in third party funding. He holds a Ph.D. and a (German) Habilitation in Computer Science, and an interdisciplinary Ph.D. in Human Biology. Currently, Jan is a Privatdozent at the Technical University of Graz and a research group leader at the Institute for Artificial Intelligence in Medicine (IKIM) at the Essen University Hospital.

Publications

2026

Large language models enable prognostic stratification of cancer patients using real-world clinical notes Niklas Kiermeyer, Tim Lenfers, Amin Dada, Julian Friedrich, Sameh Khattab, Eric Knop, Jan Egger, Markus Pauly, Andreas Jung, Grégoire Montavon, Jens T. Siveke, Marcel Wiesweg, Stefan Kasper, Ulf Peter Neumann, Frederick Klauschen, Sylvia Hartmann, Martin Schuler, Philipp Keyl, Jens Kleesiek, Julius Keyl PLOS Digital Health ++nnU-Net: Scaling nnU-Net with Prefix-Based Data Augmentation Ana Sofia Ferreira Santos, André Ferreira, Gijs Luijten, Naida Solak, Lisle Faray de Paiva, Behrus Hinrichs-Puladi, Jens Kleesiek, Jan Egger, Victor Alves arXiv Explainable AI Predicts Hematoxicity from Cancer Treatment Using Multimodal Real-World Data Julius Keyl, Philipp Keyl, Tim Lenfers, René Hosch, Niklas Kiermeyer, Simon Schallenberg, Moon-Sung Kim, Sebastian Bauer, Nikolaos Bechrakis, Michael Forsting, Dagmar Fuehrer-Sakel, Sied Kebir, Viktor Grünwald, Boris Hadaschik, Johannes Haubold, Ken Herrmann, Stefan Kasper, Rainer Kimmig, Stephan Lang, Tienush Rassaf, Alexander Roesch, Dirk Schadendorf, Jens T. Siveke, Martin Stuschke, Ulrich Sure, Matthias Totzeck, Anja Welt, Marcel Wiesweg, Jan Egger, Sylvia Hartmann, Grégoire Montavon, Felix Nensa, Klaus-Robert Müller, Martin Schuler, Jens Kleesiek, Frederick Klauschen medRxiv Achieving Over 10× Faster Sample Generation with Conditional Denoising Diffusion André Ferreira, Gijs Luijten, Behrus Hinrichs-Puladi, Jens Kleesiek, Victor Alves, Jan Egger Segmentation, Classification, and Synthesis for Brain Tumors and Traumatic Brain Injuries Deep Learning-derived Sarcopenia Marker Predicts Benefit from Anti-EGFR Therapy in Patients with RAS Wild-Type Metastatic Colorectal Cancer Julius Keyl, René Hosch, Fabian Hörst, Philipp Keyl, Amin Dada, Johannes Haubold, Jannis Straus, Jan Egger, Arndt Stahler, Annika Kurreck, Alexej Ballhausen, Sebastian Stintzing, Stefan Fruehauf, Lothar Müller, Annabel H. S. Alig, Tanja Trarbach, Sylvia Hartmann, Felix Nensa, Jens Kleesiek, Stefan Kasper, Martin Schuler, Dominik P. Modest Clinical Cancer Research From screen to space: evaluating Siemens’ Cinematic Reality application for medical imaging on the Apple Vision Pro Gijs Luijten, Lisle Faray de Paiva, Sebastian Krueger, Alexander Brost, Laura Mazilescu, Ana Sofia Ferreira Santos, Peter F. Hoyer, Jens Kleesiek, Sophia Marie-Therese Schmitz, Ulf Peter Neumann, Jan Egger Frontiers in Virtual Reality

2025

Automated CT-based sarcopenia assessment for risk stratification of patients undergoing colorectal cancer resection Johannes Vogelsang, Gernot Pucher, Fabian Hörst, René Hosch, Johannes Haubold, Philipp Keyl, Christopher Sauer, David Albers, Peter Markus, Jan P. Neuhaus, Andreas D. Rink, Jürgen Treckmann, Ulf Peter Neumann, Kai Nassenstein, Michael Forsting, Hideo A. Baba, Jan Egger, Stefan Kasper, Martin Schuler, Felix Nensa, Jens Kleesiek, Julius Keyl Clinical Surgical Oncology Performing the HINTS-exam using a mixed-reality head-mounted display in patients with acute vestibular syndrome: a feasibility study Nadia Sadok, Gijs Luijten, Fin Hendrik Bahnsen, Christina Gsaxner, Lorenz Peters, Theda Eichler, Theresa Rombach, Stephan Lang, Sameh Khattab, Jens Kleesiek, Dagny Holle, Moritz Meyer, Jan Egger Frontiers in Neurology 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. Virtual reality support during systemic cancer therapy to improve anxiety/depressive symptoms and reduce toxicity in patients with gastrointestinal cancers—OncoVR Stefan Kasper, S. Liszio, K. Schorrmann, M. Gerigk, S. Jovic, Oliver Basu, K. Kostbade, B. Goraus, Abdelrahman Elsakka, Behrus Puladi, Jens Kleesiek, Martin Schuler, Gijs Luijten, Jan Egger ESMO Gastrointestinal Oncology Decoding pan-cancer treatment outcomes using multimodal real-world data and explainable artificial intelligence Julius Keyl, Philipp Keyl, Grégoire Montavon, René Hosch, Alexander Brehmer, Liliana Mochmann, Philipp Jurmeister, Gabriel Dernbach, Moon-Sung Kim, Sven Koitka, Sebastian Bauer, Nikolaos Bechrakis, Michael Forsting, Dagmar Führer-Sakel, Martin Glas, Viktor Grünwald, Boris Hadaschik, Johannes Haubold, Ken Herrmann, Stefan Kasper, Rainer Kimmig, Stephan Lang, Tienush Rassaf, Alexander Roesch, Dirk Schadendorf, Jens T. Siveke, Martin Stuschke, Ulrich Sure, Matthias Totzeck, Anja Welt, Marcel Wiesweg, Hideo A. Baba, Felix Nensa, Jan Egger, Klaus-Robert Müller, Martin Schuler, Frederick Klauschen, Jens Kleesiek Nature Cancer 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 Comparative Analysis of nnUNet and MedNeXt for Head and Neck Tumor Segmentation in MRI-Guided Radiotherapy Nikoo Moradi, André Ferreira, Behrus Puladi, Jens Kleesiek, Emad Fatemizadeh, Gijs Luijten, Victor Alves, Jan Egger Head and Neck Tumor Segmentation for MR-Guided Applications Spacewalker: Traversing Representation Spaces for Fast Interactive Exploration and Annotation of Unstructured Data Lukas Heine, Fabian Hörst, Jana Fragemann, Gijs Luijten, Jan Egger, Fin Hendrik Bahnsen, Saquib Sarfraz, Jens Kleesiek, Constantin Seibold, M. Saquib Sarfraz Machine Learning Methods in Visualisation for Big Data (EuroVis Workshop) Why does my medical AI look at pictures of birds? Exploring the efficacy of transfer learning across domain boundaries Frederic Jonske, Moon-Sung Kim, Enrico Nasca, Janis Evers, Johannes Haubold, René Hosch, Felix Nensa, Michael Kamp, Constantin Seibold, Jan Egger, Jens Kleesiek Computer Methods and Programs in Biomedicine

2024

Brain Tumour Removing and Missing Modality Generation using 3D WDM André Ferreira, Gijs Luijten, Behrus Puladi, Jens Kleesiek, Victor Alves, Jan Egger arXiv Improved Multi-Task Brain Tumour Segmentation with Synthetic Data Augmentation André Ferreira, Tiago Jesus, Behrus Puladi, Jens Kleesiek, Victor Alves, Jan Egger arXiv Results from the autoPET challenge on fully automated lesion segmentation in oncologic PET/CT imaging Sergios Gatidis, Marcel Früh, Matthias P. Fabritius, Sijing Gu, Konstantin Nikolaou, Christian la Fougère, Jin Ye, Junjun He, Yige Peng, Lei Bi, Jun Ma, Bo Wang, Jia Zhang, Yukun Huang, Lars Heiliger, Zdravko Marinov, Rainer Stiefelhagen, Jan Egger, Jens Kleesiek, Ludovic Sibille, Lei Xiang, Simone Bendazzoli, Mehdi Astaraki, Michael Ingrisch, Clemens C. Cyran, Thomas Küstner Nature Machine Intelligence Establishing Medical Intelligence - Leveraging FHIR to Improve Clinical Management: a retrospective cohort and clinical implementation study Alexander Brehmer, Christopher Sauer, Jayson Salazar Rodríguez, Kelsey Herrmann, Moon-Sung Kim, Julius Keyl, Fin Hendrik Bahnsen, Benedikt Frank, Martin Koehrmann, Tienush Rassaf, Amir-Abbas Mahabadi, Boris Hadaschik, Christopher Darr, Ken Herrmann, Susanne Tan, Jan Buer, Thorsten Brenner, Hans Christian Reinhardt, Felix Nensa, Michael Gertz, Jan Egger, Jens Kleesiek Journal of Medical Internet Research 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 Der mobile Patient Jan Egger, Jens Kleesiek Human Hospital: wertschätzend. sinnstiftend. menschlich. Multisensory Extended Reality Applications Offer Benefits for Volumetric Biomedical Image Analysis in Research and Medicine Kathrin Krieger, Jan Egger, Jens Kleesiek, Matthias Gunzer, Jianxu Chen Journal of Imaging Informatics in Medicine Tumor likelihood estimation on MRI prostate data by utilizing k-Space information Moritz Rempe, Fabian Hörst, Constantin Seibold, Boris Hadaschik, Marco Schlimbach, Jan Egger, Kevin Kröninger, Felix Breuer, Martin Blaimer, Jens Kleesiek arXiv Deep Learning-based Point Cloud Registration for Augmented Reality-guided Surgery Maximilian Weber, Daniel Wild, Jens Kleesiek, Jan Egger, Christina Gsaxner 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 Deep PCCT: Photon Counting Computed Tomography Deep Learning Applications Review Ana Carolina Alves, André Ferreira, Gijs Luijten, Jens Kleesiek, Behrus Puladi, Jan Egger, Victor Alves arXiv Diminished Reality for Emerging Applications in Medicine through Inpainting Christina Gsaxner, Shohei Mori, Gijs Luijten, Viet Duc Vu, Timo van Meegdenburg, Gabriele A. Krombach, Jens Kleesiek, Eck Ulrich, Nassir Navab, Yan Guo, Xiaojun Chen, Frank Hölzle, Behrus Puladi, Jan Egger Response to the comment on “The impact and opportunities of large language models like ChatGPT in oral and maxillofacial surgery: a narrative review” Behrus Puladi, Christina Gsaxner, Jens Kleesiek, Frank Hölzle, Rainer Röhrig, Jan Egger International Journal of Oral and Maxillofacial Surgery Accelerating Artificial Intelligence-based Whole Slide Image Analysis with an Optimized Preprocessing Pipeline Fabian Hörst, Sajad H. Schaheer, Giulia Baldini, Fin Hendrik Bahnsen, Jan Egger, Jens Kleesiek Bildverarbeitung für die Medizin 2024 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 Deep Interactive Segmentation of Medical Images: A Systematic Review and Taxonomy Zdravko Marinov, Paul F. Jäger, Jan Egger, Jens Kleesiek, Rainer Stiefelhagen IEEE Transactions on Pattern Analysis and Machine Intelligence Designing and Implementing an Interactive Cloud Platform for Teaching Machine Learning with Medical Data Frederic Jonske, Kevin Osthues, Amin Dada, Enrico Nasca, Jana Fragemann, Julian Alff, Oleh Bakumenko, Marcel Birnbach, Maxim Kondratenko, Lars Reinike, Benjamin Schulz, Fabian Siethoff, Tobias Simon, Joey Wang, Nils Zhang, Fin Hendrik Bahnsen, Jan Egger, Moon-Sung Kim, Maria Lymbery, Jens Kleesiek, Johannes Kraus Artificial Intelligence for Security: Enhancing Protection in a Changing World Designing and Implementing an Interactive Cloud Platform for Teaching Machine Learning with Medical Data Frederic Jonske, Kevin Osthues, Amin Dada, Enrico Nasca, Jana Fragemann, Julian Alff, Oleh Bakumenko, Marcel Birnbach, Maxim Kondratenko, Lars Reinike, Benjamin Schulz, Fabian Siethoff, Tobias Simon, Joey Wang, Nils Zhang, Fin Hendrik Bahnsen, Jan Egger, Moon-Sung Kim, Maria Lymbery, Jens Kleesiek, Johannes Kraus Artificial Intelligence for Security: Enhancing Protection in a Changing World k-strip: A novel segmentation algorithm in k-space for the application of skull stripping Moritz Rempe, Florian Mentzel, Kelsey L. Pomykala, Johannes Haubold, Felix Nensa, Kevin Kroeninger, Jan Egger, Jens Kleesiek Computer Methods and Programs in Biomedicine 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 What is Diminished Virtuality? A Directional and Layer-Based Taxonomy for the Reality-Virtuality Continuum Jan Egger, Christina Gsaxner, Jens Kleesiek, Behrus Puladi JMIR XR and Spatial Computing

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 Decoding pan-cancer treatment outcomes using multimodal real-world data and explainable artificial intelligence Julius Keyl, Philipp Keyl, Grégoire Montavon, René Hosch, Alexander Brehmer, Liliana Mochmann, Philipp Jurmeister, Gabriel Dernbach, Moon-Sung Kim, Sven Koitka, Sebastian Bauer, Nikolaos Bechrakis, Michael Forsting, Dagmar Fuehrer-Sakel, Martin Glas, Viktor Gruenwald, Boris Hadaschik, Johannes Haubold, Ken Herrmann, Stefan Kasper, Rainer Kimmig, Tienush Rassaf, Alexander Roesch, Dirk Schadendorf, Jens T. Siveke, Martin Stuschke, Ulrich Sure, Matthias Totzeck, Anja Welt, Marcel Wiesweg, Hideo A. Baba, Felix Nensa, Jan Egger, Klaus-Robert Mueller, Martin Schuler, Frederick Klauschen, Jens Kleesiek medRxiv The impact and opportunities of large language models like ChatGPT in oral and maxillofacial surgery: a narrative review Behrus Puladi, Christina Gsaxner, Jens Kleesiek, Frank Hölzle, Rainer Röhrig, Jan Egger International Journal of Oral and Maxillofacial Surgery 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 Improvement in Disease Diagnosis in Computed Tomography Images by Correlating Organ Volumes with Disease Occurrences in Humans Timo van Meegdenburg, Jens Kleesiek, Jan Egger, Sören Perrey BioMedInformatics Virtual Reality, Augmented Reality, Augmented Virtuality, or Mixed Reality in Cardiopulmonary Resuscitation: Which Extended Reality am I Using for Teaching Adult Basic Life Support? Nino Fijačko, Špela Metličar, Jens Kleesiek, Jan Egger, Todd P Chang Resuscitation Apple Vision Pro for Healthcare: \"The Ultimate Display\"? Jan Egger, Christina Gsaxner, Xiaojun Chen, Jiang Bian, Jens Kleesiek, Behrus Puladi arXiv Histology-Based Prediction of Therapy Response to Neoadjuvant Chemotherapy for Esophageal and Esophagogastric Junction Adenocarcinomas Using Deep Learning Fabian Hörst, Saskia Ting, Sven-Thorsten Liffers, Kelsey L. Pomykala, Katja Steiger, Markus Albertsmeier, Martin K. Angele, Sylvie Lorenzen, Michael Quante, Wilko Weichert, Jan Egger, Jens T. Siveke, Jens Kleesiek JCO Clinical Cancer Informatics Information extraction from weakly structured radiological reports with natural language queries Amin Dada, Tim Leon Ufer, Moon-Sung Kim, Max Hasin, Nicola Spieker, Michael Forsting, Felix Nensa, Jan Egger, Jens Kleesiek European Radiology 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 CellViT: Vision Transformers for Precise Cell Segmentation and Classification Fabian Hörst, Moritz Rempe, Lukas Heine, Constantin Seibold, Julius Keyl, Giulia Baldini, Selma Ugurel, Jens T. Siveke, Barbara Grünwald, Jan Egger, Jens Kleesiek arXiv Establishing Medical Intelligence - Leveraging FHIR to Improve Clinical Management Alexander Brehmer, Christopher Sauer, Jayson Salazar, Kelsey Hermmann, Moon-Sung Kim, Julius Keyl, Fin Hendrik Bahnsen, Benedikt Frank, Martin Köhrmann, Tienush Rassaf, Amir-Abbas Mahabadi, Boris Hadaschik, Christopher Darr, Ken Herrmann, Susanne Tan, Jan Buer, Thorsten Brenner, Hans Christian Reinhardt, Felix Nensa, Michael Gertz, Jan Egger, Jens Kleesiek The autoPET challenge: Towards fully automated lesion segmentation in oncologic PET/CT imaging Sergios Gatidis, Marcel Früh, , Matthias Fabritius, Sijing Gu, Christian la Fougère, Jin Ye, Junjun He, Yige Peng, Lei Bi, Jun Ma, Bo Wang, Jia Zhang, Huang, Lars Heiliger, Zdravko Marinov, Rainer Stiefelhagen, Jan Egger, Jens Kleesiek, Ludovic Sibille, Lei Xiang, Simone Bendazolli, Mehdi Astaraki, Bernhard Schölkopf, Michael Ingrisch, Clemens C. Cyran, Thomas Küstner 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 Valuing vicinity: Memory attention framework for context-based semantic segmentation in histopathology Oliver Ester, Fabian Hörst, Constantin Seibold, Julius Keyl, Saskia Ting, Nikolaos Vasileiadis, Jessica Schmitz, Philipp Ivanyi, Viktor Grünwald, Jan Hinrich Bräsen, Jan Egger, Jens Kleesiek Computerized Medical Imaging and Graphics An Opinion on ChatGPT in Health Care—Written by Humans Only Jens Kleesiek, Yonghui Wu, Gregor Stiglic, Jan Egger, Jiang Bian Journal of Nuclear Medicine ChatGPT in Healthcare: A Taxonomy and Systematic Review Jianning Li, Amin Dada, Jens Kleesiek, Jan Egger medRxiv Histology-based Prediction of Therapy Response to Neoadjuvant Chemotherapy for Esophageal and Esophagogastric Junction Adenocarcinomas Using Deep Learning Fabian Hörst, Saskia Ting, Sven-Thorsten Liffers, Kelsey L. Pomykala, Katja Steiger, Markus Albertsmeier, Marting K. Angele, Sylvie Lorenzen, Michael Quante, Wilko Weichert, Jan Egger, Jens T. Siveke, Jens Kleesiek 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 Evaluation of thresholding methods for the quantifcation of 68Ga‑PSMA‑11 PET molecular tumor volume and their efect on survival prediction in patients with advanced prostate cancer undergoing 177Lu‑PSMA‑617 radioligand therapy Moon-Sung Kim, Robert Seifert, Jana Fragemann, David Kersting, Jacob M. Murray, Frederic Jonske, Kelsey L. Pomykala, Jan Egger, Wolfgang P. Fendler, Ken Herrmann, Jens Kleesiek European Journal of Nuclear Medicine and Molecular Imaging 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 Lean Study Host: Towards an Automated Pipeline for Multi-Center Study Hosting Lukas Heine, Fabian Hörst, Enrico Nasca, Jens T. Siveke, Jan Egger, Moon-Sung Kim, Fin Hendrik Bahnsen, Jens Kleesiek Proceedings of the 57th Hawaii International Conference on System Sciences 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 'A net for everyone': fully personalized and unsupervised neural networks trained with longitudinal data from a single patient Christian Strack, Kelsey L. Pomykala, Heinz-Peter Schlemmer, Jan Egger, Jens Kleesiek arXiv Valuing Vicinity: Memory attention framework for context-based semantic segmentation in histopathology Oliver Ester, Fabian Hörst, Constantin Seibold, Julius Keyl, Saskia Ting, Nikolaos Vasileiadis, Jessica Schmitz, Philipp Ivanyi, Viktor Grünwald, Jan Hinrich Bräsen, Jan Egger, Jens Kleesiek 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 Deep Learning–driven classification of external DICOM studies for PACS archiving Frederic Jonske, Maximilian Dederichs, Moon-Sung Kim, Julius Keyl, Jan Egger, Lale Umutlu, Michael Forsting, Felix Nensa, Jens Kleesiek European Radiology 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 k-strip: A novel segmentation algorithm in k-space for the application of skull stripping Moritz Rempe, Florian Mentzel, Kelsey L. Pomykala, Johannes Haubold, Felix Nensa, Kevin Kröninger, Jan Egger, Jens Kleesiek 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 Review of Disentanglement Approaches for Medical Applications: Towards Solving the Gordian Knot of Generative Models in Healthcare Jana Fragemann, Lynton Ardizzone, Jan Egger, Jens Kleesiek, Mad Workshop Stochastic Modeling of Inhomogeneities in the Aortic Wall and Uncertainty Quantification using a Bayesian Encoder-Decoder Surrogate Sascha Ranftl, Malte Rolf-Pissarczyk, Gloria Wolkerstorfer, Antonio Pepe, Jan Egger, Wolfgang von der Linden, Gerhard A. Holzapfel 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 Beyond Medical Imaging-A Review of Multimodal Deep Learning in Radiology Lars Heiliger, Anjany Sekuboyina, Björn Menze, Jan Egger, Jens Kleesiek TechRxiv 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 Studierfenster: an Open Science Cloud-Based Medical Imaging Analysis Platform Jan Egger, Daniel Wild, Maximilian Weber, Christopher A. Ramirez Bedoya, Florian Karner, Alexander Prutsch, Michael Schmied, Christina Dionysio, Dominik Krobath, Yuan Jin

2021

Computer-Aided Oral and Maxillofacial Surgery: Developments, Applications, and Future Perspectives Jan Egger, Xiaojun Chen Academic Press 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 patch-based-approach for aortic landmarking Michael Schmied, Antonio Pepe, Jan Egger Medical Imaging 2021: Biomedical Applications in Molecular, Structural, and Functional Imaging 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 Augmented reality in oral and maxillofacial surgery Christina Gsaxner, Ulrich Eck, Dieter Schmalstieg, Nassir Navab, Jan Egger Computer-Aided Oral and Maxillofacial Surgery 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 Deep learning and generative adversarial networks in oral and maxillofacial surgery Antonio Pepe, Gianpaolo Francesco Trotta, Christina Gsaxner, Antonio Brunetti, Giacomo Donato Cascarano, Vitoantonio Bevilacqua, Dinggang Shen, Jan Egger 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 Effects of Pre-Operative Risk Factors on Intensive Care Unit Length of Stay (ICU-LOS) in Major Oral and Maxillofacial Cancer Surgery Juergen Wallner, Michael Schwaiger, Sarah-Jayne Edmondson, Irene Mischak, Jan Egger, Matthias Feichtinger, Wolfgang Zemann, Mauro Pau 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 PCA-Skull: 3D Skull Shape Modelling Using Principal Component Analysis Lei Yu, Jianning Li, Jan Egger Cranial Implant Design Challenge Radiomics in head and neck cancer Maria Gonçalves, Christina Gsaxner, Jan Egger, Victor Alves Computer-Aided Oral and Maxillofacial Surgery 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

2020

Towards the automatization of cranial implant design in cranioplasty Jianning Li, Jan Egger Cham: Springer