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Jan has over 10 years of experience in developing algorithms in medical image analysis and image-guided therapies, including five 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 (http://www.studierfenster.at) and MedShapeNet (https://medshapenet.ikim.nrw), 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 is Professor and holds a Ph.D. and a (German) Habilitation in Computer Science, and an interdisciplinary Ph.D. in Human Biology. Currently, Jan has a dual appointment at the Institute for Artificial Intelligence in Medicine (IKIM) at the Essen University Hospital (UKE) in Germany and the Institute of Computer Graphics and Vision (ICG) of the Graz University of Technology (TU Graz) in Austria, and he is a Privatdozent in AI in Medicine.
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Identification

Personal identification

Full name
Jan Egger

Citation names

  • Egger, Jan

Author identifiers

Ciência ID
6617-7E32-1916
ORCID iD
0000-0002-5225-1982

Knowledge fields

  • Exact Sciences - Computer and Information Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
German (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Affiliation

Science

Category
Host institution 		Employer
2021/08/01 - Current Researcher (Research) Universitätsklinikum Essen, Germany
Universität Duisburg-Essen - Campus Essen, Germany
Outputs

Publications

Book chapter
  1. Gian Marco Melito; Antonio Pepe; Alireza Jafarinia; Thomas Krispel; Jan Egger. "Optimizing Aortic Segmentation with an Innovative Quality Assessment: The Role of Global Sensitivity Analysis". 2024.
    10.1007/978-3-031-53241-2_9
  2. Fabian Hörst; Sajad H. Schaheer; Giulia Baldini; Fin H. Bahnsen; Jan Egger; Jens Kleesiek. "Accelerating Artificial Intelligence-based Whole Slide Image Analysis with an Optimized Preprocessing Pipeline". 2024.
    10.1007/978-3-658-44037-4_91
  3. Antonio Pepe; Gabriel Mistelbauer; Christina Gsaxner; Jianning Li; Dominik Fleischmann; Dieter Schmalstieg; Jan Egger. "Semi-supervised Virtual Regression of Aortic Dissections Using 3D Generative Inpainting". 2020.
    10.1007/978-3-030-62469-9_12
  4. Jianning Li; Jan Egger. "Dataset Descriptor for the AutoImplant Cranial Implant Design Challenge". 2020.
    10.1007/978-3-030-64327-0_2
  5. Yuan Jin; Jianning Li; Jan Egger. "High-Resolution Cranial Implant Prediction via Patch-Wise Training". 2020.
    10.1007/978-3-030-64327-0_11
  6. Matthias Eder; Jianning Li; Jan Egger. "Learning Volumetric Shape Super-Resolution for Cranial Implant Design". 2020.
    10.1007/978-3-030-64327-0_12
  7. Jianning Li; Antonio Pepe; Christina Gsaxner; Gord von Campe; Jan Egger. "A Baseline Approach for AutoImplant: The MICCAI 2020 Cranial Implant Design Challenge". 2020.
    10.1007/978-3-030-60946-7_8
  8. Mauro Sylos Labini; Christina Gsaxner; Antonio Pepe; Juergen Wallner; Jan Egger; Vitoantonio Bevilacqua. "Depth-Awareness in a System for Mixed-Reality Aided Surgical Procedures". 2019.
    10.1007/978-3-030-26766-7_65
  9. Christina Gsaxner; Antonio Pepe; Jürgen Wallner; Dieter Schmalstieg; Jan Egger. "Markerless Image-to-Face Registration for Untethered Augmented Reality in Head and Neck Surgery". 2019.
    10.1007/978-3-030-32254-0_27
Journal article
  1. Ila Motmaen; Kunpeng Xie; Leon Schönbrunn; Jeff Berens; Kim Grunert; Anna Maria Plum; Johannes Raufeisen; et al. "Insights into Predicting Tooth Extraction from Panoramic Dental Images: Artificial Intelligence vs. Dentists". Clinical Oral Investigations (2024): https://doi.org/10.1007/s00784-024-05781-5.
    10.1007/s00784-024-05781-5
  2. Claire Melchior; Peter Isfort; Till Braunschweig; Max Witjes; Vincent Van den Bosch; Ashkan Rashad; Jan Egger; et al. "Development and validation of a cadaveric porcine pseudotumor model for oral cancer biopsy and resection training". BMC Medical Education (2024): https://doi.org/10.1186/s12909-024-05224-5.
    10.1186/s12909-024-05224-5
  3. Jianning Li; Amin Dada; Behrus Puladi; Jens Kleesiek; Jan Egger. "ChatGPT in healthcare: A taxonomy and systematic review". Computer Methods and Programs in Biomedicine (2024): https://doi.org/10.1016/j.cmpb.2024.108013.
    10.1016/j.cmpb.2024.108013
  4. Jasper J.E. Moors; Zhibin Xu; Kunpeng Xie; Ashkan Rashad; Jan Egger; Rainer Röhrig; Frank Hölzle; Behrus Puladi. "Full-thickness skin graft versus split-thickness skin graft for radial forearm free flap donor site closure: protocol for a systematic review and meta-analysis". Systematic Reviews (2024): https://doi.org/10.1186/s13643-024-02471-x.
    10.1186/s13643-024-02471-x
  5. Malik Sallam; Amwaj Al-Farajat; Jan Egger. "Envisioning the Future of ChatGPT in Healthcare: Insights and Recommendations from a Systematic Identification of Influential Research and a Call for Papers". Jordan Medical Journal (2024): https://doi.org/10.35516/jmj.v58i1.2285.
    10.35516/jmj.v58i1.2285
  6. Jan Egger; Christina Gsaxner; Jens Kleesiek; Behrus Puladi. "What is Diminished Virtuality? A Directional and Layer-Based Taxonomy for the Reality-Virtuality Continuum". JMIR XR and Spatial Computing (2024): https://doi.org/10.2196/52904.
    10.2196/52904
  7. Claudius Melzig; Sibylle Hartmann; Andrea Steuwe; Jan Egger; Thuy D. Do; Philipp Geisbüsch; Hans-Ulrich Kauczor; Fabian Rengier; Matthias A. Fink. "BMI-Adapted Double Low-Dose Dual-Source Aortic CT for Endoleak Detection after Endovascular Repair: A Prospective Intra-Individual Diagnostic Accuracy Study". Diagnostics (2024): https://doi.org/10.3390/diagnostics14030280.
    10.3390/diagnostics14030280
  8. Moritz Rempe; Florian Mentzel; Kelsey L. Pomykala; Johannes Haubold; Felix Nensa; Kevin Kroeninger; Jan Egger; Jens Kleesiek. "k-strip: A novel segmentation algorithm in k-space for the application of skull stripping". Computer Methods and Programs in Biomedicine (2024): https://doi.org/10.1016/j.cmpb.2023.107912.
    10.1016/j.cmpb.2023.107912
  9. Timo van Meegdenburg; Jens Kleesiek; Jan Egger; Sören Perrey. "Improvement in Disease Diagnosis in Computed Tomography Images by Correlating Organ Volumes with Disease Occurrences in Humans". BioMedInformatics (2023): https://doi.org/10.3390/biomedinformatics3030036.
    10.3390/biomedinformatics3030036
  10. Jiangchang Xu; Bolun Zeng; Jan Egger; Chunliang Wang; Örjan Smedby; Xiaoyi Jiang; Xiaojun Chen. "A review on AI-based medical image computing in head and neck surgery". Physics in Medicine & Biology (2022): https://doi.org/10.1088/1361-6560/ac840f.
    10.1088/1361-6560/ac840f
  11. Jan Egger; Christina Gsaxner; Antonio Pepe; Kelsey L. Pomykala; Frederic Jonske; Manuel Kurz; Jianning Li; Jens Kleesiek. "Medical deep learning—A systematic meta-review". Computer Methods and Programs in Biomedicine (2022): https://doi.org/10.1016/j.cmpb.2022.106874.
    10.1016/j.cmpb.2022.106874
  12. Gonçalves, Maria; Gsaxner, Christina; Ferreira, André; Li, Jianning; Puladi, Behrus; Kleesiek, Jens; Egger, Jan; Alves, Victor. "Radiomics in head and neck cancer outcome predictions". (2022): https://hdl.handle.net/1822/81081.
    10.3390/diagnostics12112733
  13. Juergen Wallner; Michael Schwaiger; Sarah-Jayne Edmondson; Irene Mischak; Jan Egger; Matthias Feichtinger; Wolfgang Zemann; Mauro Pau. "Effects of Pre-Operative Risk Factors on Intensive Care Unit Length of Stay (ICU-LOS) in Major Oral and Maxillofacial Cancer Surgery". Cancers (2021): https://doi.org/10.3390/cancers13163937.
    10.3390/cancers13163937
  14. Christina Gsaxner; Antonio Pepe; Jianning Li; Una Ibrahimpasic; Jürgen Wallner; Dieter Schmalstieg; Jan Egger. "Augmented Reality for Head and Neck Carcinoma Imaging: Description and Feasibility of an Instant Calibration, Markerless Approach". Computer Methods and Programs in Biomedicine (2021): https://doi.org/10.1016/j.cmpb.2020.105854.
    10.1016/j.cmpb.2020.105854
  15. Li, Jianning; Gsaxner, Christina; Pepe, Antonio; Morais, Ana; Alves, Victor; von Campe, Gord; Wallner, Juergen; Egger, Jan. "Synthetic skull bone defects for automatic patient-specific craniofacial implant design". (2021): https://hdl.handle.net/1822/78113.
    10.1038/s41597-021-00806-0
  16. Li, Jianning; Pimentel, Pedro; Szengel, Angelika; Ehlke, Moritz; Lamecker, Hans; Zachow, Stefan; Estacio, Laura; et al. "AutoImplant 2020 - First MICCAI Challenge on Automatic Cranial Implant Design". (2021): https://hdl.handle.net/1822/78123.
    10.1109/tmi.2021.3077047
  17. Christina Gsaxner; Abir Jaafar Hussain; Peter M. Roth; Jürgen Wallner; Jan Egger. "Exploit fully automatic low-level segmented PET data for training high-level deep learning algorithms for the corresponding CT data". PLOS ONE (2019): https://doi.org/10.1371/journal.pone.0212550.
    10.1371/journal.pone.0212550
  18. Jan Egger; Jose Manuel Garcia Aznar; Jürgen Wallner; Markus Gall; Xiaojun Chen; Katja Schwenzer-Zimmerer; Knut Reinbacher; Dieter Schmalstieg. "Computer-aided position planning of miniplates to treat facial bone defects". PLOS ONE (2017): https://doi.org/10.1371/journal.pone.0182839.
    10.1371/journal.pone.0182839
Preprint
  1. Ila Motmaen; Kunpeng Xie; Leon Schönbrunn; Jeff Berens; Kim Grunert; Anna Maria Plum; Johannes Raufeisen; et al. "Insights into Predicting Tooth Extraction from Panoramic Dental Images: Artificial Intelligence vs. Dentists". 2024. https://doi.org/10.1101/2024.04.22.24306189.
    10.1101/2024.04.22.24306189
  2. Jan Egger; Christina Gsaxner; Jens Kleesiek; Behrus Puladi. "What is Diminished Virtuality? A Directional and Layer-Based Taxonomy for the Reality-Virtuality Continuum (Preprint)". 2023. https://doi.org/10.2196/preprints.52904.
    10.2196/preprints.52904
  3. Jianning Li; David G Ellis; Antonio Pepe; Christina Gsaxner; Michele R. Aizenberg; Jens Kleesiek; Jan Egger. "Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model". 2022. https://doi.org/10.36227/techrxiv.19582846.
    10.36227/techrxiv.19582846
  4. Jianning Li; David G Ellis; Antonio Pepe; Christina Gsaxner; Michele R. Aizenberg; Jens Kleesiek; Jan Egger. "Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model". 2022. https://doi.org/10.36227/techrxiv.19582846.v1.
    10.36227/techrxiv.19582846.v1
  5. Jianning Li; Christina Gsaxner; Antonio Pepe; Dieter Schmalstieg; Jens Kleesiek; Jan Egger. "Sparse Convolutional Neural Networks for Medical Image Analysis". 2022. https://doi.org/10.36227/techrxiv.19137518.v2.
    10.36227/techrxiv.19137518.v2
  6. Jana Fragemann; Lynton Ardizzone; Jan Egger; Jens Kleesiek; Mad Workshop. "Review of Disentanglement Approaches for Medical Applications: Towards Solving the Gordian Knot of Generative Models in Healthcare". 2022. https://doi.org/10.36227/techrxiv.19364897.
    10.36227/techrxiv.19364897
  7. Jana Fragemann; Lynton Ardizzone; Jan Egger; Jens Kleesiek; Mad Workshop. "Review of Disentanglement Approaches for Medical Applications: Towards Solving the Gordian Knot of Generative Models in Healthcare". 2022. https://doi.org/10.36227/techrxiv.19364897.v1.
    10.36227/techrxiv.19364897.v1
  8. Lars Heiliger; Anjany Sekuboyina; Bjoern Menze; Jan Egger; Jens Kleesiek. "Beyond Medical Imaging - A Review of Multimodal Deep Learning in Radiology". 2022. https://doi.org/10.36227/techrxiv.19103432.
    10.36227/techrxiv.19103432
  9. Jianning Li; Christina Gsaxner; Antonio Pepe; Dieter Schmalstieg; Jens Kleesiek; Jan Egger. "Sparse Convolutional Neural Networks for Medical Image Analysis". 2022. https://doi.org/10.36227/techrxiv.19137518.
    10.36227/techrxiv.19137518
  10. Jianning Li; Christina Gsaxner; Antonio Pepe; Dieter Schmalstieg; Jens Kleesiek; Jan Egger. "Sparse Convolutional Neural Networks for Medical Image Analysis". 2022. https://doi.org/10.36227/techrxiv.19137518.v1.
    10.36227/techrxiv.19137518.v1
  11. Lars Heiliger; Anjany Sekuboyina; Bjoern Menze; Jan Egger; Jens Kleesiek. "Beyond Medical Imaging - A Review of Multimodal Deep Learning in Radiology". 2022. https://doi.org/10.36227/techrxiv.19103432.v1.
    10.36227/techrxiv.19103432.v1
Thesis / Dissertation
  1. Morais, Ana Rita André. "Automated computer-aided design of cranial implants: a deep learning approach". Master, 2018. https://hdl.handle.net/1822/64157.

Other

Other output
  1. Automated computer-aided design of cranial implants using a deep volumetric convolutional denoising autoencoder. Computer-aided Design (CAD) software enables the design of patient-specific cranial implants, but it often requires of a lot of manual user-interactions. This paper proposes a Deep Learning (DL) approach towards the automated CAD of cranial implants, allowing the design process to be less user-dependent and even less time-consuming. The problem of reconstructing a cranial defect, which is essentia. 2019. Morais, Ana; Egger, Jan; Alves, Victor. http://hdl.handle.net/1822/71391.
    10.1007/978-3-030-16187-3_15
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023 - 2023 Capacities of Machine and Deep Learning: Importance of an unlimited source of highquality data for medical tasks
Co-supervisor
 Engenharia Biomédica (PhD)
Universidade do Minho, Portugal