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Virtual and Augmented Reality Module for 3D Reconstruction

Virtual and Augmented Reality Module for 3D Reconstruction

Jan Egger (ORCID: 0000-0002-5225-1982)
  • Grant DOI 10.55776/KLI678
  • Funding program Clinical Research
  • Status ended
  • Start July 1, 2018
  • End September 30, 2021
  • Funding amount € 360,486
  • Project website

Disciplines

Computer Sciences (10%); Clinical Medicine (40%); Medical Engineering (30%); Environmental Engineering, Applied Geosciences (20%)

Keywords

    Maxillofacial Surgery, Bone Defect Reconstruction, Segmentation, Navigation, Augmented and Virtual Reality, 3D Printed Implant

Abstract Final report

This interdisciplinary research project between computer science and medicine targets the development of a comprehensive image-guided tool for head and neck surgery with the main focus on mandibular fractures and mid-facial fractures. The tool supports the physicians in all treatment stages (diagnosis, planning, intervention and monitoring) and can also be used during clinical traineeship. A key point is the development of an algorithm for the semi-automatic and automatic segmentation of bone structures and soft tissue in CT and MRI acquisitions. A segmentation enables a three-dimensional localization, quantification and visualization of biological structures in a very short time. Based on the radiological images from the clinical routine, treatment diagnosis can be visualized, and surgical planning processes or alternative surgery options can be simulated. In addition, the postoperative simulation results can be presented preoperatively in a photo-realistic manner. In particular, this will be applied in the reposition of bony structures, the reconstruction of facial defects and the removal of tumors in complex anatomical areas. Moreover, we plan the development of patient-individual three-dimensional implants, which will 3D printed in- house for comparison with the external manufactured ones and for clinical usage. Furthermore, the medical personnel can be supported in real-time during surgery by an interactive navigation, where Augmented Reality integrates computer-generated objects into the operation field. The application reduces surgical complications and ensures a successful treatment result by pre- and intraoperative simulations. Hence, the number of necessary corrective surgeries and the operation time needed can be reduced, and a higher patient survival rate can be achieved. In addition, the combination with Virtual Reality glasses allows the virtual training of operations during medical education. The objective of the project is the establishment of an open source tool as basis for further research and developments for the participating universities. Currently, comparable tools are protected by strict licensing conditions and not accessible without restrictions for academic research. Existing software for clinical practice is not functionally stable enough and has too high error rates. Additionally, the usage imposes high financial costs, which makes a widespread application not possible. Finally, Augmented Reality in the clinical routine is an important topic for current surgical research and cannot be ignored by modern medical universities.

In this interdisciplinary research project between computer science and medicine, image-supported tools for head and neck surgery were developed, which support physicians in all medical phases (diagnosis, operation planning, intervention and control), but can also be used in teaching. One aspect of the project was the development of algorithms for the semi-automatic and automatic segmentation of bony structures and soft tissue based on CT and MRI data sets. The segmentation enables the three-dimensional localization, quantification and visualization of anatomical structures in a short time. Based on radiological image data from the clinical routine, treatment plans can be quickly visualized, and surgical planning processes or operative treatment options can be simulated. This is mainly used in the repositioning of bony structures, in the reconstruction of facial defects and in the removal of tumors in areas with complex anatomy. Furthermore, an augmented reality (AR) tool was developed with which the medical staff can be supported in real time by interactive visualization and navigation, even during an intervention. Using AR, virtual, computer-generated objects can be integrated into the real, physical surroundings. With the developed tool, anatomical structures and planning information are visualized directly on the patient, pre- or intra-operatively, and surgeons are guided interactively to the target anatomy. This can reduce surgical complications and ensure a successful treatment outcome. Consequently, the number of necessary corrective operations and the required operating time can be reduced. As part of the project, open-source applications were created as a basis for the further development at the participating universities. Similar applications are currently protected by strict licenses and are not fully accessible to academic research.

Research institution(s)
  • Technische Universität Graz - 100%
Project participants
  • Jan Egger, Medizinische Universität Graz , former principal investigator
  • Jürgen Wallner, Medizinische Universität Graz , former principal investigator
  • Dieter Schmalstieg, Technische Universität Graz , associated research partner
International project participants
  • Xiaojun Chen, Shanghai Jiao Tong University - China
  • Malgorzata Kolodziej, Justus-Liebig-Universität Gießen - Germany
  • Ti-Chiun Chang, Siemens Corporate Research - USA

Research Output

  • 1617 Citations
  • 76 Publications
  • 5 Datasets & models
Publications
  • 2024
    Title GAN-based generation of realistic 3D volumetric data: A systematic review and taxonomy.
    DOI 10.1016/j.media.2024.103100
    Type Other
    Author Ferreira A
    Pages 103100
  • 2024
    Title Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model.
    DOI 10.1007/s10916-024-02066-y
    Type Journal Article
    Author Ellis Dg
    Journal Journal of medical systems
    Pages 55
  • 2020
    Title A Baseline Approach for AutoImplant: the MICCAI 2020 Cranial Implant Design Challenge
    DOI 10.48550/arxiv.2006.12449
    Type Preprint
    Author Li J
  • 2020
    Title Biofunctional Glycol-Modified Polyethylene Terephthalate and Thermoplastic Polyurethane Implants by Extrusion-Based Additive Manufacturing for Medical 3D Maxillofacial Defect Reconstruction
    DOI 10.3390/polym12081751
    Type Journal Article
    Author Katschnig M
    Journal Polymers
    Pages 1751
    Link Publication
  • 2020
    Title Design and Development of a Web-based Tool for Inpainting of Dissected Aortae in Angiography Images
    DOI 10.48550/arxiv.2005.02760
    Type Preprint
    Author Prutsch A
  • 2020
    Title An Online Platform for Automatic Skull Defect Restoration and Cranial Implant Design
    DOI 10.48550/arxiv.2006.00980
    Type Preprint
    Author Li J
  • 2020
    Title A Baseline Approach for AutoImplant: The MICCAI 2020 Cranial Implant Design Challenge
    DOI 10.1007/978-3-030-60946-7_8
    Type Book Chapter
    Author Li J
    Publisher Springer Nature
    Pages 75-84
  • 2020
    Title Detection, segmentation, simulation and visualization of aortic dissections: A review
    DOI 10.1016/j.media.2020.101773
    Type Journal Article
    Author Pepe A
    Journal Medical Image Analysis
    Pages 101773
  • 2020
    Title Semi-supervised Virtual Regression of Aortic Dissections Using 3D Generative Inpainting
    DOI 10.1007/978-3-030-62469-9_12
    Type Book Chapter
    Author Pepe A
    Publisher Springer Nature
    Pages 130-140
  • 2020
    Title Augmented Reality for Head and Neck Carcinoma Imaging: Description and Feasibility of an Instant Calibration, Markerless Approach
    DOI 10.1016/j.cmpb.2020.105854
    Type Journal Article
    Author Gsaxner C
    Journal Computer Methods and Programs in Biomedicine
    Pages 105854
  • 2020
    Title Single-Shot Deep Volumetric Regression for Mobile Medical Augmented Reality
    DOI 10.1007/978-3-030-60946-7_7
    Type Book Chapter
    Author Karner F
    Publisher Springer Nature
    Pages 64-74
  • 2020
    Title High-Resolution Cranial Implant Prediction via Patch-Wise Training
    DOI 10.1007/978-3-030-64327-0_11
    Type Book Chapter
    Author Jin Y
    Publisher Springer Nature
    Pages 94-103
  • 2020
    Title Dataset Descriptor for the AutoImplant Cranial Implant Design Challenge
    DOI 10.1007/978-3-030-64327-0_2
    Type Book Chapter
    Author Li J
    Publisher Springer Nature
    Pages 10-15
  • 2019
    Title Depth-Awareness in a System for Mixed-Reality Aided Surgical Procedures
    DOI 10.1007/978-3-030-26766-7_65
    Type Book Chapter
    Author Sylos Labini M
    Publisher Springer Nature
    Pages 716-726
  • 2019
    Title Exploit fully automatic low-level segmented PET data for training high-level deep learning algorithms for the corresponding CT data
    DOI 10.48550/arxiv.1903.02871
    Type Preprint
    Author Gsaxner C
  • 2019
    Title Client/Server Based Online Environment for Manual Segmentation of Medical Images
    DOI 10.48550/arxiv.1904.08610
    Type Preprint
    Author Wild D
  • 2019
    Title Facial model collection for medical augmented reality in oncologic cranio-maxillofacial surgery
    DOI 10.1038/s41597-019-0327-8
    Type Journal Article
    Author Gsaxner C
    Journal Scientific Data
    Pages 310
    Link Publication
  • 2022
    Title AVT: Multicenter aortic vessel tree CTA dataset collection with ground truth segmentation masks
    DOI 10.1016/j.dib.2022.107801
    Type Journal Article
    Author Radl L
    Journal Data in Brief
    Pages 107801
    Link Publication
  • 2022
    Title Studierfenster: an Open Science Cloud-Based Medical Imaging Analysis Platform
    DOI 10.1007/s10278-021-00574-8
    Type Journal Article
    Author Egger J
    Journal Journal of Digital Imaging
    Pages 340-355
    Link Publication
  • 2022
    Title k-strip: A novel segmentation algorithm in k-space for the application of skull stripping
    DOI 10.48550/arxiv.2205.09706
    Type Preprint
    Author Rempe M
  • 2022
    Title Medical deep learning—A systematic meta-review
    DOI 10.1016/j.cmpb.2022.106874
    Type Journal Article
    Author Egger J
    Journal Computer Methods and Programs in Biomedicine
    Pages 106874
    Link Publication
  • 2022
    Title Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model
    DOI 10.48550/arxiv.2204.05703
    Type Preprint
    Author Li J
  • 2022
    Title Radiomics in head and neck cancer outcome predictions
    DOI 10.18154/rwth-conv-250627
    Type Other
    Author Gonçalves M
    Link Publication
  • 2022
    Title Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model
    DOI 10.36227/techrxiv.19582846
    Type Preprint
    Author Ellis D
  • 2019
    Title Automated Computer-aided Design of Cranial Implants Using a Deep Volumetric Convolutional Denoising Autoencoder
    DOI 10.1007/978-3-030-16187-3_15
    Type Book Chapter
    Author Morais A
    Publisher Springer Nature
    Pages 151-160
  • 2019
    Title A Client/Server based Online Environment for the Calculation of Medical Segmentation Scores
    DOI 10.1109/embc.2019.8856481
    Type Conference Proceeding Abstract
    Author Weber M
    Pages 3463-3467
  • 2019
    Title Using Synthetic Training Data for Deep Learning-Based GBM Segmentation
    DOI 10.1109/embc.2019.8856297
    Type Conference Proceeding Abstract
    Author Lindner L
    Pages 6724-6729
  • 2021
    Title Inside-Out Instrument Tracking for Surgical Navigation in Augmented Reality
    DOI 10.1145/3489849.3489863
    Type Conference Proceeding Abstract
    Author Gsaxner C
    Pages 1-11
  • 2021
    Title Deep learning—a first meta-survey of selected reviews across scientific disciplines, their commonalities, challenges and research impact
    DOI 10.7717/peerj-cs.773
    Type Journal Article
    Author Egger J
    Journal PeerJ Computer Science
    Link Publication
  • 2021
    Title Learning to Rearrange Voxels in Binary Segmentation Masks for Smooth Manifold Triangulation
    DOI 10.1007/978-3-030-92652-6_5
    Type Book Chapter
    Author Li J
    Publisher Springer Nature
    Pages 45-62
  • 2021
    Title MUG500+: Database of 500 high-resolution healthy human skulls and 29 craniotomy skulls and implants
    DOI 10.1016/j.dib.2021.107524
    Type Journal Article
    Author Li J
    Journal Data in Brief
    Pages 107524
    Link Publication
  • 2021
    Title Effects of Pre-Operative Risk Factors on Intensive Care Unit Length of Stay (ICU-LOS) in Major Oral and Maxillofacial Cancer Surgery
    DOI 10.3390/cancers13163937
    Type Journal Article
    Author Wallner J
    Journal Cancers
    Pages 3937
    Link Publication
  • 2020
    Title Deep Learning -- A first Meta-Survey of selected Reviews across Scientific Disciplines, their Commonalities, Challenges and Research Impact
    DOI 10.48550/arxiv.2011.08184
    Type Preprint
    Author Egger J
  • 2020
    Title A review on the applications of virtual reality, augmented reality and mixed reality in surgical simulation: an extension to different kinds of surgery
    DOI 10.1080/17434440.2021.1860750
    Type Journal Article
    Author Lungu A
    Journal Expert Review of Medical Devices
    Pages 47-62
  • 2023
    Title Why does my medical AI look at pictures of birds? Exploring the efficacy of transfer learning across domain boundaries
    DOI 10.48550/arxiv.2306.17555
    Type Other
    Author Jonske F
    Link Publication
  • 2022
    Title The HoloLens in Medicine: A systematic Review and Taxonomy
    DOI 10.48550/arxiv.2209.03245
    Type Preprint
    Author Gsaxner C
  • 2018
    Title Pattern Recognition and Mixed Reality for Computer-Aided Maxillofacial Surgery and Oncological Assessment
    DOI 10.1109/bmeicon.2018.8609921
    Type Conference Proceeding Abstract
    Author Pepe A
    Pages 1-5
  • 2024
    Title Brain Tumour Removing and Missing Modality Generation using 3D WDM
    DOI 10.48550/arxiv.2411.04630
    Type Preprint
    Author Ferreira A
    Link Publication
  • 2024
    Title Improved Multi-Task Brain Tumour Segmentation with Synthetic Data Augmentation
    DOI 10.48550/arxiv.2411.04632
    Type Preprint
    Author Ferreira A
    Link Publication
  • 2024
    Title k-strip: A novel segmentation algorithm in k-space for the application of skull stripping.
    DOI 10.1016/j.cmpb.2023.107912
    Type Journal Article
    Author Mentzel F
    Journal Computer methods and programs in biomedicine
    Pages 107912
  • 2023
    Title The HoloLens in medicine: A systematic review and taxonomy.
    DOI 10.1016/j.media.2023.102757
    Type Other
    Author Gsaxner C
    Pages 102757
  • 2022
    Title Gender-specific differences in haemostatic parameters and their influence on blood loss in bimaxillary surgery
    DOI 10.1007/s00784-021-04347-z
    Type Journal Article
    Author Schwaiger M
    Journal Clinical Oral Investigations
    Pages 3765-3779
    Link Publication
  • 2022
    Title Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model
    DOI 10.36227/techrxiv.19582846.v1
    Type Preprint
    Author Ellis D
  • 2022
    Title Radiomics in Head and Neck Cancer Outcome Predictions
    DOI 10.3390/diagnostics12112733
    Type Journal Article
    Author Gonçalves M
    Journal Diagnostics
    Pages 2733
    Link Publication
  • 2022
    Title Open-Source Skull Reconstruction with MONAI
    DOI 10.48550/arxiv.2211.14051
    Type Preprint
    Author Li J
  • 2021
    Title AI-based Aortic Vessel Tree Segmentation for Cardiovascular Diseases Treatment: Status Quo
    DOI 10.48550/arxiv.2108.02998
    Type Preprint
    Author Jin Y
  • 2021
    Title Synthetic skull bone defects for automatic patient-specific craniofacial implant design
    DOI 10.1038/s41597-021-00806-0
    Type Journal Article
    Author Li J
    Journal Scientific Data
    Pages 36
    Link Publication
  • 2021
    Title AutoImplant 2020-First MICCAI Challenge on Automatic Cranial Implant Design
    DOI 10.1109/tmi.2021.3077047
    Type Journal Article
    Author Li J
    Journal IEEE Transactions on Medical Imaging
    Pages 2329-2342
  • 2018
    Title Human upper-body inverse kinematics for increased embodiment in consumer-grade virtual reality
    DOI 10.1145/3281505.3281529
    Type Conference Proceeding Abstract
    Author Parger M
    Pages 1-10
  • 2018
    Title PET-Train: Automatic Ground Truth Generation from PET Acquisitions for Urinary Bladder Segmentation in CT Images using Deep Learning
    DOI 10.1109/bmeicon.2018.8609954
    Type Conference Proceeding Abstract
    Author Gsaxner C
    Pages 1-5
  • 2018
    Title Clinical evaluation of semi-automatic opensource algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action
    DOI 10.48550/arxiv.1805.08604
    Type Preprint
    Author Wallner J
  • 2018
    Title Anatomy of the Le Fort I segment: Are arterial variations a potential risk factor for avascular bone necrosis in Le Fort I osteotomies?
    DOI 10.1016/j.jcms.2018.04.023
    Type Journal Article
    Author Bruneder S
    Journal Journal of Cranio-Maxillofacial Surgery
    Pages 1285-1295
  • 2018
    Title Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action
    DOI 10.1371/journal.pone.0196378
    Type Journal Article
    Author Wallner J
    Journal PLOS ONE
    Link Publication
  • 2023
    Title Open-source skull reconstruction with MONAI
    DOI 10.18154/rwth-conv-252675
    Type Other
    Author Ferreira A
    Link Publication
  • 2023
    Title Open-source skull reconstruction with MONAI
    DOI 10.1016/j.softx.2023.101432
    Type Journal Article
    Author Ferreira A
    Journal SoftwareX
  • 2023
    Title Automated cross-sectional view selection in CT angiography of aortic dissections with uncertainty awareness and retrospective clinical annotations.
    DOI 10.1016/j.compbiomed.2023.107365
    Type Journal Article
    Author Egger J
    Journal Computers in biology and medicine
    Pages 107365
  • 2021
    Title Automatic skull defect restoration and cranial implant generation for cranioplasty
    DOI 10.1016/j.media.2021.102171
    Type Journal Article
    Author Li J
    Journal Medical Image Analysis
    Pages 102171
  • 2021
    Title Learning to Rearrange Voxels in Binary Segmentation Masks for Smooth Manifold Triangulation
    DOI 10.48550/arxiv.2108.05269
    Type Preprint
    Author Li J
  • 2021
    Title A review on patient-specific facial and cranial implant design using Artificial Intelligence (AI) techniques
    DOI 10.1080/17434440.2021.1969914
    Type Journal Article
    Author Memon A
    Journal Expert Review of Medical Devices
    Pages 985-994
  • 2021
    Title An online platform for automatic skull defect restoration and cranial implant design
    DOI 10.1117/12.2580719
    Type Conference Proceeding Abstract
    Author Li J
    Pages 59
    Link Publication
  • 2021
    Title SkullBreak / SkullFix – Dataset for automatic cranial implant design and a benchmark for volumetric shape learning tasks
    DOI 10.1016/j.dib.2021.106902
    Type Journal Article
    Author Kodym O
    Journal Data in Brief
    Pages 106902
    Link Publication
  • 2021
    Title Sparse Convolutional Neural Network for Skull Reconstruction
    DOI 10.1007/978-3-030-92652-6_7
    Type Book Chapter
    Author Kroviakov A
    Publisher Springer Nature
    Pages 80-94
  • 2021
    Title PCA-Skull: 3D Skull Shape Modelling Using Principal Component Analysis
    DOI 10.1007/978-3-030-92652-6_9
    Type Book Chapter
    Author Yu L
    Publisher Springer Nature
    Pages 105-115
  • 2021
    Title Automated cross-sectional view selection in CT angiography of aortic dissections with uncertainty awareness and retrospective clinical annotations
    DOI 10.48550/arxiv.2111.11269
    Type Preprint
    Author Pepe A
  • 2020
    Title Towards the Automatization of Cranial Implant Design in Cranioplasty - First Challenge, AutoImplant 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 8, 2020, Proceedings
    DOI 10.1007/978-3-030-64327-0
    Type Book
    editors Li J, Egger J
    Publisher Springer International Publishing
  • 2020
    Title Medical Deep Learning -- A systematic Meta-Review
    DOI 10.48550/arxiv.2010.14881
    Type Preprint
    Author Egger J
  • 2020
    Title Differences in adhesion between 1C-PUR and MUF wood adhesives to (ligno)cellulosic surfaces revealed by nanoindentation
    DOI 10.1016/j.ijadhadh.2019.102507
    Type Journal Article
    Author Herzele S
    Journal International Journal of Adhesion and Adhesives
    Pages 102507
    Link Publication
  • 2020
    Title A review on computer-aided design and manufacturing of patient-specific maxillofacial implants
    DOI 10.1080/17434440.2020.1736040
    Type Journal Article
    Author Memon A
    Journal Expert Review of Medical Devices
    Pages 345-356
    Link Publication
  • 2016
    Title Drug trapping in hERG K + channels: (not) a matter of drug size?
    DOI 10.1039/c5md00443h
    Type Journal Article
    Author Linder T
    Journal MedChemComm
    Pages 512-518
    Link Publication
  • 2019
    Title A review on multiplatform evaluations of semi-automatic open-source based image segmentation for cranio-maxillofacial surgery
    DOI 10.1016/j.cmpb.2019.105102
    Type Journal Article
    Author Wallner J
    Journal Computer Methods and Programs in Biomedicine
    Pages 105102
  • 2019
    Title A Marker-Less Registration Approach for Mixed Reality–Aided Maxillofacial Surgery: a Pilot Evaluation
    DOI 10.1007/s10278-019-00272-6
    Type Journal Article
    Author Pepe A
    Journal Journal of Digital Imaging
    Pages 1008-1018
    Link Publication
  • 2019
    Title Markerless Image-to-Face Registration for Untethered Augmented Reality in Head and Neck Surgery
    DOI 10.1007/978-3-030-32254-0_27
    Type Book Chapter
    Author Gsaxner C
    Publisher Springer Nature
    Pages 236-244
  • 2019
    Title Computed tomography data collection of the complete human mandible and valid clinical ground truth models
    DOI 10.1038/sdata.2019.3
    Type Journal Article
    Author Wallner J
    Journal Scientific Data
    Pages 190003
    Link Publication
  • 2019
    Title Exploit fully automatic low-level segmented PET data for training high-level deep learning algorithms for the corresponding CT data
    DOI 10.1371/journal.pone.0212550
    Type Journal Article
    Author Gsaxner C
    Journal PLOS ONE
    Link Publication
  • 2019
    Title Free thoracodorsal, perforator-scapular flap based on the angular artery (TDAP-Scap-aa): Clinical experiences and description of a novel technique for single flap reconstruction of extensive oromandibular defects
    DOI 10.1016/j.jcms.2019.07.021
    Type Journal Article
    Author Pau M
    Journal Journal of Cranio-Maxillofacial Surgery
    Pages 1617-1625
  • 2016
    Title Uncertainty budgeting in fold change determination and implications for non-targeted metabolomics studies in model systems
    DOI 10.1039/c6an01342b
    Type Journal Article
    Author Ortmayr K
    Journal Analyst
    Pages 80-90
Datasets & models
  • 2021 Link
    Title Metadata record for: Synthetic skull bone defects for automatic patient-specific craniofacial implant design
    DOI 10.6084/m9.figshare.13265225
    Type Database/Collection of data
    Public Access
    Link Link
  • 2021 Link
    Title MUG500+ Repository
    DOI 10.6084/m9.figshare.9616319.v19
    Type Database/Collection of data
    Public Access
    Link Link
  • 2020 Link
    Title Metadata record for: Facial model collection for medical augmented reality in oncologic cranio-maxillofacial surgery
    DOI 10.6084/m9.figshare.11284757
    Type Database/Collection of data
    Public Access
    Link Link
  • 2019 Link
    Title Medical Augmented Reality Facial Data Collection
    DOI 10.6084/m9.figshare.8857007.v2
    Type Database/Collection of data
    Public Access
    Link Link
  • 2019 Link
    Title Mandibular CT Dataset Collection
    DOI 10.6084/m9.figshare.6167726.v6
    Type Database/Collection of data
    Public Access
    Link Link

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