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11th Biomedical Engineering International Conference, BMEiCON 2018

作者： Gsaxner, Christina Pfarrkirchner, Birgit Lindner, Lydia Pepe, Antonio Roth, Peter M. Egger, Jan Wallner, Jurgen Inst. of Computer Graphics and Vision Graz University of Technology Graz Austria Department of Maxillofacial Surgery Medical University of Graz Graz Austria Computer Algorithms for Medicine Laboratory Graz Austria

ISBN: (纸本)9781538657249

In this contribution, we propose an automatic ground truth generation approach that utilizes Positron Emission Tomography (PET) acquisitions to train neural networks for automatic urinary bladder segmentation in Computed Tomography (CT) images. We evaluated different deep learning architectures to segment the urinary bladder. However, deep neural networks require a large amount of training data, which is currently the main bottleneck in the medical field, because ground truth labels have to be created by medical experts on a time-consuming slice-by-slice basis. To overcome this problem, we generate the training data set from the PET data of combined PET/CT acquisitions. This can be achieved by applying simple thresholding to the PET data, where the radiotracer accumulates very distinct in the urinary bladder. However, the ultimate goal is to entirely skip PET imaging and its additional radiation exposure in the future, and only use CT images for segmentation. © 2018 IEEE.

关键词： Positron emission tomography

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Fully Convolutional Mandible Segmentation on a valid Ground- Truth Dataset

Fully Convolutional Mandible Segmentation on a valid Ground-...

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Annual International Conference of the IEEE Engineering in medicine and Biology Society (EMBC)

作者： Jan Egger Birgit Pfarrkirchner Christina Gsaxner Lydia Lindner Dieter Schmalstieg Jürgen Wallner Technische Universitat Graz Graz Steiermark AT Computer Algorithms for Medicine Laboratory Graz Austria

This contribution presents the automatic segmentation of the lower jawbone (mandible) in humans' computed tomography (CT) images with the support of trained deep learning networks. CT acquisitions from the mandible frequently include radiological artifacts e.g., from metal dental restorations, ostheosynthesis materials or include trauma related free pieces of bones with missing bone contour anatomy. As a result, manual outlining these slices to generate the ground truth for evaluating segmentation algorithms lead to massive uncertainties and results in significant interphysician disagreement. Simply excluding these slices is also not the option of choice, regarding the treatment outcome. Hence, we defined strict inclusion and exclusion criteria for our datasets to avoid subjectivity or occurring bias in the ground-truth creation. Amongst others, datasets must display a complete physiological mandible without teeth. According to these data selection criteria such images are difficult to find since they originate from the clinical routine and therefore need a medical indication (such as trauma or pathologic lesions) to be provided as CT data. Furthermore, to prove the adequateness of our ground-truth, clinical experts segmented all cases twice manually, showing the great qualitative and quantitative agreement between them. Our dataset collection and the corresponding ground truth is an absolute novelty and the first serious evaluation of segmentation algorithms for the mandible.

关键词： Image segmentation Computed tomography Training Bones Network topology Topology

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Depth-Awareness in a System for Mixed-Reality Aided Surgical Procedures 15th

Depth-Awareness in a System for Mixed-Reality Aided Surgical...

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15th International Conference on Intelligent Computing, ICIC 2019

作者： Sylos Labini, Mauro Gsaxner, Christina Pepe, Antonio Wallner, Juergen Egger, Jan Bevilacqua, Vitoantonio Institute for Computer Graphics and Vision Faculty of Computer Science and Biomedical Engineering Graz University of Technology Graz Austria Computer Algorithms for Medicine Laboratory Graz Austria Department of Electrical and Information Engineering Polytechnic University of Bari Bari Italy Department of Oral and Maxillofacial Surgery Medical University of Graz Graz Austria

ISBN: (纸本)9783030267650

computer-assisted surgery is a trending topic in research, with many different approaches which aim at supporting surgeons in the operating room. Existing surgical planning and navigation solutions are often considered to be distracting, unintuitive or hard to interpret. In this work, we address this issue with an approach based on mixed reality devices like Microsoft HoloLens. We assess the depth sensing capabilities of Microsoft HoloLens, and the potential benefit they could bring to computer-assisted surgery applications. © 2019, Springer Nature Switzerland AG.

关键词： Mixed reality

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Semi-supervised Virtual Regression of Aortic Dissections Using 3D Generative Inpainting 2nd

Semi-supervised Virtual Regression of Aortic Dissections Usi...

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2nd International Workshop on Thoracic Image Analysis, TIA 2020 Held in Conjunction with Medical Image Computing and computer-Assisted Intervention Conference, MICCAI 2020

作者： Pepe, Antonio Mistelbauer, Gabriel Gsaxner, Christina Li, Jianning Fleischmann, Dominik Schmalstieg, Dieter Egger, Jan Institute of Computer Graphics and Vision Graz University of Technology Graz Austria School of Medicine Department of Radiology Stanford University StanfordCA United States Computer Algorithms in Medicine Laboratory Graz Austria Department of Simulation and Graphics University of Magdeburg Magdeburg Germany Department of Oral and Maxillofacial Surgery Medical University of Graz Graz Austria

ISBN: (纸本)9783030624682

Aortic dissection (AD) is a condition of the main artery of the human body, resulting in the formation of a new flow channel, or false lumen (FL). The disease is usually diagnosed with a computed tomography angiography (CTA) scan during the acute phase. A better understanding of the causes of AD requires knowledge of aortic geometry prior to the event, which is available only in very rare circumstances. In this work, we propose an approach to reconstruct the aorta before the formation of a dissection by performing 3D inpainting with a two-stage generative adversarial network (GAN). In the first stage of our two-stage GAN, a network is trained on the 3D edge information of the healthy aorta to reconstruct the aortic wall. The second stage infers the image information of the aorta to reconstruct the entire dataset. We train our two-stage GAN with 3D patches from 55 non-dissected aortic datasets and evaluate it on 20 more non-dissected datasets, demonstrating that our proposed 3D architecture outperforms its 2D counterpart. To obtain pre-dissection aortae, we mask the entire FL in AD datasets. Finally, we provide qualitative feedback from a renown expert on the obtained pre-dissection cases. © 2020, Springer Nature Switzerland AG.

关键词： Generative adversarial networks

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Multicenter aortic vessel tree extraction using deep learning

Multicenter aortic vessel tree extraction using deep learnin...

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Medical Imaging 2023: Biomedical Applications in Molecular, Structural, and Functional Imaging

作者： Scharinger, Bernhard Pepe, Antonio Jin, Yuan Gsaxner, Christina Li, Jianning Egger, Jan Graz University of Technology Institute for Computer Graphics and Vision Inffeldgasse 16c/II GrazA-8010 Austria Computer Algorithms for Medicine Laboratory Graz Austria Girardetstrasse 2 Essen45131 Germany Research Center for Connected Healthcare Big Data Zhejiang Lab Zhejiang Hangzhou311121 China

ISBN: (纸本)9781510660410

The aorta is the largest vessel of the human body and its pathological degenerations, such as dissections and aneurysms, can be life threatening. An automatic and fast segmentation of the aorta can therefore be a helpful tool to quickly identify an abnormal anatomy. The segmentation of the aortic vessel tree (AVT) typically requires extensive manual labor, but, in recent years, progress in deep learning techniques made the automation of this process viable. For this purpose, we tested different deep learning networks to segment the aortic vessel tree from computed tomography angiography (CTA) scans with a deep neural network consisting of an encoder-decoder architecture with skip connections and an optional self-attention block. The networks were trained on a dataset of 56 CTA scans from three different sources and resulted in Dice score similarities between 0.043-0.897. Generally, the classical U-Nets performed better than the ones containing a self-attention block, indicating that they might diminish performance for AVT segmentation. The quality of the resulting segmentations was highly dependent on the CTA image quality, especially on the contrast between the aorta and the surrounding tissues. However, the trained deep neural network can segment CTA scans well with limited computational resources and training data. © COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.

关键词： Deep neural networks

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Aortic dissection maps: Comprehensive visualization of aortic dissections for risk assessment

Aortic dissection maps: Comprehensive visualization of aorti...

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2016 Eurographics Workshop on Visual Computing for Biology and medicine, VCBM 2016

作者： Mistelbauer, G. Schmidt, J. Sailer, A.M. Bäumler, K. Walters, S. Fleischmann, D. Institute of Computer Graphics and Algorithms TU Wien Vienna Austria Otto-von-Guericke University Magdeburg Germany AIT Austrian Institute of Technology Austria 3D and Quantitative Imaging Laboratory Department of Radiology Stanford University School of Medicine CA United States

ISBN: (纸本)9783038680109

Aortic dissection is a life threatening condition of the aorta, characterized by separation of its wall layers into a true and false lumen. A subset of patients require immediate surgical or endovascular repair. All survivors of the acute phase need long-term surveillance with imaging to monitor chronic degeneration and dilatation of the false lumen and prevent late adverse events such as rupture, or malperfusion. We introduce four novel plots displaying features of aortic dissections known or presumed to be associated with risk of future adverse events: Aortic diameter, the blood supply (outflow) to the aortic branches from the true and false lumen, the previous treatment, and an estimate of adverse event-free probabilities in one, two and 5 years. Aortic dissection maps, the composite visualization of these plots, provide a baseline for visual comparison of the complex features and associated risk of aortic dissection. These maps may lead to more individualized monitoring and improved, patient-centric treatment planning in the future. © 2016 The Author(s) Eurographics Proceedings © 2016 The Eurographics Association.

关键词： Visualization

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An Online Platform for Automatic Skull Defect Restoration and Cranial Implant Design

arXiv

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arXiv 2020年

作者： Li, Jianning Pepe, Antonio Gsaxner, Christina Egger, Jan Institute of Computer Graphics and Vision Graz University of Technology Computer Algorithms for Medicine Laboratory Graz Austria Department of Oral and Maxillofacial Surgery Medical University of Graz

We introduce a fully automatic system for cranial implant design, a common task in cranioplasty operations. The system is currently integrated in Studierfenster (http://***/), an online, cloud-based medical image processing platform for medical imaging applications. Enhanced by deep learning algorithms, the system automatically restores the missing part of a skull (i.e., skull shape completion) and generates the desired implant by subtracting the defective skull from the completed skull. The generated implant can be downloaded in the STereoLithography (.stl) format directly via the browser interface of the system. The implant model can then be sent to a 3D printer for in loco implant manufacturing. Furthermore, thanks to the standard format, the user can thereafter load the model into another application for post-processing whenever necessary. Such an automatic cranial implant design system can be integrated into the clinical practice to improve the current routine for surgeries related to skull defect repair (e.g., cranioplasty). Our system, although currently intended for educational and research use only, can be seen as an application of additive manufacturing for fast, patient-specific implant design. Copyright © 2020, The Authors. All rights reserved.

关键词： 3D printers

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Enhanced Data Augmentation Using Synthetic Data for Brain Tumour Segmentation 1

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Challenge on Brain Tumor Segmentation, BraTS 2023, International Challenge on Cross-Modality Domain Adaptation for Medical Image Segmentation, CrossMoDA 2023, held in conjunction with the Medical Image Computing for computer Assisted Intervention Conference, MICCAI 2023

作者： Ferreira, André Solak, Naida Li, Jianning Dammann, Philipp Kleesiek, Jens Alves, Victor Egger, Jan Center Algoritmi/LASI University of Minho Braga4710-057 Portugal Computer Algorithms for Medicine Laboratory Graz Austria University Medicine Essen Girardetstraße 2 Essen45131 Germany University Medicine Essen Hufelandstraße 55 Essen45147 Germany Partner Site Essen Hufelandstraße 55 Essen45147 Germany Institute of Computer Graphics and Vision Graz University of Technology Inffeldgasse 16 Graz8010 Austria Department of Neurosurgery and Spine Surgery University Hospital Essen Essen Germany

ISBN: (数字)9783031761638

ISBN: (纸本)9783031761621

Deep Learning is the state-of-the-art technology for segmenting brain tumours. However, this requires a lot of high-quality data, which is difficult to obtain, especially in the medical field. Therefore, our solutions address this problem by using unconventional mechanisms for data augmentation. Generative adversarial networks and registration are used to massively increase the amount of available samples for training three different deep learning models for adult glioma segmentation, the Task 1 of the BraTS 2023 challenge. The first model is the standard nnU-Net, the second is the Swin UNETR and the third is the winning solution of the BraTS 2021 Challenge. The entire pipeline is built on the nnU-Net implementation, except for the generation of the synthetic data. The use of convolutional algorithms and transformers is able to fill each other’s knowledge gaps. Our solution achieves the lesion-wise Dice metric of 0.8851, 0.8719, 0.8685 and lesion-wise HD95 of 22.838, 22.974, 16.713 (whole tumour, tumour core and enhancing tumour) on the testing cohort. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.

关键词： Generative adversarial networks

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Exploit fully automatic low-level segmented PET data for training high-level deep learning algorithms for the corresponding CT data

arXiv

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arXiv 2019年

作者： Gsaxner, Christina Roth, Peter M. Wallner, Jürgen Egger, Jan Institute for Computer Graphics and Vision Faculty of Computer Science and Biomedical Engineering Graz University of Technology Graz Austria Computer Algorithms for Medicine Laboratory Graz Austria Department of Oral & Maxillofacial Surgery Medical University of Graz Auenbruggerplatz Styria Austria

We present an approach for fully automatic urinary bladder segmentation in CT images with artificial neural networks in this study. Automatic medical image analysis has become an invaluable tool in the different treatment stages of diseases. Especially medical image segmentation plays a vital role, since segmentation is often the initial step in an image analysis pipeline. Since deep neural networks have made a large impact on the field of image processing in the past years, we use two different deep learning architectures to segment the urinary bladder. Both of these architectures are based on pre-trained classification networks that are adapted to perform semantic segmentation. Since deep neural networks require a large amount of training data, specifically images and corresponding ground truth labels, we furthermore propose a method to generate such a suitable training data set from Positron Emission Tomography/Computed Tomography image data. This is done by applying thresholding to the Positron Emission Tomography data for obtaining a ground truth and by utilizing data augmentation to enlarge the dataset. In this study, we discuss the influence of data augmentation on the segmentation results, and compare and evaluate the proposed architectures in terms of qualitative and quantitative segmentation performance. The results presented in this study allow concluding that deep neural networks can be considered a promising approach to segment the urinary bladder in CT images. Copyright © 2019, The Authors. All rights reserved.

关键词： Deep neural networks

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IRIS: Interactive real-time feedback image segmentation with deep learning

IRIS: Interactive real-time feedback image segmentation with...

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Medical Imaging 2020: Biomedical Applications in Molecular, Structural, and Functional Imaging

作者： Pepe, Antonio Schussnig, Richard Li, Jianning Gsaxner, Christina Chen, Xiaojun Fries, Thomas-Peter Egger, Jan Stanford University School of Medicine Department of Radiology 300 Pasteur Dr StanfordCA United States Graz University of Technology Institute of Computer Graphics and Vision Inffeldgasse 16c/II GrazA-8010 Austria Computer Algorithms for Medicine Laboratory GrazA-8010 Austria Graz University of Technology Institute of Structural Analysis Lessingstraße 25/II GrazA-8010 Austria Medical University of Graz Department of Oral and Maxillofacial Surgery Auenbruggerplatz 5/1 GrazA-8036 Austria Shanghai Jiao Tong University School of Mechanical Engineering 800 Dong Chuan Road Shanghai200240 China

ISBN: (纸本)9781510634015

Volumetric examinations of the aorta are nowadays of crucial importance for the management of critical pathologies such as aortic dissection, aortic aneurism, and other pathologies, which affect the morphology of the artery. These examinations usually begin with the acquisition of a Computed Tomography Angiography (CTA) scan from the patient, which is later on postprocessed to reconstruct the 3D geometry of the aorta. The first postprocessing step is referred to as segmentation. Different algorithms have been suggested for the segmentation of the aorta;including interactive methods, as well as fully automatic methods. Interactive methods need to be fine-tuned on each single CTA scan and result in longer duration of the process, whereas fully automatic methods require the possession of a large amount of labeled training data. In this work, we introduce a hybrid approach by combining a deep learning method with a consolidated interaction technique. In particular, we trained a 2D and a 3D U-Net on a limited number of patches extracted from 25 labeled CTA scans. Afterwards, we use an interactive approach, which consists in defining a region of interest (ROI) by just placing a seed point. This seed point is later used as the center of a 2D or 3D patch to be fed to the 2D or 3D U-Net, respectively. Due to the low content variation of these patches, this method allows to correctly segment the ROIs without the need for parameter tuning for each dataset and with a smaller training dataset, requiring the same minimal interaction as state-of-the-art interactive methods. Later on, the new segmented CTA scans can be further used to train a convolutional network for a fully automatic approach. © 2020 SPIE

关键词： Angiography

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