Objective: Surveillance imaging of chronic aortic diseases, such as dissections, relies on obtaining and comparing cross-sectional diameter measurements at predefined aortic landmarks, over time. Due to a lack of robust tools, the orientation of the cross-sectional planes is defined manually by highly trained operators. We show how manual annotations routinely collected in a clinic can be efficiently used to ease this task, despite the presence of a non-negligible interoperator variability in the measurements. Impact: Ill-posed but repetitive imaging tasks can be eased or automated by leveraging imperfect, retrospective clinical annotations. Methodology: In this work, we combine convolutional neural networks and uncertainty quantification methods to predict the orientation of such cross-sectional planes. We use clinical data randomly processed by 11 operators for training, and test on a smaller set processed by 3 independent operators to assess interoperator variability. Results: Our analysis shows that manual selection of cross-sectional planes is characterized by 95% limits of agreement (LOA) of $10.6^\circ$ and $21.4^\circ$ per angle. Our method showed to decrease static error by $3.57^\circ$ ($40.2$%) and $4.11^\circ$ ($32.8$%) against state of the art and LOA by $5.4^\circ$ ($49.0$%) and $16.0^\circ$ ($74.6$%) against manual processing. Conclusion: This suggests that pre-existing annotations can be an inexpensive resource in clinics to ease ill-posed and repetitive tasks like cross-section extraction for surveillance of aortic dissections.
Medical images, especially volumetric images, are of high resolution and often exceed the capacity of standard desktop GPUs. As a result, most deep learning-based medical image analysis tasks require the input images to be downsampled, often substantially, before these can be fed to a neural network. However, downsampling can lead to a loss of image quality, which is undesirable especially in reconstruction tasks, where the fine geometric details need to be preserved. In this paper, we propose that high-resolution images can be reconstructed in a coarse-to-fine fashion, where a deep learning algorithm is only responsible for generating a coarse representation of the image, which consumes moderate GPU memory. For producing the high-resolution outcome, we propose two novel methods: learned voxel rearrangement of the coarse output and hierarchical image synthesis. Compared to the coarse output, the high-resolution counterpart allows for smooth surface triangulation, which can be 3D-printed in the highest possible quality. Experiments of this paper are carried out on the dataset of AutoImplant 2021 (https://autoimplant2021.grand-challenge.org/), a MICCAI challenge on cranial implant design. The dataset contains high-resolution skulls that can be viewed as 2D manifolds embedded in a 3D space. Codes associated with this study can be accessed at https://github.com/Jianningli/voxel_rearrangement.
The aortic vessel tree is composed of the aorta and its branching arteries, and plays a key role in supplying the whole body with blood. Aortic diseases, like aneurysms or dissections, can lead to an aortic rupture, whose treatment with open surgery is highly risky. Therefore, patients commonly undergo drug treatment under constant monitoring, which requires regular inspections of the vessels through imaging. The standard imaging modality for diagnosis and monitoring is computed tomography (CT), which can provide a detailed picture of the aorta and its branching vessels if combined with a contrast agent, resulting in a CT angiography (CTA). Optimally, the whole aortic vessel tree geometry from consecutive CTAs, are overlaid and compared. This allows to not only detect changes in the aorta, but also more peripheral vessel tree changes, caused by the primary pathology or newly developed. When performed manually, this reconstruction requires slice by slice contouring, which could easily take a whole day for a single aortic vessel tree and, hence, is not feasible in clinical practice. Automatic or semi-automatic vessel tree segmentation algorithms, on the other hand, can complete this task in a fraction of the manual execution time and run in parallel to the clinical routine of the clinicians. In this paper, we systematically review computing techniques for the automatic and semi-automatic segmentation of the aortic vessel tree. The review concludes with an in-depth discussion on how close these state-of-the-art approaches are to an application in clinical practice and how active this research field is, taking into account the number of publications, datasets and challenges.
Deep learning belongs to the field of artificial intelligence, where machines perform tasks that typically require some kind of human intelligence. Deep learning tries to achieve this by mimicking the learning of a human brain. Similar to the basic structure of a brain, which consists of (billions of) neurons and connections between them, a deep learning algorithm consists of an artificial neural network, which resembles the biological brain structure. Mimicking the learning process of humans with their senses, deep learning networks are fed with (sensory) data, like texts, images, videos or sounds. These networks outperform the state-of-the-art methods in different tasks and, because of this, the whole field saw an exponential growth during the last years. This growth resulted in way over 10 000 publications per year in the last years. For example, the search engine PubMed alone, which covers only a sub-set of all publications in the medical field, provides over 11 000 results for the search term $'$deep learning$'$ in Q3 2020, and ~90% of these results are from the last three years. Consequently, a complete overview over the field of deep learning is already impossible to obtain and, in the near future, it will potentially become difficult to obtain an overview over a subfield. However, there are several review articles about deep learning, which are focused on specific scientific fields or applications, for example deep learning advances in computer vision or in specific tasks like object detection. With these surveys as a foundation, the aim of this contribution is to provide a first high-level, categorized meta-analysis of selected reviews on deep learning across different scientific disciplines and outline the research impact that they already have during a short period of time.
Deep learning had a remarkable impact in different scientific disciplines during the last years. This was demonstrated in numerous tasks, where deep learning algorithms were able to outperform the state-of-art methods, also in image processing and analysis. Moreover, deep learning delivers good results in tasks like autonomous driving, which could not have been performed automatically before. There are even applications where deep learning outperformed humans, like object recognition or games. Another field in which this development is showing a huge potential is the medical domain. With the collection of large quantities of patient records and data, and a trend towards personalized treatments, there is a great need for an automatic and reliable processing and analysis of this information. Patient data is not only collected in clinical centres, like hospitals, but it relates also to data coming from general practitioners, healthcare smartphone apps or online websites, just to name a few. This trend resulted in new, massive research efforts during the last years. In Q2/2020, the search engine PubMed returns already over 11.000 results for the search term $'$deep learning$'$, and around 90% of these publications are from the last three years. Hence, a complete overview of the field of $'$medical deep learning$'$ is almost impossible to obtain and getting a full overview of medical sub-fields gets increasingly more difficult. Nevertheless, several review and survey articles about medical deep learning have been presented within the last years. They focused, in general, on specific medical scenarios, like the analysis of medical images containing specific pathologies. With these surveys as foundation, the aim of this contribution is to provide a very first high-level, systematic meta-review of medical deep learning surveys.
In this study, we present a baseline approach for AutoImplant (https://autoimplant.grand-challenge.org/) - the cranial implant design challenge, which, as suggested by the organizers, can be formulated as a volumetric shape learning task. In this task, the defective skull, the complete skull and the cranial implant are represented as binary voxel grids. To accomplish this task, the implant can be either reconstructed directly from the defective skull or obtained by taking the difference between a defective skull and a complete skull. In the latter case, a complete skull has to be reconstructed given a defective skull, which defines a volumetric shape completion problem. Our baseline approach for this task is based on the former formulation, i.e., a deep neural network is trained to predict the implants directly from the defective skulls. The approach generates high-quality implants in two steps: First, an encoder-decoder network learns a coarse representation of the implant from down-sampled, defective skulls; The coarse implant is only used to generate the bounding box of the defected region in the original high-resolution skull. Second, another encoder-decoder network is trained to generate a fine implant from the bounded area. On the test set, the proposed approach achieves an average dice similarity score (DSC) of 0.8555 and Hausdorff distance (HD) of 5.1825 mm. The code is publicly available at https://github.com/Jianningli/autoimplant.
We introduce a fully automatic system for cranial implant design, a common task in cranioplasty operations. The system is currently integrated in Studierfenster (http://studierfenster.tugraz.at/), 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.
Medical imaging is an important tool for the diagnosis and the evaluation of an aortic dissection (AD); a serious condition of the aorta, which could lead to a life-threatening aortic rupture. AD patients need life-long medical monitoring of the aortic enlargement and of the disease progression, subsequent to the diagnosis of the aortic dissection. Since there is a lack of 'healthy-dissected' image pairs from medical studies, the application of inpainting techniques offers an alternative source for generating them by doing a virtual regression from dissected aortae to healthy aortae; an indirect way to study the origin of the disease. The proposed inpainting tool combines a neural network, which was trained on the task of inpainting aortic dissections, with an easy-to-use user interface. To achieve this goal, the inpainting tool has been integrated within the 3D medical image viewer of StudierFenster (www.studierfenster.at). By designing the tool as a web application, we simplify the usage of the neural network and reduce the initial learning curve.
Segmentation is a key step in analyzing and processing medical images. Due to the low fault tolerance in medical imaging, manual segmentation remains the de facto standard in this domain. Besides, efforts to automate the segmentation process often rely on large amounts of manually labeled data. While existing software supporting manual segmentation is rich in features and delivers accurate results, the necessary time to set it up and get comfortable using it can pose a hurdle for the collection of large datasets. This work introduces a client/server based online environment, referred to as Studierfenster (studierfenster.at), that can be used to perform manual segmentations directly in a web browser. The aim of providing this functionality in the form of a web application is to ease the collection of ground truth segmentation datasets. Providing a tool that is quickly accessible and usable on a broad range of devices, offers the potential to accelerate this process. The manual segmentation workflow of Studierfenster consists of dragging and dropping the input file into the browser window and slice-by-slice outlining the object under consideration. The final segmentation can then be exported as a file storing its contours and as a binary segmentation mask. In order to evaluate the usability of Studierfenster, a user study was performed. The user study resulted in a mean of 6.3 out of 7.0 possible points given by users, when asked about their overall impression of the tool. The evaluation also provides insights into the results achievable with the tool in practice, by presenting two ground truth segmentations performed by physicians.