Back to the Roots: Reconstructing Large and Complex Cranial Defects using an Image-based Statistical Shape Model.

Designing implants for large and complex cranial defects is a challenging task, even for professional designers. Current efforts on automating the design process focused mainly on convolutional neural networks (CNN), which have produced state-of-the-art results on reconstructing synthetic defects. However, existing CNN-based methods have been difficult to translate to clinical practice in cranioplasty, as their performance on large and complex cranial defects remains unsatisfactory. In this paper, we present a statistical shape model (SSM) built directly on the segmentation masks of the skulls represented as binary voxel occupancy grids and evaluate it on several cranial implant design datasets. Results show that, while CNN-based approaches outperform the SSM on synthetic defects, they are inferior to SSM when it comes to large, complex and real-world defects. Experienced neurosurgeons evaluate the implants generated by the SSM to be feasible for clinical use after minor manual corrections. Datasets and the SSM model are publicly available at https://github.com/Jianningli/ssm .

3D surgical instrument collection for computer vision and extended reality.

The availability of computational hardware and developments in (medical) machine learning (MML) increases medical mixed realities' (MMR) clinical usability. Medical instruments have played a vital role in surgery for ages. To further accelerate the implementation of MML and MMR, three-dimensional (3D) datasets of instruments should be publicly available. The proposed data collection consists of 103, 3D-scanned medical instruments from the clinical routine, scanned with structured light scanners. The collection consists, for example, of instruments, like retractors, forceps, and clamps. The collection can be augmented by generating likewise models using 3D software, resulting in an inflated dataset for analysis. The collection can be used for general instrument detection and tracking in operating room settings, or a freeform marker-less instrument registration for tool tracking in augmented reality. Furthermore, for medical simulation or training scenarios in virtual reality and medical diminishing reality in mixed reality. We hope to ease research in the field of MMR and MML, but also to motivate the release of a wider variety of needed surgical instrument datasets.

Sparse convolutional neural network for high-resolution skull shape completion and shape super-resolution.

Traditional convolutional neural network (CNN) methods rely on dense tensors, which makes them suboptimal for spatially sparse data. In this paper, we propose a CNN model based on sparse tensors for efficient processing of high-resolution shapes represented as binary voxel occupancy grids. In contrast to a dense CNN that takes the entire voxel grid as input, a sparse CNN processes only on the non-empty voxels, thus reducing the memory and computation overhead caused by the sparse input data. We evaluate our method on two clinically relevant skull reconstruction tasks: (1) given a defective skull, reconstruct the complete skull (i.e., skull shape completion), and (2) given a coarse skull, reconstruct a high-resolution skull with fine geometric details (shape super-resolution). Our method outperforms its dense CNN-based counterparts in the skull reconstruction task quantitatively and qualitatively, while requiring substantially less memory for training and inference. We observed that, on the 3D skull data, the overall memory consumption of the sparse CNN grows approximately linearly during inference with respect to the image resolutions. During training, the memory usage remains clearly below increases in image resolution-an [Formula: see text] increase in voxel number leads to less than [Formula: see text] increase in memory requirements. Our study demonstrates the effectiveness of using a sparse CNN for skull reconstruction tasks, and our findings can be applied to other spatially sparse problems. We prove this by additional experimental results on other sparse medical datasets, like the aorta and the heart. Project page at https://github.com/Jianningli/SparseCNN .

Augmented Reality-Guided Apicoectomy Based on Maxillofacial CBCT Scans.

Implementation of augmented reality (AR) image guidance systems using preoperative cone beam computed tomography (CBCT) scans in apicoectomies promises to help surgeons overcome iatrogenic complications associated with this procedure. This study aims to evaluate the intraoperative feasibility and usability of HoloLens 2, an established AR image guidance device, in the context of apicoectomies. Three experienced surgeons carried out four AR-guided apicoectomies each on human cadaver head specimens. Preparation and operating times of each procedure, as well as the subjective usability of HoloLens for AR image guidance in apicoectomies using the System Usability Scale (SUS), were measured. In total, twelve AR-guided apicoectomies on six human cadaver head specimens were performed (n = 12). The average preparation time amounted to 162 (±34) s. The surgical procedure itself took on average 9 (±2) min. There was no statistically significant difference between the three surgeons. Quantification of the usability of HoloLens revealed a mean SUS score of 80.4 (±6.8), indicating an "excellent" usability level. In conclusion, this study implies the suitability, practicality, and simplicity of AR image guidance systems such as the HoloLens in apicoectomies and advocates their routine implementation.

Automated cross-sectional view selection in CT angiography of aortic dissections with uncertainty awareness and retrospective clinical annotations.

Surveillance imaging of patients with chronic aortic diseases, such as aneurysms and dissections, relies on obtaining and comparing cross-sectional diameter measurements along the aorta at predefined aortic landmarks, over time. The orientation of the cross-sectional measuring planes at each landmark is currently defined manually by highly trained operators. Centerline-based approaches are unreliable in patients with chronic aortic dissection, because of the asymmetric flow channels, differences in contrast opacification, and presence of mural thrombus, making centerline computations or measurements difficult to generate and reproduce. In this work, we present three alternative approaches - INS, MCDS, MCDbS - based on convolutional neural networks and uncertainty quantification methods to predict the orientation (ϕ,θ) of such cross-sectional planes. For the monitoring of chronic aortic dissections, we show how a dataset of 162 CTA volumes with overall 3273 imperfect manual annotations routinely collected in a clinic can be efficiently used to accomplish this task, despite the presence of non-negligible interoperator variabilities in terms of mean absolute error (MAE) and 95% limits of agreement (LOA). We show how, despite the large limits of agreement in the training data, the trained model provides faster and more reproducible results than either an expert user or a centerline method. The remaining disagreement lies within the variability produced by three independent expert annotators and matches the current state of the art, providing a similar error, but in a fraction of the time.

Towards clinical applicability and computational efficiency in automatic cranial implant design: An overview of the AutoImplant 2021 cranial implant design challenge.

Cranial implants are commonly used for surgical repair of craniectomy-induced skull defects. These implants are usually generated offline and may require days to weeks to be available. An automated implant design process combined with onsite manufacturing facilities can guarantee immediate implant availability and avoid secondary intervention. To address this need, the AutoImplant II challenge was organized in conjunction with MICCAI 2021, catering for the unmet clinical and computational requirements of automatic cranial implant design. The first edition of AutoImplant (AutoImplant I, 2020) demonstrated the general capabilities and effectiveness of data-driven approaches, including deep learning, for a skull shape completion task on synthetic defects. The second AutoImplant challenge (i.e., AutoImplant II, 2021) built upon the first by adding real clinical craniectomy cases as well as additional synthetic imaging data. The AutoImplant II challenge consisted of three tracks. Tracks 1 and 3 used skull images with synthetic defects to evaluate the ability of submitted approaches to generate implants that recreate the original skull shape. Track 3 consisted of the data from the first challenge (i.e., 100 cases for training, and 110 for evaluation), and Track 1 provided 570 training and 100 validation cases aimed at evaluating skull shape completion algorithms at diverse defect patterns. Track 2 also made progress over the first challenge by providing 11 clinically defective skulls and evaluating the submitted implant designs on these clinical cases. The submitted designs were evaluated quantitatively against imaging data from post-craniectomy as well as by an experienced neurosurgeon. Submissions to these challenge tasks made substantial progress in addressing issues such as generalizability, computational efficiency, data augmentation, and implant refinement. This paper serves as a comprehensive summary and comparison of the submissions to the AutoImplant II challenge. Codes and models are available at https://github.com/Jianningli/Autoimplant_II.

The HoloLens in medicine: A systematic review and taxonomy.

The HoloLens (Microsoft Corp., Redmond, WA), a head-worn, optically see-through augmented reality (AR) display, is the main player in the recent boost in medical AR research. In this systematic review, we provide a comprehensive overview of the usage of the first-generation HoloLens within the medical domain, from its release in March 2016, until the year of 2021. We identified 217 relevant publications through a systematic search of the PubMed, Scopus, IEEE Xplore and SpringerLink databases. We propose a new taxonomy including use case, technical methodology for registration and tracking, data sources, visualization as well as validation and evaluation, and analyze the retrieved publications accordingly. We find that the bulk of research focuses on supporting physicians during interventions, where the HoloLens is promising for procedures usually performed without image guidance. However, the consensus is that accuracy and reliability are still too low to replace conventional guidance systems. Medical students are the second most common target group, where AR-enhanced medical simulators emerge as a promising technology. While concerns about human-computer interactions, usability and perception are frequently mentioned, hardly any concepts to overcome these issues have been proposed. Instead, registration and tracking lie at the core of most reviewed publications, nevertheless only few of them propose innovative concepts in this direction. Finally, we find that the validation of HoloLens applications suffers from a lack of standardized and rigorous evaluation protocols. We hope that this review can advance medical AR research by identifying gaps in the current literature, to pave the way for novel, innovative directions and translation into the medical routine.

Radiomics in Head and Neck Cancer Outcome Predictions.

Head and neck cancer has great regional anatomical complexity, as it can develop in different structures, exhibiting diverse tumour manifestations and high intratumoural heterogeneity, which is highly related to resistance to treatment, progression, the appearance of metastases, and tumour recurrences. Radiomics has the potential to address these obstacles by extracting quantitative, measurable, and extractable features from the region of interest in medical images. Medical imaging is a common source of information in clinical practice, presenting a potential alternative to biopsy, as it allows the extraction of a large number of features that, although not visible to the naked eye, may be relevant for tumour characterisation. Taking advantage of machine learning techniques, the set of features extracted when associated with biological parameters can be used for diagnosis, prognosis, and predictive accuracy valuable for clinical decision-making. Therefore, the main goal of this contribution was to determine to what extent the features extracted from Computed Tomography (CT) are related to cancer prognosis, namely Locoregional Recurrences (LRs), the development of Distant Metastases (DMs), and Overall Survival (OS). Through the set of tumour characteristics, predictive models were developed using machine learning techniques. The tumour was described by radiomic features, extracted from images, and by the clinical data of the patient. The performance of the models demonstrated that the most successful algorithm was XGBoost, and the inclusion of the patients' clinical data was an asset for cancer prognosis. Under these conditions, models were created that can reliably predict the LR, DM, and OS status, with the area under the ROC curve (AUC) values equal to 0.74, 0.84, and 0.91, respectively. In summary, the promising results obtained show the potential of radiomics, once the considered cancer prognosis can, in fact, be expressed through CT scans.

Medical deep learning-A systematic meta-review.

Deep learning has remarkably impacted several different scientific disciplines over the last few years. For example, in image processing and analysis, deep learning algorithms were able to outperform other cutting-edge methods. Additionally, deep learning has delivered state-of-the-art results in tasks like autonomous driving, outclassing previous attempts. There are even instances where deep learning outperformed humans, for example with object recognition and gaming. Deep learning is also showing vast potential in 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 automated and reliable processing and analysis of health information. Patient data is not only collected in clinical centers, like hospitals and private practices, but also by mobile healthcare apps or online websites. The abundance of collected patient data and the recent growth in the deep learning field has resulted in a large increase in research efforts. In Q2/2020, the search engine PubMed returned already over 11,000 results for the search term 'deep learning', and around 90% of these publications are from the last three years. However, even though PubMed represents the largest search engine in the medical field, it does not cover all medical-related publications. Hence, a complete overview of the field of 'medical deep learning' is almost impossible to obtain and acquiring a full overview of medical sub-fields is becoming increasingly more difficult. Nevertheless, several review and survey articles about medical deep learning have been published within the last few years. They focus, in general, on specific medical scenarios, like the analysis of medical images containing specific pathologies. With these surveys as a foundation, the aim of this article is to provide the first high-level, systematic meta-review of medical deep learning surveys.

Studierfenster: an Open Science Cloud-Based Medical Imaging Analysis Platform.

Imaging modalities such as computed tomography (CT) and magnetic resonance imaging (MRI) are widely used in diagnostics, clinical studies, and treatment planning. Automatic algorithms for image analysis have thus become an invaluable tool in medicine. Examples of this are two- and three-dimensional visualizations, image segmentation, and the registration of all anatomical structure and pathology types. In this context, we introduce Studierfenster ( www.studierfenster.at ): a free, non-commercial open science client-server framework for (bio-)medical image analysis. Studierfenster offers a wide range of capabilities, including the visualization of medical data (CT, MRI, etc.) in two-dimensional (2D) and three-dimensional (3D) space in common web browsers, such as Google Chrome, Mozilla Firefox, Safari, or Microsoft Edge. Other functionalities are the calculation of medical metrics (dice score and Hausdorff distance), manual slice-by-slice outlining of structures in medical images, manual placing of (anatomical) landmarks in medical imaging data, visualization of medical data in virtual reality (VR), and a facial reconstruction and registration of medical data for augmented reality (AR). More sophisticated features include the automatic cranial implant design with a convolutional neural network (CNN), the inpainting of aortic dissections with a generative adversarial network, and a CNN for automatic aortic landmark detection in CT angiography images. A user study with medical and non-medical experts in medical image analysis was performed, to evaluate the usability and the manual functionalities of Studierfenster. When participants were asked about their overall impression of Studierfenster in an ISO standard (ISO-Norm) questionnaire, a mean of 6.3 out of 7.0 possible points were achieved. The evaluation also provided insights into the results achievable with Studierfenster in practice, by comparing these with two ground truth segmentations performed by a physician of the Medical University of Graz in Austria. In this contribution, we presented an online environment for (bio-)medical image analysis. In doing so, we established a client-server-based architecture, which is able to process medical data, especially 3D volumes. Our online environment is not limited to medical applications for humans. Rather, its underlying concept could be interesting for researchers from other fields, in applying the already existing functionalities or future additional implementations of further image processing applications. An example could be the processing of medical acquisitions like CT or MRI from animals [Clinical Pharmacology & Therapeutics, 84(4):448-456, 68], which get more and more common, as veterinary clinics and centers get more and more equipped with such imaging devices. Furthermore, applications in entirely non-medical research in which images/volumes need to be processed are also thinkable, such as those in optical measuring techniques, astronomy, or archaeology.

AVT: Multicenter aortic vessel tree CTA dataset collection with ground truth segmentation masks.

In this article, we present a multicenter aortic vessel tree database collection, containing 56 aortas and their branches. The datasets have been acquired with computed tomography angiography (CTA) scans and each scan covers the ascending aorta, the aortic arch and its branches into the head/neck area, the thoracic aorta, the abdominal aorta and the lower abdominal aorta with the iliac arteries branching into the legs. For each scan, the collection provides a semi-automatically generated segmentation mask of the aortic vessel tree (ground truth). The scans come from three different collections and various hospitals, having various resolutions, which enables studying the geometry/shape variabilities of human aortas and its branches from different geographic locations. Furthermore, creating a robust statistical model of the shape of human aortic vessel trees, which can be used for various tasks such as the development of fully-automatic segmentation algorithms for new, unseen aortic vessel tree cases, e.g. by training deep learning-based approaches. Hence, the collection can serve as an evaluation set for automatic aortic vessel tree segmentation algorithms.

Deep learning-a first meta-survey of selected reviews across scientific disciplines, their commonalities, challenges and research impact.

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 drawing inspiration from 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 already over 11,000 results in Q3 2020 for the search term 'deep learning', and around 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-survey 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. The categories (computer vision, language processing, medical informatics and additional works) have been chosen according to the underlying data sources (image, language, medical, mixed). In addition, we review the common architectures, methods, pros, cons, evaluations, challenges and future directions for every sub-category.

MUG500+: Database of 500 high-resolution healthy human skulls and 29 craniotomy skulls and implants.

In this article, we present a skull database containing 500 healthy skulls segmented from high-resolution head computed-tomography (CT) scans and 29 defective skulls segmented from craniotomy head CTs. Each healthy skull contains the complete anatomical structures of human skulls, including the cranial bones, facial bones and other subtle structures. For each craniotomy skull, a part of the cranial bone is missing, leaving a defect on the skull. The defects have various sizes, shapes and positions, depending on the specific pathological conditions of each patient. Along with each craniotomy skull, a cranial implant, which is designed manually by an expert and can fit with the defect, is provided. Considering the large volume of the healthy skull collection, the dataset can be used to study the geometry/shape variabilities of human skulls and create a robust statistical model of the shape of human skulls, which can be used for various tasks such as cranial implant design. The craniotomy collection can serve as an evaluation set for automatic cranial implant design algorithms.

Automatic skull defect restoration and cranial implant generation for cranioplasty.

A fast and fully automatic design of 3D printed patient-specific cranial implants is highly desired in cranioplasty - the process to restore a defect on the skull. We formulate skull defect restoration as a 3D volumetric shape completion task, where a partial skull volume is completed automatically. The difference between the completed skull and the partial skull is the restored defect; in other words, the implant that can be used in cranioplasty. To fulfill the task of volumetric shape completion, a fully data-driven approach is proposed. Supervised skull shape learning is performed on a database containing 167 high-resolution healthy skulls. In these skulls, synthetic defects are injected to create training and evaluation data pairs. We propose a patch-based training scheme tailored for dealing with high-resolution and spatially sparse data, which overcomes the disadvantages of conventional patch-based training methods in high-resolution volumetric shape completion tasks. In particular, the conventional patch-based training is applied to images of high resolution and proves to be effective in tasks such as segmentation. However, we demonstrate the limitations of conventional patch-based training for shape completion tasks, where the overall shape distribution of the target has to be learnt, since it cannot be captured efficiently by a sub-volume cropped from the target. Additionally, the standard dense implementation of a convolutional neural network tends to perform poorly on sparse data, such as the skull, which has a low voxel occupancy rate. Our proposed training scheme encourages a convolutional neural network to learn from the high-resolution and spatially sparse data. In our study, we show that our deep learning models, trained on healthy skulls with synthetic defects, can be transferred directly to craniotomy skulls with real defects of greater irregularity, and the results show promise for clinical use. Project page: https://github.com/Jianningli/MIA.

AutoImplant 2020-First MICCAI Challenge on Automatic Cranial Implant Design.

The aim of this paper is to provide a comprehensive overview of the MICCAI 2020 AutoImplant Challenge. The approaches and publications submitted and accepted within the challenge will be summarized and reported, highlighting common algorithmic trends and algorithmic diversity. Furthermore, the evaluation results will be presented, compared and discussed in regard to the challenge aim: seeking for low cost, fast and fully automated solutions for cranial implant design. Based on feedback from collaborating neurosurgeons, this paper concludes by stating open issues and post-challenge requirements for intra-operative use. The codes can be found at https://github.com/Jianningli/tmi.

SkullBreak / SkullFix - Dataset for automatic cranial implant design and a benchmark for volumetric shape learning tasks.

The article introduces two complementary datasets intended for the development of data-driven solutions for cranial implant design, which remains to be a time-consuming and laborious task in current clinical routine of cranioplasty. The two datasets, referred to as the SkullBreak and SkullFix in this article, are both adapted from a public head CT collection CQ500 (http://headctstudy.qure.ai/dataset) with CC BY-NC-SA 4.0 license. The SkullBreak contains 114 and 20 complete skulls, each accompanied by five defective skulls and the corresponding cranial implants, for training and evaluation respectively. The SkullFix contains 100 triplets (complete skull, defective skull and the implant) for training and 110 triplets for evaluation. The SkullFix dataset was first used in the MICCAI 2020 AutoImplant Challenge (https://autoimplant.grand-challenge.org/) and the ground truth, i.e., the complete skulls and the implants in the evaluation set are held private by the organizers. The two datasets are not overlapping and differ regarding data selection and synthetic defect creation and each serves as a complement to the other. Besides cranial implant design, the datasets can be used for the evaluation of volumetric shape learning algorithms, such as volumetric shape completion. This article gives a description of the two datasets in detail.

Synthetic skull bone defects for automatic patient-specific craniofacial implant design.

Patient-specific craniofacial implants are used to repair skull bone defects after trauma or surgery. Currently, cranial implants are designed and produced by third-party suppliers, which is usually time-consuming and expensive. Recent advances in additive manufacturing made the in-hospital or in-operation-room fabrication of personalized implants feasible. However, the implants are still manufactured by external companies. To facilitate an optimized workflow, fast and automatic implant manufacturing is highly desirable. Data-driven approaches, such as deep learning, show currently great potential towards automatic implant design. However, a considerable amount of data is needed to train such algorithms, which is, especially in the medical domain, often a bottleneck. Therefore, we present CT-imaging data of the craniofacial complex from 24 patients, in which we injected various artificial cranial defects, resulting in 240 data pairs and 240 corresponding implants. Based on this work, automatic implant design and manufacturing processes can be trained. Additionally, the data of this work build a solid base for researchers to work on automatic cranial implant designs.

Augmented Reality for Head and Neck Carcinoma Imaging: Description and Feasibility of an Instant Calibration, Markerless Approach.

BACKGROUND AND OBJECTIVE: Augmented reality (AR) can help to overcome current limitations in computer assisted head and neck surgery by granting "X-ray vision" to physicians. Still, the acceptance of AR in clinical applications is limited by technical and clinical challenges. We aim to demonstrate the benefit of a marker-free, instant calibration AR system for head and neck cancer imaging, which we hypothesize to be acceptable and practical for clinical use. METHODS: We implemented a novel AR system for visualization of medical image data registered with the head or face of the patient prior to intervention. Our system allows the localization of head and neck carcinoma in relation to the outer anatomy. Our system does not require markers or stationary infrastructure, provides instant calibration and allows 2D and 3D multi-modal visualization for head and neck surgery planning via an AR head-mounted display. We evaluated our system in a pre-clinical user study with eleven medical experts. RESULTS: Medical experts rated our application with a system usability scale score of 74.8 ± 15.9, which signifies above average, good usability and clinical acceptance. An average of 12.7 ± 6.6 minutes of training time was needed by physicians, before they were able to navigate the application without assistance. CONCLUSIONS: Our AR system is characterized by a slim and easy setup, short training time and high usability and acceptance. Therefore, it presents a promising, novel tool for visualizing head and neck cancer imaging and pre-surgical localization of target structures.

Detection, segmentation, simulation and visualization of aortic dissections: A review.

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. The disease is usually diagnosed with a computed tomography angiography scan during the acute phase. A better understanding of the causes of AD requires knowledge of the aortic geometry (segmentation), including the true and false lumina, which is very time-consuming to reconstruct when performed manually on a slice-by-slice basis. Hence, different automatic and semi-automatic medical image analysis approaches have been proposed for this task over the last years. In this review, we present and discuss these computing techniques used to segment dissected aortas, also in regard to the detection and visualization of clinically relevant information and features from dissected aortas for customized patient-specific treatments.