Deep Medial Voxels: Learned Medial Axis Approximations for Anatomical Shape Modeling

Shape reconstruction from imaging volumes is a recurring need in medical image analysis. Common workflows start with a segmentation step, followed by careful post-processing and,finally, ad hoc meshing algorithms. As this sequence can be timeconsuming, neural networks are trained to reconstruct shapes through template deformation. These networks deliver state-ofthe-art results without manual intervention, but, so far, they have primarily been evaluated on anatomical shapes with little topological variety between individuals. In contrast, other works favor learning implicit shape models, which have multiple benefits for meshing and visualization. Our work follows this direction by introducing deep medial voxels, a semi-implicit representation that faithfully approximates the topological skeleton from imaging volumes and eventually leads to shape reconstruction via convolution surfaces. Our reconstruction technique shows potential for both visualization and computer simulations.

DeepDR: Deep Structure-Aware RGB-D Inpainting for Diminished Reality

Diminished reality (DR) refers to the removal of real objects from the environment by virtually replacing them with their background. Modern DR frameworks use inpainting to hallucinate unobserved regions. While recent deep learning-based inpainting is promising, the DR use case is complicated by the need to generate coherent structure and 3D geometry (i.e., depth), in particular for advanced applications, such as 3D scene editing. In this paper, we propose DeepDR, a first RGB-D inpainting framework fulfilling all requirements of DR: Plausible image and geometry inpainting with coherent structure, running at real-time frame rates, with minimal temporal artifacts. Our structure-aware generative network allows us to explicitly condition color and depth outputs on the scene semantics, overcoming the difficulty of reconstructing sharp and consistent boundaries in regions with complex backgrounds. Experimental results show that the proposed framework can outperform related work qualitatively and quantitatively.

The HoloLens in Medicine: A systematic Review and Taxonomy

The HoloLens (Microsoft Corp., Redmond, WA), a head-worn, optically see-through augmented reality display, is the main player in the recent boost in medical augmented reality research. In medical settings, the HoloLens enables the physician to obtain immediate insight into patient information, directly overlaid with their view of the clinical scenario, the medical student to gain a better understanding of complex anatomies or procedures, and even the patient to execute therapeutic tasks with improved, immersive guidance. 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, were attention is shifting towards it's successor, the HoloLens 2. We identified 171 relevant publications through a systematic search of the PubMed and Scopus databases. We analyze these publications in regard to their intended use case, technical methodology for registration and tracking, data sources, visualization as well as validation and evaluation. We find that, although the feasibility of using the HoloLens in various medical scenarios has been shown, increased efforts in the areas of precision, reliability, usability, workflow and perception are necessary to establish AR in clinical practice.

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

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.

DetectFusion: Detecting and Segmenting Both Known and Unknown Dynamic Objects in Real-time SLAM

We present DetectFusion, an RGB-D SLAM system that runs in real-time and can robustly handle semantically known and unknown objects that can move dynamically in the scene. Our system detects, segments and assigns semantic class labels to known objects in the scene, while tracking and reconstructing them even when they move independently in front of the monocular camera. In contrast to related work, we achieve real-time computational performance on semantic instance segmentation with a novel method combining 2D object detection and 3D geometric segmentation. In addition, we propose a method for detecting and segmenting the motion of semantically unknown objects, thus further improving the accuracy of camera tracking and map reconstruction. We show that our method performs on par or better than previous work in terms of localization and object reconstruction accuracy, while achieving about 20 FPS even if the objects are segmented in each frame.

Clinical evaluation of semi-automatic opensource algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action

Computer assisted technologies based on algorithmic software segmentation are an increasing topic of interest in complex surgical cases. However - due to functional instability, time consuming software processes, personnel resources or licensed-based financial costs many segmentation processes are often outsourced from clinical centers to third parties and the industry. Therefore, the aim of this trial was to assess the practical feasibility of an easy available, functional stable and licensed-free segmentation approach to be used in the clinical practice. In this retrospective, randomized, controlled trail the accuracy and accordance of the open-source based segmentation algorithm GrowCut (GC) was assessed through the comparison to the manually generated ground truth of the same anatomy using 10 CT lower jaw data-sets from the clinical routine. Assessment parameters were the segmentation time, the volume, the voxel number, the Dice Score (DSC) and the Hausdorff distance (HD). Overall segmentation times were about one minute. Mean DSC values of over 85% and HD below 33.5 voxel could be achieved. Statistical differences between the assessment parameters were not significant (p<0.05) and correlation coefficients were close to the value one (r > 0.94). Complete functional stable and time saving segmentations with high accuracy and high positive correlation could be performed by the presented interactive open-source based approach. In the cranio-maxillofacial complex the used method could represent an algorithmic alternative for image-based segmentation in the clinical practice for e.g. surgical treatment planning or visualization of postoperative results and offers several advantages. Systematic comparisons to other segmentation approaches or with a greater data amount are areas of future works.

In-depth Assessment of an Interactive Graph-based Approach for the Segmentation for Pancreatic Metastasis in Ultrasound Acquisitions of the Liver with two Specialists in Internal Medicine

The manual outlining of hepatic metastasis in (US) ultrasound acquisitions from patients suffering from pancreatic cancer is common practice. However, such pure manual measurements are often very time consuming, and the results repeatedly differ between the raters. In this contribution, we study the in-depth assessment of an interactive graph-based approach for the segmentation for pancreatic metastasis in US images of the liver with two specialists in Internal Medicine. Thereby, evaluating the approach with over one hundred different acquisitions of metastases. The two physicians or the algorithm had never assessed the acquisitions before the evaluation. In summary, the physicians first performed a pure manual outlining followed by an algorithmic segmentation over one month later. As a result, the experts satisfied in up to ninety percent of algorithmic segmentation results. Furthermore, the algorithmic segmentation was much faster than manual outlining and achieved a median Dice Similarity Coefficient (DSC) of over eighty percent. Ultimately, the algorithm enables a fast and accurate segmentation of liver metastasis in clinical US images, which can support the manual outlining in daily practice.

Algorithm guided outlining of 105 pancreatic cancer liver metastases in Ultrasound

Manual segmentation of hepatic metastases in ultrasound images acquired from patients suffering from pancreatic cancer is common practice. Semiautomatic measurements promising assistance in this process are often assessed using a small number of lesions performed by examiners who already know the algorithm. In this work, we present the application of an algorithm for the segmentation of liver metastases due to pancreatic cancer using a set of 105 different images of metastases. The algorithm and the two examiners had never assessed the images before. The examiners first performed a manual segmentation and, after five weeks, a semiautomatic segmentation using the algorithm. They were satisfied in up to 90% of the cases with the semiautomatic segmentation results. Using the algorithm was significantly faster and resulted in a median Dice similarity score of over 80%. Estimation of the inter-operator variability by using the intra class correlation coefficient was good with 0.8. In conclusion, the algorithm facilitates fast and accurate segmentation of liver metastases, comparable to the current gold standard of manual segmentation.

Computer-aided position planning of miniplates to treat facial bone defects

In this contribution, a software system for computer-aided position planning of miniplates to treat facial bone defects is proposed. The intra-operatively used bone plates have to be passively adapted on the underlying bone contours for adequate bone fragment stabilization. However, this procedure can lead to frequent intra-operatively performed material readjustments especially in complex surgical cases. Our approach is able to fit a selection of common implant models on the surgeon's desired position in a 3D computer model. This happens with respect to the surrounding anatomical structures, always including the possibility of adjusting both the direction and the position of the used osteosynthesis material. By using the proposed software, surgeons are able to pre-plan the out coming implant in its form and morphology with the aid of a computer-visualized model within a few minutes. Further, the resulting model can be stored in STL file format, the commonly used format for 3D printing. Using this technology, surgeons are able to print the virtual generated implant, or create an individually designed bending tool. This method leads to adapted osteosynthesis materials according to the surrounding anatomy and requires further a minimum amount of money and time.

Interactive Outlining of Pancreatic Cancer Liver Metastases in Ultrasound Images

Ultrasound (US) is the most commonly used liver imaging modality worldwide. Due to its low cost, it is increasingly used in the follow-up of cancer patients with metastases localized in the liver. In this contribution, we present the results of an interactive segmentation approach for liver metastases in US acquisitions. A (semi-) automatic segmentation is still very challenging because of the low image quality and the low contrast between the metastasis and the surrounding liver tissue. Thus, the state of the art in clinical practice is still manual measurement and outlining of the metastases in the US images. We tackle the problem by providing an interactive segmentation approach providing real-time feedback of the segmentation results. The approach has been evaluated with typical US acquisitions from the clinical routine, and the datasets consisted of pancreatic cancer metastases. Even for difficult cases, satisfying segmentations results could be achieved because of the interactive real-time behavior of the approach. In total, 40 clinical images have been evaluated with our method by comparing the results against manual ground truth segmentations. This evaluation yielded to an average Dice Score of 85% and an average Hausdorff Distance of 13 pixels.