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Semantic segmentation is a challenging computer vision task demanding a significant amount of pixel-level annotated data. Producing such data is a time-consuming and costly process, especially for domains with a scarcity of experts, such as medicine or forensic anthropology. While numerous semi-supervised approaches have been developed to make the most from the limited labeled data and ample amount of unlabeled data, domain-specific real-world datasets often have characteristics that both reduce the effectiveness of off-the-shelf state-of-the-art methods and also provide opportunities to create new methods that exploit these characteristics. We propose and evaluate a semi-supervised method that reuses available labels for unlabeled images of a dataset by exploiting existing similarities, while dynamically weighting the impact of these reused labels in the training process. We evaluate our method on a large dataset of human decomposition images and find that our method, while conceptually simple, outperforms state-of-the-art consistency and pseudo-labeling-based methods for the segmentation of this dataset. This paper includes graphic content of human decomposition.

\cite{rohe2016co} proposed Stochastic co-Blockmodel (ScBM) as a tool for detecting community structure of binary directed graph data in network studies. However, ScBM completely ignores node weight, and is unable to explain the block structure of directed weighted network which appears in various areas, such as biology, sociology, physiology and computer science. Here, to model directed weighted network, we introduce a Directed Distribution-Free model by releasing ScBM's distribution restriction. We also build an extension of the proposed model by considering variation of node degree. Our models do not require a specific distribution on generating elements of adjacency matrix but only a block structure on the expected adjacency matrix. Spectral algorithms with theoretical guarantee on consistent estimation of node label are presented to identify communities. Our proposed methods are illustrated by simulated and empirical examples.

LiDAR sensors are a powerful tool for robot simultaneous localization and mapping (SLAM) in unknown environments, but the raw point clouds they produce are dense, computationally expensive to store, and unsuited for direct use by downstream autonomy tasks, such as motion planning. For integration with motion planning, it is desirable for SLAM pipelines to generate lightweight geometric map representations. Such representations are also particularly well-suited for man-made environments, which can often be viewed as a so-called "Manhattan world" built on a Cartesian grid. In this work we present a 3D LiDAR SLAM algorithm for Manhattan world environments which extracts planar features from point clouds to achieve lightweight, real-time localization and mapping. Our approach generates plane-based maps which occupy significantly less memory than their point cloud equivalents, and are suited towards fast collision checking for motion planning. By leveraging the Manhattan world assumption, we target extraction of orthogonal planes to generate maps which are more structured and organized than those of existing plane-based LiDAR SLAM approaches. We demonstrate our approach in the high-fidelity AirSim simulator and in real-world experiments with a ground rover equipped with a Velodyne LiDAR. For both cases, we are able to generate high quality maps and trajectory estimates at a rate matching the sensor rate of 10 Hz.

Robustly classifying ground infrastructure such as roads and street crossings is an essential task for mobile robots operating alongside pedestrians. While many semantic segmentation datasets are available for autonomous vehicles, models trained on such datasets exhibit a large domain gap when deployed on robots operating in pedestrian spaces. Manually annotating images recorded from pedestrian viewpoints is both expensive and time-consuming. To overcome this challenge, we propose TrackletMapper, a framework for annotating ground surface types such as sidewalks, roads, and street crossings from object tracklets without requiring human-annotated data. To this end, we project the robot ego-trajectory and the paths of other traffic participants into the ego-view camera images, creating sparse semantic annotations for multiple types of ground surfaces from which a ground segmentation model can be trained. We further show that the model can be self-distilled for additional performance benefits by aggregating a ground surface map and projecting it into the camera images, creating a denser set of training annotations compared to the sparse tracklet annotations. We qualitatively and quantitatively attest our findings on a novel large-scale dataset for mobile robots operating in pedestrian areas. Code and dataset will be made available at //trackletmapper.cs.uni-freiburg.de.

Exploration of unknown environments is a fundamental problem in robotics and an essential component in numerous applications of autonomous systems. A major challenge in exploring unknown environments is that the robot has to plan with the limited information available at each time step. While most current approaches rely on heuristics and assumption to plan paths based on these partial observations, we instead propose a novel way to integrate deep learning into exploration by leveraging 3D scene completion for informed, safe, and interpretable exploration mapping and planning. Our approach, SC-Explorer, combines scene completion using a novel incremental fusion mechanism and a newly proposed hierarchical multi-layer mapping approach, to guarantee safety and efficiency of the robot. We further present an informative path planning method, leveraging the capabilities of our mapping approach and a novel scene-completion-aware information gain. While our method is generally applicable, we evaluate it in the use case of a Micro Aerial Vehicle (MAV). We thoroughly study each component in high-fidelity simulation experiments using only mobile hardware, and show that our method can speed up coverage of an environment by 73% compared to the baselines with only minimal reduction in map accuracy. Even if scene completions are not included in the final map, we show that they can be used to guide the robot to choose more informative paths, speeding up the measurement of the scene with the robot's sensors by 35%. We validate our system on a fully autonomous MAV, showing rapid and reliable scene coverage even in a complex cluttered environment. We make our methods available as open-source.

The extraction of contrast-filled vessels from X-ray coronary angiography(XCA) image sequence has important clinical significance for intuitively diagnosis and therapy. In this study, XCA image sequence O is regarded as a three-dimensional tensor input, vessel layer H is a sparse tensor, and background layer B is a low-rank tensor. Using tensor nuclear norm(TNN) minimization, a novel method for vessel layer extraction based on tensor robust principal component analysis(TRPCA) is proposed. Furthermore, considering the irregular movement of vessels and the dynamic interference of surrounding irrelevant tissues, the total variation(TV) regularized spatial-temporal constraint is introduced to separate the dynamic background E. Subsequently, for the vessel images with uneven contrast distribution, a two-stage region growth(TSRG) method is utilized for vessel enhancement and segmentation. A global threshold segmentation is used as the pre-processing to obtain the main branch, and the Radon-Like features(RLF) filter is used to enhance and connect broken minor segments, the final vessel mask is constructed by combining the two intermediate results. We evaluated the visibility of TV-TRPCA algorithm for foreground extraction and the accuracy of TSRG algorithm for vessel segmentation on real clinical XCA image sequences and third-party database. Both qualitative and quantitative results verify the superiority of the proposed methods over the existing state-of-the-art approaches.

Optical coherence tomography (OCT) is a micrometer-scale, volumetric imaging modality that has become a clinical standard in ophthalmology. OCT instruments image by raster-scanning a focused light spot across the retina, acquiring sequential cross-sectional images to generate volumetric data. Patient eye motion during the acquisition poses unique challenges: Non-rigid, discontinuous distortions can occur, leading to gaps in data and distorted topographic measurements. We present a new distortion model and a corresponding fully-automatic, reference-free optimization strategy for computational motion correction in orthogonally raster-scanned, retinal OCT volumes. Using a novel, domain-specific spatiotemporal parametrization of forward-warping displacements, eye motion can be corrected continuously for the first time. Parameter estimation with temporal regularization improves robustness and accuracy over previous spatial approaches. We correct each A-scan individually in 3D in a single mapping, including repeated acquisitions used in OCT angiography protocols. Specialized 3D forward image warping reduces median runtime to < 9 s, fast enough for clinical use. We present a quantitative evaluation on 18 subjects with ocular pathology and demonstrate accurate correction during microsaccades. Transverse correction is limited only by ocular tremor, whereas submicron repeatability is achieved axially (0.51 um median of medians), representing a dramatic improvement over previous work. This allows assessing longitudinal changes in focal retinal pathologies as a marker of disease progression or treatment response, and promises to enable multiple new capabilities such as supersampled/super-resolution volume reconstruction and analysis of pathological eye motion occuring in neurological diseases.

Since the preparation of labeled data for training semantic segmentation networks of point clouds is a time-consuming process, weakly supervised approaches have been introduced to learn from only a small fraction of data. These methods are typically based on learning with contrastive losses while automatically deriving per-point pseudo-labels from a sparse set of user-annotated labels. In this paper, our key observation is that the selection of what samples to annotate is as important as how these samples are used for training. Thus, we introduce a method for weakly supervised segmentation of 3D scenes that combines self-training with active learning. The active learning selects points for annotation that likely result in performance improvements to the trained model, while the self-training makes efficient use of the user-provided labels for learning the model. We demonstrate that our approach leads to an effective method that provides improvements in scene segmentation over previous works and baselines, while requiring only a small number of user annotations.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.