Due to the increasing availability of whole slide scanners facilitating digitization of histopathological tissue, there is a strong demand for the development of computer based image analysis systems. In this work, the focus is on the segmentation of the glomeruli constituting a highly relevant structure in renal histopathology, which has not been investigated before in combination with CNNs. We propose two different CNN cascades for segmentation applications with sparse objects. These approaches are applied to the problem of glomerulus segmentation and compared with conventional fully-convolutional networks. Overall, with the best performing cascade approach, single CNNs are outperformed and a pixel-level Dice similarity coefficient of 0.90 is obtained. Combined with qualitative and further object-level analyses the obtained results are assessed as excellent also compared to recent approaches. In conclusion, we can state that especially one of the proposed cascade networks proved to be a highly powerful tool for segmenting the renal glomeruli providing best segmentation accuracies and also keeping the computing time at a low level.
To circumvent the need for large annotated training data, @cite_16 proposed an unsupervised segmentation algorithm. The authors aim at segmenting the Bowman's capsule surrounding the glomerulus by applying a color-based segmentation approach. The segmentation method consists of k-means clustering after thresholding including morphological operations. The inherent problem here is, that the Bowman's capsule is not always visible, depending on the staining protocol as well as the cutting plane (Fig. , ). Therefore, this method is not capable of generating a reliable precise segmentation of all objects.
@cite_16
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Convolutional neural networks (CNNs) have shown remarkable results over the last several years for a wide range of computer vision tasks. A new architecture recently introduced by , referred to as a capsule networks with dynamic routing, has shown great initial results for digit recognition and small image classification. The success of capsule networks lies in their ability to preserve more information about the input by replacing max-pooling layers with convolutional strides and dynamic routing, allowing for preservation of part-whole relationships in the data. This preservation of the input is demonstrated by reconstructing the input from the output capsule vectors. Our work expands the use of capsule networks to the task of object segmentation for the first time in the literature. We extend the idea of convolutional capsules with locally-connected routing and propose the concept of deconvolutional capsules. Further, we extend the masked reconstruction to reconstruct the positive input class. The proposed convolutional-deconvolutional capsule network, called SegCaps, shows strong results for the task of object segmentation with substantial decrease in parameter space. As an example application, we applied the proposed SegCaps to segment pathological lungs from low dose CT scans and compared its accuracy and efficiency with other U-Net-based architectures. SegCaps is able to handle large image sizes (512 x 512) as opposed to baseline capsules (typically less than 32 x 32). The proposed SegCaps reduced the number of parameters of U-Net architecture by 95.4 while still providing a better segmentation accuracy. Systemic Lupus Erythematosus involvement of the kidneys is associated with high morbidity and mortality. Inter-observer variability can also lead to an incorrect assessment of the disease. Computer aided image analysis can potentially be used to advance the understanding, diagnosis and treatment of Lupus. Our research focuses on the image analysis of kidney biopsies for quantifying tissue characteristics relevant to Lupus. In this paper we describe an algorithm for identifying glomeruli in H&E stained mouse renal biopsies. The proposed approach uses color segmentation to identify all objects in the image that potentially correspond to the Bowman's space around the glomeruli. This is followed by a perceptual grouping procedure to group objects based on their size, location and orientation. We present an unsupervised multilevel segmentation scheme for automatically segmenting grayscale and color images.Fuzzy 2-partition entropy is combined with Graph Cut to form a bi-level segmentation operator that splits a given region into 2 parts based on both global optimal threshold and local spatial coherence.A multilevel segmentation scheme iteratively performs on selected regions and color channels, producing a coarse-to-fine hierarchy of segments.The presented algorithm is evaluated using the Berkeley Segmentation Database and achieves competitive results compared with the state-of-the-art methods. The fuzzy c-partition entropy has been widely adopted as a global optimization technique for finding the optimal thresholds when performing multilevel gray image segmentation. Nevertheless, existing fuzzy c-partition entropy approaches generally have two limitations, i.e., partition number cneeds to be manually tuned for different input and the methods can process grayscale images only. To address these two limitations, an unsupervised multilevel segmentation algorithm is presented in this paper. The core step of our algorithm is a bi-level segmentation operator, which uses binary graph cuts to maximize both fuzzy 2-partition entropy and segmentation smoothness. By iteratively performing this bi-level segmentation operator, multilevel image segmentation is achieved in a hierarchical manner: Starting from the input color image, our algorithm first picks the color channel that can best segment the image into two labels, and then iteratively selects channels to further split each labels until convergence. The experimental results demonstrate the presented hierarchical segmentation scheme can efficiently segment both grayscale and color images. Quantitative evaluations over classic gray images and the Berkeley Segmentation Database show that our method is comparable to the state-of-the-art multi-scale segmentation methods, yet has the advantage of being unsupervised, efficient, and easy to implement. In this paper, we present a superpixel segmentation algorithm called linear spectral clustering (LSC), which is capable of producing superpixels with both high boundary adherence and visual compactness for natural images with low computational costs. In LSC, a normalized cuts-based formulation of image segmentation is adopted using a distance metric that measures both the color similarity and the space proximity between image pixels. However, rather than directly using the traditional eigen-based algorithm, we approximate the similarity metric through a deliberately designed kernel function such that pixel values can be explicitly mapped to a high-dimensional feature space. We then apply the conclusion that by appropriately weighting each point in this feature space, the objective functions of the weighted K-means and the normalized cuts share the same optimum points. Consequently, it is possible to optimize the cost function of the normalized cuts by iteratively applying simple K-means clustering in the proposed feature space. LSC possesses linear computational complexity and high memory efficiency, since it avoids both the decomposition of the affinity matrix and the generation of the large kernel matrix. By utilizing the underlying mathematical equivalence between the two types of seemingly different methods, LSC successfully preserves global image structures through efficient local operations. Experimental results show that LSC performs as well as or even better than the state-of-the-art superpixel segmentation algorithms in terms of several commonly used evaluation metrics in image segmentation. The applicability of LSC is further demonstrated in two related computer vision tasks. Conventional unsupervised image segmentation methods use color and geometric information and apply clustering algorithms over pixels. They preserve object boundaries well but often suffer from over-segmentation due to noise and artifacts in the images. In this paper, we contribute on a preprocessing step for image smoothing, which alleviates the burden of conventional unsupervised image segmentation and enhance their performance. Our approach relies on a convolutional autoencoder (CAE) with the total variation loss (TVL) for unsupervised learning. We show that, after our CAE-TVL preprocessing step, the over-segmentation effect is significantly reduced using the same unsupervised image segmentation methods. We evaluate our approach using the BSDS500 image segmentation benchmark dataset and show the performance enhancement introduced by our approach in terms of both increased segmentation accuracy and reduced computation time. We examine the robustness of the trained CAE and show that it is directly applicable to other natural scene images. The morphology of glands has been used routinely by pathologists to assess the malignancy degree of adenocarcinomas. Accurate segmentation of glands from histology images is a crucial step to obtain reliable morphological statistics for quantitative diagnosis. In this paper, we proposed an efficient deep contour-aware network (DCAN) to solve this challenging problem under a unified multi-task learning framework. In the proposed network, multi-level contextual features from the hierarchical architecture are explored with auxiliary supervision for accurate gland segmentation. When incorporated with multi-task regularization during the training, the discriminative capability of intermediate features can be further improved. Moreover, our network can not only output accurate probability maps of glands, but also depict clear contours simultaneously for separating clustered objects, which further boosts the gland segmentation performance. This unified framework can be efficient when applied to large-scale histopathological data without resorting to additional steps to generate contours based on low-level cues for post-separating. Our method won the 2015 MICCAI Gland Segmentation Challenge out of 13 competitive teams, surpassing all the other methods by a significant margin. In this work, we address the problem of performing class specific unsupervised object segmentation, i.e., automatic segmentation without annotated training images. We propose a hybrid graph model (HGM) to integrate recognition and segmentation into a unified process. The vertices of a hybrid graph represent the entities associated to the object class or local image features. The vertices are connected by directed edges and or undirected ones, which represent the dependence between the shape priors of the class (for recognition) and the similarity between the color texture priors within an image (for segmentation), respectively. By simultaneously considering the Markov chain formed by the directed subgraph and the minimal cut of the undirected subgraph, the likelihood that the vertices belong to the underlying class can be computed. Given a set of images each containing objects of the same class, our HGM based method automatically identifies in each image the area that the objects occupy. Experiments on 14 sets of images show promising results. The watershed is one of the latest segmentation tools developed in mathematical morphology. In order to prevent its oversegmentation, the notion of dynamics of a minimum, based on geodesic reconstruction, has been proposed. In this paper, we extend the notion of dynamics to the contour arcs. This notion acts as a measure of the saliency of the contour. Contrary to the dynamics of minima, our concept reflects the extension and shape of the corresponding object in the image. This representation is also much more natural, because it is expressed in terms of partitions of the plane, i.e., segmentations. A hierarchical segmentation process is then derived, which gives a compact description of the image, containing all the segmentations one can obtain by the notion of dynamics, by means of a simple thresholding. Finally, efficient algorithms for computing the geodesic reconstruction as well as the dynamics of contours are presented. We present an approach for autonomous interactive object segmentation by a humanoid robot. The visual segmentation of unknown objects in a complex scene is an important prerequisite for e.g. object learning or grasping, but extremely difficult to achieve through passive observation only. Our approach uses the manipulative capabilities of humanoid robots to induce motion on the object and thus integrates the robots manipulation and sensing capabilities to segment previously unknown objects. We show that this is possible without any human guidance or pre-programmed knowledge, and that the resulting motion allows for reliable and complete segmentation of new objects in an unknown and cluttered environment. We extend our previous work, which was restricted to textured objects, by devising new methods for the generation of object hypotheses and the estimation of their motion after being pushed by the robot. These methods are mainly based on the analysis of motion of color annotated 3D points obtained from stereo vision, and allow the segmentation of textured as well as non-textured rigid objects. In order to evaluate the quality of the obtained segmentations, they are used to train a simple object recognizer. The approach has been implemented and tested on the humanoid robot ARMAR-III, and the experimental results confirm its applicability on a wide variety of objects even in highly cluttered scenes. We present a method for multi-class segmentation from RGB-D data in a realistic warehouse picking setting. The method computes pixel-wise probabilities and combines them to find a coherent object segmentation. It reliably segments objects in cluttered scenarios, even when objects are translucent, reflective, highly deformable, have fuzzy surfaces, or consist of loosely coupled components. The robust performance results from the exploitation of problem structure inherent to the warehouse setting. The proposed method proved its capabilities as part of our winning entry to the 2015 Amazon Picking Challenge. We present a detailed experimental analysis of the contribution of different information sources, compare our method to standard segmentation techniques, and assess possible extensions that further enhance the algorithm's capabilities. We release our software and data sets as open source. This paper introduces to use semi-supervised learning for large scale image co segmentation. Different from traditional unsupervised cosegmentation that does not use any segmentation ground truth, semi-supervised cosegmentation exploits the similarity from both the very limited training image foregrounds, as well as the common object shared between the large number of unsegmented images. This would be a much practical way to effectively co segment a large number of related images simultaneously, where previous unsupervised co segmentation work poorly due to the large variances in appearance between different images and the lack of segmentation ground truth for guidance in co segmentation. For semi-supervised co segmentation in large scale, we propose an effective method by minimizing an energy function, which consists of the inter-image distance, the intra-image distance and the balance term. We also propose an iterative updating algorithm to efficiently solve this energy function, which decomposes the original energy minimization problem into sub-problems, and updates each image alternatively to reduce the number of variables in each sub-problem for computation efficiency. Experiment results on iCoseg and Pascal VOC datasets show that the proposed co segmentation method can effectively co segment hundreds of images in less than one minute. And our semi-supervised co segmentation is able to outperform both unsupervised co segmentation as well as fully supervised single image segmentation, especially when the training data is limited. We present in this paper a superpixel segmentation algorithm called Linear Spectral Clustering (LSC), which produces compact and uniform superpixels with low computational costs. Basically, a normalized cuts formulation of the superpixel segmentation is adopted based on a similarity metric that measures the color similarity and space proximity between image pixels. However, instead of using the traditional eigen-based algorithm, we approximate the similarity metric using a kernel function leading to an explicitly mapping of pixel values and coordinates into a high dimensional feature space. We revisit the conclusion that by appropriately weighting each point in this feature space, the objective functions of weighted K-means and normalized cuts share the same optimum point. As such, it is possible to optimize the cost function of normalized cuts by iteratively applying simple K-means clustering in the proposed feature space. LSC is of linear computational complexity and high memory efficiency and is able to preserve global properties of images. Experimental results show that LSC performs equally well or better than state of the art superpixel segmentation algorithms in terms of several commonly used evaluation metrics in image segmentation. Performing data augmentation for learning deep neural networks is well known to be important for training visual recognition systems. By artificially increasing the number of training examples, it helps reducing overfitting and improves generalization. For object detection, classical approaches for data augmentation consist of generating images obtained by basic geometrical transformations and color changes of original training images. In this work, we go one step further and leverage segmentation annotations to increase the number of object instances present on training data. For this approach to be successful, we show that modeling appropriately the visual context surrounding objects is crucial to place them in the right environment. Otherwise, we show that the previous strategy actually hurts. With our context model, we achieve significant mean average precision improvements when few labeled examples are available on the VOC’12 benchmark. Unsupervised over-segmentation of an image into regions of perceptually similar pixels, known as super pixels, is a widely used preprocessing step in segmentation algorithms. Super pixel methods reduce the number of regions that must be considered later by more computationally expensive algorithms, with a minimal loss of information. Nevertheless, as some information is inevitably lost, it is vital that super pixels not cross object boundaries, as such errors will propagate through later steps. Existing methods make use of projected color or depth information, but do not consider three dimensional geometric relationships between observed data points which can be used to prevent super pixels from crossing regions of empty space. We propose a novel over-segmentation algorithm which uses voxel relationships to produce over-segmentations which are fully consistent with the spatial geometry of the scene in three dimensional, rather than projective, space. Enforcing the constraint that segmented regions must have spatial connectivity prevents label flow across semantic object boundaries which might otherwise be violated. Additionally, as the algorithm works directly in 3D space, observations from several calibrated RGB+D cameras can be segmented jointly. Experiments on a large data set of human annotated RGB+D images demonstrate a significant reduction in occurrence of clusters crossing object boundaries, while maintaining speeds comparable to state-of-the-art 2D methods. We present a fully unsupervised method for morphological segmentation. Unlike many morphological segmentation systems, our method is based on semantic features rather than orthographic features. In order to capture word meanings, word embeddings are obtained from a two-level neural network [11]. We compute the semantic similarity between words using the neural word embeddings, which forms our baseline segmentation model. We model morphotactics with a bigram language model based on maximum likelihood estimates by using the initial segmentations from the baseline. Results show that using semantic features helps to improve morphological segmentation especially in agglutinating languages like Turkish. Our method shows competitive performance compared to other unsupervised morphological segmentation systems. This paper presents a comparison study between 10 automatic and six interactive methods for liver segmentation from contrast-enhanced CT images. It is based on results from the "MICCAI 2007 Grand Challenge" workshop, where 16 teams evaluated their algorithms on a common database. A collection of 20 clinical images with reference segmentations was provided to train and tune algorithms in advance. Participants were also allowed to use additional proprietary training data for that purpose. All teams then had to apply their methods to 10 test datasets and submit the obtained results. Employed algorithms include statistical shape models, atlas registration, level-sets, graph-cuts and rule-based systems. All results were compared to reference segmentations five error measures that highlight different aspects of segmentation accuracy. All measures were combined according to a specific scoring system relating the obtained values to human expert variability. In general, interactive methods reached higher average scores than automatic approaches and featured a better consistency of segmentation quality. However, the best automatic methods (mainly based on statistical shape models with some additional free deformation) could compete well on the majority of test images. The study provides an insight in performance of different segmentation approaches under real-world conditions and highlights achievements and limitations of current image analysis techniques. Despite the recent success of deep-learning based semantic segmentation, deploying a pre-trained road scene segmenter to a city whose images are not presented in the training set would not achieve satisfactory performance due to dataset biases. Instead of collecting a large number of annotated images of each city of interest to train or refine the segmenter, we propose an unsupervised learning approach to adapt road scene segmenters across different cities. By utilizing Google Street View and its timemachine feature, we can collect unannotated images for each road scene at different times, so that the associated static-object priors can be extracted accordingly. By advancing a joint global and class-specific domain adversarial learning framework, adaptation of pre-trained segmenters to that city can be achieved without the need of any user annotation or interaction. We show that our method improves the performance of semantic segmentation in multiple cities across continents, while it performs favorably against state-of-the-art approaches requiring annotated training data. Despite the recent success of deep-learning based semantic segmentation, deploying a pre-trained road scene segmenter to a city whose images are not presented in the training set would not achieve satisfactory performance due to dataset biases. Instead of collecting a large number of annotated images of each city of interest to train or refine the segmenter, we propose an unsupervised learning approach to adapt road scene segmenters across different cities. By utilizing Google Street View and its time-machine feature, we can collect unannotated images for each road scene at different times, so that the associated static-object priors can be extracted accordingly. By advancing a joint global and class-specific domain adversarial learning framework, adaptation of pre-trained segmenters to that city can be achieved without the need of any user annotation or interaction. We show that our method improves the performance of semantic segmentation in multiple cities across continents, while it performs favorably against state-of-the-art approaches requiring annotated training data. Real-time 3D perception of the surrounding environment is a crucial precondition for the reliable and safe application of mobile service robots in domestic environments. Using a RGB-D camera, we present a system for acquiring and processing 3D (semantic) information at frame rates of up to 30Hz that allows a mobile robot to reliably detect obstacles and segment graspable objects and supporting surfaces as well as the overall scene geometry. Using integral images, we compute local surface normals. The points are then clustered, segmented, and classified in both normal space and spherical coordinates. The system is tested in different setups in a real household environment. The results show that the system is capable of reliably detecting obstacles at high frame rates, even in case of obstacles that move fast or do not considerably stick out of the ground. The segmentation of all planes in the 3D data even allows for correcting characteristic measurement errors and for reconstructing the original scene geometry in far ranges. We propose a novel approach for solving the perceptual grouping problem in vision. Rather than focusing on local features and their consistencies in the image data, our approach aims at extracting the global impression of an image. We treat image segmentation as a graph partitioning problem and propose a novel global criterion, the normalized cut, for segmenting the graph. The normalized cut criterion measures both the total dissimilarity between the different groups as well as the total similarity within the groups. We show that an efficient computational technique based on a generalized eigenvalue problem can be used to optimize this criterion. We applied this approach to segmenting static images, as well as motion sequences, and found the results to be very encouraging.