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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Training a fully convolutional network for pixel-wise (or voxel-wise) image segmentation normally requires a large number of training images with corresponding ground truth label maps. However, it is a challenge to obtain such a large training set in the medical imaging domain, where expert annotations are time-consuming and difficult to obtain. In this paper, we propose a semi-supervised learning approach, in which a segmentation network is trained from both labelled and unlabelled data. The network parameters and the segmentations for the unlabelled data are alternately updated. We evaluate the method for short-axis cardiac MR image segmentation and it has demonstrated a high performance, outperforming a baseline supervised method. The mean Dice overlap metric is 0.92 for the left ventricular cavity, 0.85 for the myocardium and 0.89 for the right ventricular cavity. It also outperforms a state-of-the-art multi-atlas segmentation method by a large margin and the speed is substantially faster. Quantitative magnetic resonance analysis often requires accurate, robust, and reliable automatic extraction of anatomical structures. Recently, template-warping methods incorporating a label fusion strategy have demonstrated high accuracy in segmenting cerebral structures. In this study, we propose a novel patch-based method using expert manual segmentations as priors to achieve this task. Inspired by recent work in image denoising, the proposed nonlocal patch-based label fusion produces accurate and robust segmentation. Validation with two different datasets is presented. In our experiments, the hippocampi of 80 healthy subjects and the lateral ventricles of 80 patients with Alzheimer's disease were segmented. The influence on segmentation accuracy of different parameters such as patch size and number of training subjects was also studied. A comparison with an appearance-based method and a template-based method was also carried out. The highest median kappa index values obtained with the proposed method were 0.884 for hippocampus segmentation and 0.959 for lateral ventricle segmentation. Surgical tool segmentation in endoscopic images is the first step towards pose estimation and (sub-)task automation in challenging minimally invasive surgical operations. While many approaches in the literature have shown great results using modern machine learning methods such as convolutional neural networks, the main bottleneck lies in the acquisition of a large number of manually-annotated images for efficient learning. This is especially true in surgical context, where patient-to-patient differences impede the overall generalizability. In order to cope with this lack of annotated data, we propose a self-supervised approach in a robot-assisted context. To our knowledge, the proposed approach is the first to make use of the kinematic model of the robot in order to generate training labels. The core contribution of the paper is to propose an optimization method to obtain good labels for training despite an unknown hand-eye calibration and an imprecise kinematic model. The labels can subsequently be used for fine-tuning a fully-convolutional neural network for pixel-wise classification. As a result, the tool can be segmented in the endoscopic images without needing a single manually-annotated image. Experimental results on phantom and in vivo datasets obtained using a flexible robotized endoscopy system are very promising. 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. In this paper, we present an efficient approach for unsupervised segmenta- tion of natural and textural images based on the extraction o fi mage features and a fast active contour segmentation model. We address the problem of textures where neither the gray-level information nor the boundary information is adequate for object extraction. This is often the case of natural images compose do f both homogeneous and textured regions. Because these images cannot be in generaldirectly processed by the gray-level information, we propose a new texture descripto rw hich intrinsically def ines the geometry of textures using semi-local image informatio na nd tools from differen- tial geometry. Then, we use the popular Kullback-Leibler distance to design an active contour model which distinguishes the background and textures of interest. The exis- tence of a minimizing solution to the proposed segmentationmodel is proven. Finally, at exture segmentation algorithm based on the Split-Bregma nm ethod is introduced to extract meaningful objects in a fast way. Promising synthetic and real-world results for gray-scale and color images are presented. We consider the problem of segmenting a biomedical image into anatomical regions of interest. We specifically address the frequent scenario where we have no paired training data that contains images and their manual segmentations. Instead, we employ unpaired segmentation images that we use to build an anatomical prior. Critically these segmentations can be derived from imaging data from a different dataset and imaging modality than the current task. We introduce a generative probabilistic model that employs the learned prior through a convolutional neural network to compute segmentations in an unsupervised setting. We conducted an empirical analysis of the proposed approach in the context of structural brain MRI segmentation, using a multi-study dataset of more than 14,000 scans. Our results show that an anatomical prior enables fast unsupervised segmentation which is typically not possible using standard convolutional networks. The integration of anatomical priors can facilitate CNN-based anatomical segmentation in a range of novel clinical problems, where few or no annotations are available and thus standard networks are not trainable. The code, model definitions and model weights are freely available at http: github.com adalca neuron. 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. In this paper, we propose a novel approach of learning mid-level filters from automatically discovered patch clusters for person re-identification. It is well motivated by our study on what are good filters for person re-identification. Our mid-level filters are discriminatively learned for identifying specific visual patterns and distinguishing persons, and have good cross-view invariance. First, local patches are qualitatively measured and classified with their discriminative power. Discriminative and representative patches are collected for filter learning. Second, patch clusters with coherent appearance are obtained by pruning hierarchical clustering trees, and a simple but effective cross-view training strategy is proposed to learn filters that are view-invariant and discriminative. Third, filter responses are integrated with patch matching scores in RankSVM training. The effectiveness of our approach is validated on the VIPeR dataset and the CUHK01 dataset. The learned mid-level features are complementary to existing handcrafted low-level features, and improve the best Rank-1 matching rate on the VIPeR dataset by 14 . Training deep fully convolutional neural networks (F-CNNs) for semantic image segmentation requires access to abundant labeled data. While large datasets of unlabeled image data are available in medical applications, access to manually labeled data is very limited. We propose to automatically create auxiliary labels on initially unlabeled data with existing tools and to use them for pre-training. For the subsequent fine-tuning of the network with manually labeled data, we introduce error corrective boosting (ECB), which emphasizes parameter updates on classes with lower accuracy. Furthermore, we introduce SkipDeconv-Net (SD-Net), a new F-CNN architecture for brain segmentation that combines skip connections with the unpooling strategy for upsampling. The SD-Net addresses challenges of severe class imbalance and errors along boundaries. With application to whole-brain MRI T1 scan segmentation, we generate auxiliary labels on a large dataset with FreeSurfer and fine-tune on two datasets with manual annotations. Our results show that the inclusion of auxiliary labels and ECB yields significant improvements. SD-Net segments a 3D scan in 7 secs in comparison to 30 hours for the closest multi-atlas segmentation method, while reaching similar performance. It also outperforms the latest state-of-the-art F-CNN models. In this paper we present a learning based method for vessel segmentation in angiographic videos. Vessel segmentation is an important task in medical imaging and has been investigated extensively in the past. Traditional approaches often require pre-processing steps, standard conditions or manually set seed points. Our method is automatic, fast and robust towards noise often seen in low radiation X-ray images. Furthermore, it can be easily trained and used for any kind of tubular structure. We formulate the segmentation task as a hierarchical learning problem over 3 levels: border points, cross-segments and vessel pieces, corresponding to the vessel's position, width and length. Following the marginal space learning paradigm the detection on each level is performed by a learned classifier. We use probabilistic boosting trees with Haar and steerable features. First results of segmenting the vessel which surrounds a guide wire in 200 frames are presented and future additions are discussed. 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. Abstract We introduce a new methodology that combines deep learning and level set for the automated segmentation of the left ventricle of the heart from cardiac cine magnetic resonance (MR) data. This combination is relevant for segmentation problems, where the visual object of interest presents large shape and appearance variations, but the annotated training set is small, which is the case for various medical image analysis applications, including the one considered in this paper. In particular, level set methods are based on shape and appearance terms that use small training sets, but present limitations for modelling the visual object variations. Deep learning methods can model such variations using relatively small amounts of annotated training, but they often need to be regularised to produce good generalisation. Therefore, the combination of these methods brings together the advantages of both approaches, producing a methodology that needs small training sets and produces accurate segmentation results. We test our methodology on the MICCAI 2009 left ventricle segmentation challenge database (containing 15 sequences for training, 15 for validation and 15 for testing), where our approach achieves the most accurate results in the semi-automated problem and state-of-the-art results for the fully automated challenge. This paper is the first to address the problem of unsupervised action localization in videos. Given unlabeled data without bounding box annotations, we propose a novel approach that: 1) Discovers action class labels and 2) Spatio-temporally localizes actions in videos. It begins by computing local video features to apply spectral clustering on a set of unlabeled training videos. For each cluster of videos, an undirected graph is constructed to extract a dominant set, which are known for high internal homogeneity and in-homogeneity between vertices outside it. Next, a discriminative clustering approach is applied, by training a classifier for each cluster, to iteratively select videos from the non-dominant set and obtain complete video action classes. Once classes are discovered, training videos within each cluster are selected to perform automatic spatio-temporal annotations, by first over-segmenting videos in each discovered class into supervoxels and constructing a directed graph to apply a variant of knapsack problem with temporal constraints. Knapsack optimization jointly collects a subset of supervoxels, by enforcing the annotated action to be spatio-temporally connected and its volume to be the size of an actor. These annotations are used to train SVM action classifiers. During testing, actions are localized using a similar Knapsack approach, where supervoxels are grouped together and SVM, learned using videos from discovered action classes, is used to recognize these actions. We evaluate our approach on UCF-Sports, Sub-JHMDB, JHMDB, THUMOS13 and UCF101 datasets. Our experiments suggest that despite using no action class labels and no bounding box annotations, we are able to get competitive results to the state-of-the-art supervised methods. A major problem among the elderly involves falling. The recognition of falls from video first requires the segmentation of the individual from the background. To ensure privacy, segmentation should result in a silhouette that is a binary map indicating only the body position of the individual in an image. We have previously demonstrated a segmentation method based on color that can recognize the silhouette and detect and remove shadows. After the silhouettes are obtained, we extract features and train hidden Markov models to recognize future performances of these known activities. In this paper, we present preliminary results that demonstrate the usefulness of this approach for distinguishing between a few common activities, specifically with fall detection in mind. and dynamic environments. High-level knowledge was fused with low-level feature-based classification to handle a time-varying background, and a decision process based on a fuzzy logic inference system was used to detach the moving objects from the human silhouette. One central task in silhouette extraction is background modeling. Once a background model is established, those image regions with significantly different characteristics from the background are considered foreground objects. In (5), a Least Median of Squares method was used to construct a background model, and in (6), a differencing function was proposed to extract moving human silhouettes. (7) demonstrated a non-parametric kernel density estimation method to model and subtract the human from a background. The adaptive background updating handles small motion in the background scene, such as moving tree branches. A slightly different approach outlined in (8) is based on processing in the YUV color space, and is capable of detecting shadows and extracting In this paper, the real-time segmentation of surgical instruments with color images used in minimally invasive surgery is addressed. This work has been developed in the scope of the robotized laparoscopic surgery, specifically for the detection and tracking of gray regions and accounting for images of met allic instruments inside the abdominal cavity. With this environment, the moving background due to the breathing motion, the non-uniform and time-varying lighting conditions and the presence of specularities are the main difficulties to overcome. Then, to achieve an automatic color segmentation suitable for robot control, we developed a technique based on a discriminant color feature with robustness capabilities with respect to intensity variations and specularities. We also designed an adaptive region growing with automatic region seed detection and a model-based region classification, both dedicated to laparoscopy. The foreseen application is a good training ground to evaluate the proposed technique and the effectiveness of this work has been demonstrated through experimental results with endoscopic image sequences to efficiently locate boundaries of a landmark-free needle-holder at half the video-rate. This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases. This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases. Large-scale training for semantic segmentation is challenging due to the expense of obtaining training data for this task relative to other vision tasks. We propose a novel training approach to address this difficulty. Given cheaply-obtained sparse image labelings, we propagate the sparse labels to produce guessed dense labelings. A standard CNN-based segmentation network is trained to mimic these labelings. The label-propagation process is defined via random-walk hitting probabilities, which leads to a differentiable parameterization with uncertainty estimates that are incorporated into our loss. We show that by learning the label-propagator jointly with the segmentation predictor, we are able to effectively learn semantic edges given no direct edge supervision. Experiments also show that training a segmentation network in this way outperforms the naive approach. The success and generalisation of deep learning algorithms heavily depend on learning good feature representations. In medical imaging this entails representing anatomical information, as well as properties related to the specific imaging setting. Anatomical information is required to perform further analysis, whereas imaging information is key to disentangle scanner variability and potential artefacts. The ability to factorise these would allow for training algorithms only on the relevant information according to the task. To date, such factorisation has not been attempted. In this paper, we propose a methodology of latent space factorisation relying on the cycle-consistency principle. As an example application, we consider cardiac MR segmentation, where we separate information related to the myocardium from other features related to imaging and surrounding substructures. We demonstrate the proposed method’s utility in a semi-supervised setting: we use very few labelled images together with many unlabelled images to train a myocardium segmentation neural network. Specifically, we achieve comparable performance to fully supervised networks using a fraction of labelled images in experiments on ACDC and a dataset from Edinburgh Imaging Facility QMRI. Code will be made available at https: github.com agis85 spatial_factorisation. In this paper we investigate the segmentation of closed contours in sub-cellular data using a framework that primarily combines the pairwise affinity grouping principles with a graph partitioning contour searching approach. One salient problem that precluded the application of these methods to large scale segmentation problems is the onerous computational complexity required to generate comprehensive representations that include all pairwise relationships between all pixels in the input data. To compensate for this problem a practical solution is to reduce the complexity of the input data by applying an oversegmentation technique prior to the application of the computationally demanding strands of the segmentation process. This approach opens the opportunity to build specific shape and intensity models that can be successfully employed to extract the salient structures in the input image which are further processed to identify the cycles in an undirected graph. The proposed framework has been applied to the segmentation of mitochondria membranes in electron microscopy (EM) data which are characterized by low contrast and low signal to noise ratio. The algorithm has been quantitatively evaluated using two datasets where the segmentation results have been compared with the corresponding manual annotations. The performance of the proposed algorithm has been measured using standard metrics such as Precision and Recall and the experimental results indicate a high level of segmentation accuracy.