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.
Few approaches were proposed to perform segmentation of the glomeruli. @cite_12 introduced a separate detection and segmentation stage, both based on training a supervised classification model, specifically a linear support vector machine. For detection and segmentation different versions of histogram of oriented gradient descriptors were applied. Detection was performed by means of the sliding window approach. For segmentation, a polygon-fitting technique was utilized to determine the precise outline of the objects by adding a circularity constraint. For learning to distinguish between border region and non-border regions (and not between inside and outside of a glomerulus), this method requires highly precise annotations for training. This method was developed for a specific staining (desmin) which highlights cells in glomeruli.
@cite_12
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In this paper, we address the problems of contour detection, bottom-up grouping, object detection and semantic segmentation on RGB-D data. We focus on the challenging setting of cluttered indoor scenes, and evaluate our approach on the recently introduced NYU-Depth V2 (NYUD2) dataset (, ECCV, 2012). We propose algorithms for object boundary detection and hierarchical segmentation that generalize the @math gPb-ucm approach of (TPAMI, 2011) by making effective use of depth information. We show that our system can label each contour with its type (depth, normal or albedo). We also propose a generic method for long-range amodal completion of surfaces and show its effectiveness in grouping. We train RGB-D object detectors by analyzing and computing histogram of oriented gradients on the depth image and using them with deformable part models (, TPAMI, 2010). We observe that this simple strategy for training object detectors significantly outperforms more complicated models in the literature. We then turn to the problem of semantic segmentation for which we propose an approach that classifies superpixels into the dominant object categories in the NYUD2 dataset. We design generic and class-specific features to encode the appearance and geometry of objects. We also show that additional features computed from RGB-D object detectors and scene classifiers further improves semantic segmentation accuracy. In all of these tasks, we report significant improvements over the state-of-the-art. Early detection of Ground Glass Nodule (GGN) in lung Computed Tomography (CT) images is important for lung cancer prognosis. Due to its indistinct boundaries, manual detection and segmentation of GGN is labor-intensive and problematic. In this paper, we propose a novel multi-level learning-based framework for automatic detection and segmentation of GGN in lung CT images. Our main contributions are: firstly, a multi-level statistical learning-based approach that seamlessly integrates segmentation and detection to improve the overall accuracy for GGN detection (in a subvolume). The classification is done at two levels, both voxel-level and object-level. The algorithm starts with a three-phase voxel-level classification step, using volumetric features computed per voxel to generate a GGN class-conditional probability map. GGN candidates are then extracted from this probability map by integrating prior knowledge of shape and location, and the GGN object-level classifier is used to determine the occurrence of the GGN. Secondly, an extensive set of volumetric features are used to capture the GGN appearance. Finally, to our best knowledge, the GGN dataset used for experiments is an order of magnitude larger than previous work. The effectiveness of our method is demonstrated on a dataset of 1100 subvolumes (100 containing GGNs) extracted from about 200 subjects. Background Automated segmentation of fluorescently-labeled cell nuclei in 3D confocal microscope images is essential to many studies involving morphological and functional analysis. A common source of segmentation error is tight clustering of nuclei. There is a compelling need to minimize these errors for constructing highly automated scoring systems. Methods A combination of two approaches is presented. First, an improved distance transform combining intensity gradients and geometric distance is used for the watershed step. Second, an explicit mathematical model for the anatomic characteristics of cell nuclei such as size and shape measures is incorporated. This model is constructed automatically from the data. Deliberate initial over-segmentation of the image data is performed, followed by statistical model-based merging. A confidence score is computed for each detected nucleus, measuring how well the nucleus fits the model. This is used in combination with the intensity gradient to control the merge decisions. Results Experimental validation on a set of rodent brain cell images showed 97 concordance with the human observer and significant improvement over prior methods. Conclusions Combining a gradient-weighted distance transform with a richer morphometric model significantly improves the accuracy of automated segmentation and FISH analysis. Cytometry Part A 56A:23–36, 2003. © 2003 Wiley-Liss, Inc. Contour detection has been a fundamental component in many image segmentation and object detection systems. Most previous work utilizes low-level features such as texture or saliency to detect contours and then use them as cues for a higher-level task such as object detection. However, we claim that recognizing objects and predicting contours are two mutually related tasks. Contrary to traditional approaches, we show that we can invert the commonly established pipeline: instead of detecting contours with low-level cues for a higher-level recognition task, we exploit object-related features as high-level cues for contour detection. We achieve this goal by means of a multi-scale deep network that consists of five convolutional layers and a bifurcated fully-connected sub-network. The section from the input layer to the fifth convolutional layer is fixed and directly lifted from a pre-trained network optimized over a large-scale object classification task. This section of the network is applied to four different scales of the image input. These four parallel and identical streams are then attached to a bifurcated sub-network consisting of two independently-trained branches. One branch learns to predict the contour likelihood (with a classification objective) whereas the other branch is trained to learn the fraction of human labelers agreeing about the contour presence at a given point (with a regression criterion). We show that without any feature engineering our multi-scale deep learning approach achieves state-of-the-art results in contour detection. In this paper, we propose a generalized Laplacian of Gaussian (LoG) (gLoG) filter for detecting general elliptical blob structures in images. The gLoG filter can not only accurately locate the blob centers but also estimate the scales, shapes, and orientations of the detected blobs. These functions can be realized by generalizing the common 3-D LoG scale-space blob detector to a 5-D gLoG scale-space one, where the five parameters are image-domain coordinates (x, y), scales (σx, σy), and orientation (θ), respectively. Instead of searching the local extrema of the image's 5-D gLoG scale space for locating blobs, a more feasible solution is given by locating the local maxima of an intermediate map, which is obtained by aggregating the log-scale-normalized convolution responses of each individual gLoG filter. The proposed gLoG-based blob detector is applied to both biomedical images and natural ones such as general road-scene images. For the biomedical applications on pathological and fluorescent microscopic images, the gLoG blob detector can accurately detect the centers and estimate the sizes and orientations of cell nuclei. These centers are utilized as markers for a watershed-based touching-cell splitting method to split touching nuclei and counting cells in segmentation-free images. For the application on road images, the proposed detector can produce promising estimation of texture orientations, achieving an accurate texture-based road vanishing point detection method. The implementation of our method is quite straightforward due to a very small number of tunable parameters. The automatic extraction of blood vessels in non-fluorescein eye fundus images is a tough task in applications such as diabetic retinopathy screening. However, vessel shapes have complex variations, and accurate modeling of retinal vascular structures is challenging. We have therefore developed a new approach to accurately extract blood vessels in non-fluorescein fundus images using an orientation-aware detector (OAD). The detector was designed according to the intrinsic property of vessels being locally oriented and having linearly elongated structures. We employ the OAD to extract vessel shapes with no assumptions on parametric orientations of vessel shapes. The orientations of vessels can be efficiently modeled by the energy distribution of Fourier transformation. Accordingly, both wide and thin vessels can be extracted with two-scale segmentation in which line operators are applied in large scale and the Gabor filter bank is applied in small scale. A post-processing technique, based on the path opening operation, is applied to eliminate false responses to nonvascular areas, such as retinal structures (optic disc and macula) and pathologies (exudates, hemorrhages,and microaneurysms). This makes the detector robust and structure-aware. By achieving a competitive CAL measurement of 80.82 for the DRIVE database and 68.94 for the STARE, the experimental results demonstrated that the OAD approach outperforms existing segmentation methods. Furthermore, the proposed approach effectively works with non-fluorescein fundus images and proves highly accurate and robust in complicated regions such as the central reflex, close vessels, and crossover points, despite a high level of illumination noise in the original data. We propose a novel approach to both learning and detecting local contour-based representations for mid-level features. Our features, called sketch tokens, are learned using supervised mid-level information in the form of hand drawn contours in images. Patches of human generated contours are clustered to form sketch token classes and a random forest classifier is used for efficient detection in novel images. We demonstrate our approach on both top-down and bottom-up tasks. We show state-of-the-art results on the top-down task of contour detection while being over 200x faster than competing methods. We also achieve large improvements in detection accuracy for the bottom-up tasks of pedestrian and object detection as measured on INRIA and PASCAL, respectively. These gains are due to the complementary information provided by sketch tokens to low-level features such as gradient histograms. An efficient optic disk localization and segmentation are important tasks in an automated retinal image analysis system. General-purpose edge detection algorithms often fail to segment the optic disk due to fuzzy boundaries, inconsistent image contrast or missing edge features. This paper presents a method to automatically locate and boundary detect of the optic disk. The detection procedure comprises two independent methodologies. On one hand, a location methodology obtains a pixel that belongs to the OD using iterative thresholding method followed by Principal Component Analysis techniques (PCA) and, on the other hand, a boundary segmentation methodology estimates the OD boundary by applying region-based active contour model in a variational level set formulation (RSF). The method uses an improved geometric active contour model which can not only solve the boundary leakage problem but also is less sensitive to intensity inhomogeneity The results from the RSF method were compared with conventional optic disk detection using a geometric active contour models (ACM) and later verified with hand-drawn ground truth. Results indicate 89 accuracy for identification and 95.05 average accuracy in localizing the optic disc boundary. In this paper, we focus on improving the proposal classification stage in the object detection task and present implicit negative sub-categorization and sink diversion to lift the performance by strengthening loss function in this stage. First, based on the observation that the “background” class is generally very diverse and thus challenging to be handled as a single indiscriminative class in existing state-of-the-art methods, we propose to divide the background category into multiple implicit sub-categories to explicitly differentiate diverse patterns within it. Second, since the ground truth class inevitably has low-value probability scores for certain images, we propose to add a “sink” class and divert the probabilities of wrong classes to this class when necessary, such that the ground truth label will still have a higher probability than other wrong classes even though it has low probability output. Additionally, we propose to use dilated convolution, which is widely used in the semantic segmentation task, for efficient and valuable context information extraction. Extensive experiments on PASCAL VOC 2007 and 2012 data sets show that our proposed methods based on faster R-CNN implementation can achieve state-of-the-art mAPs, i.e., 84.1 , 82.6 , respectively, and obtain 2.5 improvement on ILSVRC DET compared with that of ResNet. 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. This paper presents a new supervised method for vessel segmentation in retinal images. This method remolds the task of segmentation as a problem of cross-modality data transformation from retinal image to vessel map. A wide and deep neural network with strong induction ability is proposed to model the transformation, and an efficient training strategy is presented. Instead of a single label of the center pixel, the network can output the label map of all pixels for a given image patch. Our approach outperforms reported state-of-the-art methods in terms of sensitivity, specificity and accuracy. The result of cross-training evaluation indicates its robustness to the training set. The approach needs no artificially designed feature and no preprocessing step, reducing the impact of subjective factors. The proposed method has the potential for application in image diagnosis of ophthalmologic diseases, and it may provide a new, general, high-performance computing framework for image segmentation. In this paper, an effective model-based approach for computer-aided kidney segmentation of abdominal CT images with anatomic structure consideration is presented. This automatic segmentation system is expected to assist physicians in both clinical diagnosis and educational training. The proposed method is a coarse to fine segmentation approach divided into two stages. First, the candidate kidney region is extracted according to the statistical geometric location of kidney within the abdomen. This approach is applicable to images of different sizes by using the relative distance of the kidney region to the spine. The second stage identifies the kidney by a series of image processing operations. The main elements of the proposed system are: 1) the location of the spine is used as the landmark for coordinate references; 2) elliptic candidate kidney region extraction with progressive positioning on the consecutive CT images; 3) novel directional model for a more reliable kidney region seed point identification; and 4) adaptive region growing controlled by the properties of image homogeneity. In addition, in order to provide different views for the physicians, we have implemented a visualization tool that will automatically show the renal contour through the method of second-order neighborhood edge detection. We considered segmentation of kidney regions from CT scans that contain pathologies in clinical practice. The results of a series of tests on 358 images from 30 patients indicate an average correlation coefficient of up to 88 between automatic and manual segmentation We propose a shape-based, hierarchical part-template matching approach to simultaneous human detection and segmentation combining local part-based and global shape-template-based schemes. The approach relies on the key idea of matching a part-template tree to images hierarchically to detect humans and estimate their poses. For learning a generic human detector, a pose-adaptive feature computation scheme is developed based on a tree matching approach. Instead of traditional concatenation-style image location-based feature encoding, we extract features adaptively in the context of human poses and train a kernel-SVM classifier to separate human nonhuman patterns. Specifically, the features are collected in the local context of poses by tracing around the estimated shape boundaries. We also introduce an approach to multiple occluded human detection and segmentation based on an iterative occlusion compensation scheme. The output of our learned generic human detector can be used as an initial set of human hypotheses for the iterative optimization. We evaluate our approaches on three public pedestrian data sets (INRIA, MIT-CBCL, and USC-B) and two crowded sequences from Caviar Benchmark and Munich Airport data sets. Abstract This paper pertains to the detection of objects located in complex backgrounds. A feature-based segmentation approach to the object detection problem is pursued, where the features are computed over multiple spatial orientations and frequencies. The method proceeds as follows: a given image is passed through a bank of even-symmetric Gabor filters. A selection of these filtered images is made and each (selected) filtered image is subjected to a nonlinear (sigmoidal like) transformation. Then, a measure of texture energy is computed in a window around each transformed image pixel. The texture energy (“Gabor features”) and their spatial locations are inputted to a squared-error clustering algorithm. This clustering algorithm yields a segmentation of the original image—it assigns to each pixel in the image a cluster label that identifies the amount of mean local energy the pixel possesses across different spatial orientations and frequencies. The method is applied to a number of visual and infrared images, each one of which contains one or more objects. The region corresponding to the object is usually segmented correctly, and a unique signature of “Gabor features” is typically associated with the segment containing the object(s) of interest. Experimental results are provided to illustrate the usefulness of this object detection method in a number of problem domains. These problems arise in IVHS, military reconnaissance, fingerprint analysis, and image database query. By combining Histograms of Oriented Gradients (HOG) and Local Binary Pattern (LBP) as the feature set, we propose a novel human detection approach capable of handling partial occlusion. Two kinds of detectors, i.e., global detector for whole scanning windows and part detectors for local regions, are learned from the training data using linear SVM. For each ambiguous scanning window, we construct an occlusion likelihood map by using the response of each block of the HOG feature to the global detector. The occlusion likelihood map is then segmented by Mean-shift approach. The segmented portion of the window with a majority of negative response is inferred as an occluded region. If partial occlusion is indicated with high likelihood in a certain scanning window, part detectors are applied on the unoccluded regions to achieve the final classification on the current scanning window. With the help of the augmented HOG-LBP feature and the global-part occlusion handling method, we achieve a detection rate of 91.3 with FPPW= 10−6, 94.7 with FPPW= 10−5, and 97.9 with FPPW= 10−4 on the INRIA dataset, which, to our best knowledge, is the best human detection performance on the INRIA dataset. The global-part occlusion handling method is further validated using synthesized occlusion data constructed from the INRIA and Pascal dataset. Recently, deep convolutional neural networks (DCNNs) have significantly promoted the development of semantic image segmentation. However, previous works on learning the segmentation network often rely on a large number of ground-truths with pixel-level annotations, which usually require considerable human effort. In this paper, we explore a more challenging problem by learning to segment under image-level annotations. Specifically, our framework consists of two components. First, reliable hypotheses based localization maps are generated by incorporating the hypotheses-aware classification and cross-image contextual refinement. Second, the segmentation network can be trained in a supervised manner by these generated localization maps. We explore two network training strategies for achieving good segmentation performance. For the first strategy, a novel multi-label cross-entropy loss is proposed to train the network by directly using multiple localization maps for all classes, where each pixel contributes to each class with different weights. For the second strategy, the rough segmentation mask can be inferred from the localization maps, and then the network is optimized based on the single-label cross-entropy loss with the produced masks. We evaluate our methods on the PASCAL VOC 2012 segmentation benchmark. Extensive experimental results demonstrate the effectiveness of the proposed methods compared with the state-of-the-arts. HighlightsLocalization map generation is proposed by using the hypothesis-based classification.A novel multi-label loss is proposed to train the network based on localization maps.An effective method is proposed to predict the rough mask of the given training image.Our methods achieve new state-of-the-art results on PASCAL VOC 2012 benchmark. We address the problems of contour detection, bottom-up grouping and semantic segmentation using RGB-D data. We focus on the challenging setting of cluttered indoor scenes, and evaluate our approach on the recently introduced NYU-Depth V2 (NYUD2) dataset [27]. We propose algorithms for object boundary detection and hierarchical segmentation that generalize the gPb-ucm approach of [2] by making effective use of depth information. We show that our system can label each contour with its type (depth, normal or albedo). We also propose a generic method for long-range amodal completion of surfaces and show its effectiveness in grouping. We then turn to the problem of semantic segmentation and propose a simple approach that classifies super pixels into the 40 dominant object categories in NYUD2. We use both generic and class-specific features to encode the appearance and geometry of objects. We also show how our approach can be used for scene classification, and how this contextual information in turn improves object recognition. In all of these tasks, we report significant improvements over the state-of-the-art. 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. Abstract In many microscopy applications the images may contain both regions of low and high cell densities corresponding to different tissues or colonies at different stages of growth. This poses a challenge to most previously developed automated cell detection and counting methods, which are designed to handle either the low-density scenario (through cell detection) or the high-density scenario (through density estimation or texture analysis). The objective of this work is to detect all the instances of an object of interest in microscopy images. The instances may be partially overlapping and clustered. To this end we introduce a tree-structured discrete graphical model that is used to select and label a set of non-overlapping regions in the image by a global optimization of a classification score. Each region is labeled with the number of instances it contains – for example regions can be selected that contain two or three object instances, by defining separate classes for tuples of objects in the detection process. We show that this formulation can be learned within the structured output SVM framework and that the inference in such a model can be accomplished using dynamic programming on a tree structured region graph. Furthermore, the learning only requires weak annotations – a dot on each instance. The candidate regions for the selection are obtained as extremal region of a surface computed from the microscopy image, and we show that the performance of the model can be improved by considering a proxy problem for learning the surface that allows better selection of the extremal regions. Furthermore, we consider a number of variations for the loss function used in the structured output learning. The model is applied and evaluated over six quite disparate data sets of images covering: fluorescence microscopy, weak-fluorescence molecular images, phase contrast microscopy and histopathology images, and is shown to exceed the state of the art in performance. This paper presents a novel approach to face recognition, named Multi-resolution Histograms of Local Variation Patterns (MHLVP), in which face images are represented as the concatenation of the local spatial histogram of local variation patterns computed from the multi-resolution Gabor features. For a face image with abundant texture and shape information, aGabor feature map(GFM) is computed by convolving the image with each of the forty multi-scale and multi-orientation Gabor filters. Each GFM is then divided into small non-overlapping regions to enhance its shape information, and then Local Binary Pattern (LBP) histograms are extracted for each region and concatenated into a feature histogram to enhance the texture information in the specific GFM. Further more, all of the feature histograms extracted from the forty GFMs are further concatenated into a single feature histogram as the final representation of the given face image. Eventually, the identification is achieved by histogram intersection operation. Our experimental results on FERET face databases show that the proposed method performs terrifically better than the performance of some classical results including the best results in FERET'97.