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.
All further approaches do not focus on a segmentation but on related tasks such as tissue classification or object detection: In the work of @cite_3 the need for large annotated training data was circumvented by a weakly-supervised approach. It was shown that even with a small number of positive training samples, a detection of the glomeruli can be performed. However, a segmentation stage is missing in this work. In a study of @cite_13 various image representations were investigated to determine whether they are appropriate for distinguishing between different regions in renal pathology. The authors found that colour as well as texture representations can be utilized for distinguishing between the investigated texture classes. In a further study domain adaptation methods were investigated for patch-wise classification of renal tissue. It was shown that domain adaptation can help to improve the fit of trained models for image data showing changed properties. However, the performance of feature-based patch-wise classification was not sufficient for a reliable classification or segmentation applying a difficult-to-segment staining.
@cite_13 @cite_3
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Automatic tissue classification from medical images is an important step in pathology detection and diagnosis. Here, we deal with mammography images and present a novel supervised deep learning-based framework for region classification into semantically coherent tissues. The proposed method uses Convolutional Neural Network (CNN) to learn discriminative features automatically. We overcome the difficulty involved in a medium-size database by training the CNN in an overlapping patch-wise manner. In order to accelerate the pixel-wise automatic class prediction, we use convolutional layers instead of the classical fully connected layers. This approach results in significantly faster computation, while preserving the classification accuracy. The proposed method was tested on annotated mammography images and demonstrates promising image segmentation and tissue classification results. The advancing pervasion of digital pathology in research and clinical practice results in a strong need for image analysis techniques in the field of histopathology. Due to diverse reasons, histopathological imaging generally exhibits a high degree of variability. As automated segmentation approaches are known to be vulnerable, especially to unseen variability, we investigate several stain normalization methods to compensate for variations between different whole slide images. In a large experimental study, we investigate all combinations of five image normalization (not only stain normalization) methods as well as five image representations with respect to the classification performance in two application scenarios in kidney histopathology. Finally, we also pose the question, if color normalization is sufficient to compensate for the changed properties between whole slide images in an application scenario with few training data. Detection and classification of cell nuclei in histopathology images of cancerous tissue stained with the standard hematoxylin and eosin stain is a challenging task due to cellular heterogeneity. Deep learning approaches have been shown to produce encouraging results on histopathology images in various studies. In this paper, we propose a Spatially Constrained Convolutional Neural Network (SC-CNN) to perform nucleus detection. SC-CNN regresses the likelihood of a pixel being the center of a nucleus, where high probability values are spatially constrained to locate in the vicinity of the centers of nuclei. For classification of nuclei, we propose a novel Neighboring Ensemble Predictor (NEP) coupled with CNN to more accurately predict the class label of detected cell nuclei. The proposed approaches for detection and classification do not require segmentation of nuclei. We have evaluated them on a large dataset of colorectal adenocarcinoma images, consisting of more than 20,000 annotated nuclei belonging to four different classes. Our results show that the joint detection and classification of the proposed SC-CNN and NEP produces the highest average F1 score as compared to other recently published approaches. Prospectively, the proposed methods could offer benefit to pathology practice in terms of quantitative analysis of tissue constituents in whole-slide images, and potentially lead to a better understanding of cancer. Abstract Labeling a histopathology image as having cancerous regions or not is a critical task in cancer diagnosis; it is also clinically important to segment the cancer tissues and cluster them into various classes. Existing supervised approaches for image classification and segmentation require detailed manual annotations for the cancer pixels, which are time-consuming to obtain. In this paper, we propose a new learning method, multiple clustered instance learning (MCIL) (along the line of weakly supervised learning) for histopathology image segmentation. The proposed MCIL method simultaneously performs image-level classification (cancer vs. non-cancer image), medical image segmentation (cancer vs. non-cancer tissue), and patch-level clustering (different classes). We embed the clustering concept into the multiple instance learning (MIL) setting and derive a principled solution to performing the above three tasks in an integrated framework. In addition, we introduce contextual constraints as a prior for MCIL, which further reduces the ambiguity in MIL. Experimental results on histopathology colon cancer images and cytology images demonstrate the great advantage of MCIL over the competing methods. Breast cancer grading of histological tissue samples by visual inspection is the standard clinical practice for the diagnosis and prognosis of cancer development. An important parameter for tumor prognosis is the number of mitotic cells present in histologically stained breast cancer tissue sections. We propose a hierarchical learning workflow for automated mitosis detection in breast cancer. From an initial training set a pixel-wise classifier is learned to segment candidate cells, which are then classified into mitotic and non-mitotic cells using object shape and texture features. Our workflow banks on two open source biomedical image analysis software: “ilastik” and “CellCognition” which provide a user user friendly interface to powerful learning algorithms, with the potential of making the pathologist work an easier task. We evaluate our approach on a dataset of 35 highresolution histopathological images from 5 different specimen (provided by International Conference for Pattern Recognition 2012 contest on Mitosis Detection in Breast Cancer Histological Images). Based on the candidate segmentation our approach achieves an area-under Precision-Recall-curve of 70 on an annotated dataset, with good localization accuracy, little parameter tuning and small user effort. Source code is provided. Age-related Macular Degeneration (AMD) is a common eye disorder with high prevalence in elderly people. The disease mainly affects the central part of the retina, and could ultimately lead to permanent vision loss. Optical Coherence Tomography (OCT) is becoming the standard imaging modality in diagnosis of AMD and the assessment of its progression. However, the evaluation of the obtained volumetric scan is time consuming, expensive and the signs of early AMD are easy to miss. In this paper we propose a classification method to automatically distinguish AMD patients from healthy subjects with high accuracy. The method is based on an unsupervised feature learning approach, and processes the complete image without the need for an accurate pre-segmentation of the retina. The method can be divided in two steps: an unsupervised clustering stage that extracts a set of small descriptive image patches from the training data, and a supervised training stage that uses these patches to create a patch occurrence histogram for every image on which a random forest classifier is trained. Experiments using 384 volume scans show that the proposed method is capable of identifying AMD patients with high accuracy, obtaining an area under the Receiver Operating Curve of 0:984. Our method allows for a quick and reliable assessment of the presence of AMD pathology in OCT volume scans without the need for accurate layer segmentation algorithms. We propose a novel deep neural network architecture for semi-supervised semantic segmentation using heterogeneous annotations. Contrary to existing approaches posing semantic segmentation as a single task of region-based classification, our algorithm decouples classification and segmentation, and learns a separate network for each task. In this architecture, labels associated with an image are identified by classification network, and binary segmentation is subsequently performed for each identified label in segmentation network. The decoupled architecture enables us to learn classification and segmentation networks separately based on the training data with image-level and pixel-wise class labels, respectively. It facilitates to reduce search space for segmentation effectively by exploiting class-specific activation maps obtained from bridging layers. Our algorithm shows outstanding performance compared to other semi-supervised approaches even with much less training images with strong annotations in PASCAL VOC dataset. We propose a novel deep neural network architecture for semi-supervised semantic segmentation using heterogeneous annotations. Contrary to existing approaches posing semantic segmentation as a single task of region-based classification, our algorithm decouples classification and segmentation, and learns a separate network for each task. In this architecture, labels associated with an image are identified by classification network, and binary segmentation is subsequently performed for each identified label in segmentation network. The decoupled architecture enables us to learn classification and segmentation networks separately based on the training data with image-level and pixel-wise class labels, respectively. It facilitates to reduce search space for segmentation effectively by exploiting class-specific activation maps obtained from bridging layers. Our algorithm shows outstanding performance compared to other semi-supervised approaches with much less training images with strong annotations in PASCAL VOC dataset. Convolutional neural networks with many layers have recently been shown to achieve excellent results on many high-level tasks such as image classification, object detection and more recently also semantic segmentation. Particularly for semantic segmentation, a two-stage procedure is often employed. Hereby, convolutional networks are trained to provide good local pixel-wise features for the second step being traditionally a more global graphical model. In this work we unify this two-stage process into a single joint training algorithm. We demonstrate our method on the semantic image segmentation task and show encouraging results on the challenging PASCAL VOC 2012 dataset. The standard chronic wound assessment method based on visual examination is potentially inaccurate and also represents a significant clinical workload. Hence, computer-based systems providing quantitative wound assessment may be valuable for accurately monitoring wound healing status, with the wound area the best suited for automated analysis. Here, we present a novel approach, using support vector machines (SVM) to determine the wound boundaries on foot ulcer images captured with an image capture box, which provides controlled lighting and range. After superpixel segmentation, a cascaded two-stage classifier operates as follows: in the first stage, a set of k binary SVM classifiers are trained and applied to different subsets of the entire training images dataset, and incorrectly classified instances are collected. In the second stage, another binary SVM classifier is trained on the incorrectly classified set. We extracted various color and texture descriptors from superpixels that are used as input for each stage in the classifier training. Specifically, color and bag-of-word representations of local dense scale invariant feature transformation features are descriptors for ruling out irrelevant regions, and color and wavelet-based features are descriptors for distinguishing healthy tissue from wound regions. Finally, the detected wound boundary is refined by applying the conditional random field method. We have implemented the wound classification on a Nexus 5 smartphone platform, except for training which was done offline. Results are compared with other classifiers and show that our approach provides high global performance rates (average sensitivity = 73.3 , specificity = 94.6 ) and is sufficiently efficient for a smartphone-based image analysis. In this paper, we propose a new classification method for five categories of lung tissues in high-resolution computed tomography (HRCT) images, with feature-based image patch approximation. We design two new feature descriptors for higher feature descriptiveness, namely the rotation-invariant Gabor-local binary patterns (RGLBP) texture descriptor and multi-coordinate histogram of oriented gradients (MCHOG) gradient descriptor. Together with intensity features, each image patch is then labeled based on its feature approximation from reference image patches. And a new patch-adaptive sparse approximation (PASA) method is designed with the following main components: minimum discrepancy criteria for sparse-based classification, patch-specific adaptation for discriminative approximation, and feature-space weighting for distance computation. The patch-wise labelings are then accumulated as probabilistic estimations for region-level classification. The proposed method is evaluated on a publicly available ILD database, showing encouraging performance improvements over the state-of-the-arts. 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. In this work, we present a method for unsupervised domain adaptation. Many adversarial learning methods train domain classifier networks to distinguish the features as either a source or target and train a feature generator network to mimic the discriminator. Two problems exist with these methods. First, the domain classifier only tries to distinguish the features as a source or target and thus does not consider task-specific decision boundaries between classes. Therefore, a trained generator can generate ambiguous features near class boundaries. Second, these methods aim to completely match the feature distributions between different domains, which is difficult because of each domain's characteristics. To solve these problems, we introduce a new approach that attempts to align distributions of source and target by utilizing the task-specific decision boundaries. We propose to maximize the discrepancy between two classifiers' outputs to detect target samples that are far from the support of the source. A feature generator learns to generate target features near the support to minimize the discrepancy. Our method outperforms other methods on several datasets of image classification and semantic segmentation. The codes are available at https: github.com mil-tokyo MCD_DA Incorporation of prior knowledge about organ shape and location is key to improve performance of image analysis approaches. In particular, priors can be useful in cases where images are corrupted and contain artefacts due to limitations in image acquisition. The highly constrained nature of anatomical objects can be well captured with learning-based techniques. However, in most recent and promising techniques such as CNN-based segmentation it is not obvious how to incorporate such prior knowledge. State-of-the-art methods operate as pixel-wise classifiers where the training objectives do not incorporate the structure and inter-dependencies of the output. To overcome this limitation, we propose a generic training strategy that incorporates anatomical prior knowledge into CNNs through a new regularisation model, which is trained end-to-end. The new framework encourages models to follow the global anatomical properties of the underlying anatomy ( e.g. shape, label structure) via learnt non-linear representations of the shape. We show that the proposed approach can be easily adapted to different analysis tasks ( e.g. image enhancement, segmentation) and improve the prediction accuracy of the state-of-the-art models. The applicability of our approach is shown on multi-modal cardiac data sets and public benchmarks. In addition, we demonstrate how the learnt deep models of 3-D shapes can be interpreted and used as biomarkers for classification of cardiac pathologies. Visual codebook based quantization of robust appearance descriptors extracted from local image patches is an effective means of capturing image statistics for texture analysis and scene classification. Codebooks are usually constructed by using a method such as k-means to cluster the descriptor vectors of patches sampled either densely ('textons') or sparsely ('bags of features' based on key-points or salience measures) from a set of training images. This works well for texture analysis in homogeneous images, but the images that arise in natural object recognition tasks have far less uniform statistics. We show that for dense sampling, k-means over-adapts to this, clustering centres almost exclusively around the densest few regions in descriptor space and thus failing to code other informative regions. This gives suboptimal codes that are no better than using randomly selected centres. We describe a scalable acceptance-radius based clusterer that generates better codebooks and study its performance on several image classification tasks. We also show that dense representations outperform equivalent keypoint based ones on these tasks and that SVM or mutual information based feature selection starting from a dense codebook further improves the performance. In this paper we study the problem of the detection of semantic objects from known categories in images. Unlike existing techniques which operate at the pixel or at a patch level for recognition, we propose to rely on the categorization of image segments. Recent work has highlighted that image segments provide a sound support for visual object class recognition. In this work, we use image segments as primitives to extract robust features and train detection models for a predefined set of categories. Several segmentation algorithms are benchmarked and their performances for segment recognition are compared. We then propose two methods for enhancing the segments classification, one based on the fusion of the classification results obtained with the different segmentations, the other one based on the optimization of the global labelling by correcting local ambiguities between neighbor segments. We use as a benchmark the Microsoft MSRC-21 image database and show that our method competes with the current state-of-the-art. 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 The adaptive integration of the colour and texture attributes in the development of complex image descriptors is one of the most investigated topics of research in computer vision. The substantial interest shown by the research community in colour-texture-based segmentation is mainly motivated by two factors. The first is related to the observation that the imaged objects are often described at perceptual level by distinctive colour and texture characteristics, while the second is motivated by the large spectrum of possible applications that can be addressed by the colour-texture integration in the segmentation process. Over the past three decades a substantial number of techniques in the field of colour-texture segmentation have been reported and it is the aim of this article to thoroughly evaluate and categorise the most relevant algorithms with respect to the modality behind the integration of these two fundamental image attributes. In this paper we also provide a detailed discussion about data collections, evaluation metrics and we review the performance attained by state of the art implementations. We conclude with a discussion that samples our views on the field of colour-texture image segmentation and this is complemented with an examination of the potential future directions of research. We propose a two-class classification model for grouping. Human segmented natural images are used as positive examples. Negative examples of grouping are constructed by randomly matching human segmentations and images. In a preprocessing stage an image is over-segmented into super-pixels. We define a variety of features derived from the classical Gestalt cues, including contour, texture, brightness and good continuation. Information-theoretic analysis is applied to evaluate the power of these grouping cues. We train a linear classifier to combine these features. To demonstrate the power of the classification model, a simple algorithm is used to randomly search for good segmentations. Results are shown on a wide range of images. We investigate a principle way to progressively mine discriminative object regions using classification networks to address the weakly-supervised semantic segmentation problems. Classification networks are only responsive to small and sparse discriminative regions from the object of interest, which deviates from the requirement of the segmentation task that needs to localize dense, interior and integral regions for pixel-wise inference. To mitigate this gap, we propose a new adversarial erasing approach for localizing and expanding object regions progressively. Starting with a single small object region, our proposed approach drives the classification network to sequentially discover new and complement object regions by erasing the current mined regions in an adversarial manner. These localized regions eventually constitute a dense and complete object region for learning semantic segmentation. To further enhance the quality of the discovered regions by adversarial erasing, an online prohibitive segmentation learning approach is developed to collaborate with adversarial erasing by providing auxiliary segmentation supervision modulated by the more reliable classification scores. Despite its apparent simplicity, the proposed approach achieves 55.0 and 55.7 mean Intersection-over-Union (mIoU) scores on PASCAL VOC 2012 val and test sets, which are the new state-of-the-arts.