Currently, histopathological tissue examination by a pathologist represents the gold standard for breast lesion diagnostics. Automated classification of histopathological whole-slide images (WSIs) is challenging owing to the wide range of appearances of benign lesions and the visual similarity of ductal carcinoma in-situ (DCIS) to invasive lesions at the cellular level. Consequently, analysis of tissue at high resolutions with a large contextual area is necessary. We present context-aware stacked convolutional neural networks (CNN) for classification of breast WSIs into normal/benign, DCIS, and invasive ductal carcinoma (IDC). We first train a CNN using high pixel resolution to capture cellular level information. The feature responses generated by this model are then fed as input to a second CNN, stacked on top of the first. Training of this stacked architecture with large input patches enables learning of fine-grained (cellular) details and global tissue structures. Our system is trained and evaluated on a dataset containing 221 WSIs of hematoxylin and eosin stained breast tissue specimens. The system achieves an AUC of 0.962 for the binary classification of nonmalignant and malignant slides and obtains a three-class accuracy of 81.3% for classification of WSIs into normal/benign, DCIS, and IDC, demonstrating its potential for routine diagnostics.
Early detection of pulmonary nodules is crucial for improving prognosis of patients with lung cancer. Computer-aided detection of lung nodules in thoracic computed tomography (CT) scans has a great potential to enhance the performance of the radiologist in detecting nodules. In this paper we present a computer-aided lung nodule detection system for computed tomography (CT) scans that works in three steps. The system first segments the lung using thresholding and hole filling. From this segmentation the system extracts candidate nodules using Laplacian of Gaussian. To reject false positives among the detected candidate nodules, multiple established features are calculated. We propose a novel feature based on a spherical shell filter, which is specifically designed to distinguish between vascular structures and nodular structures. The performance of the proposed CAD system was evaluated by partaking in the ANODE09 challenge, which presents a platform for comparing automatic nodule detection programs. The results from the challenge show that our CAD system ranks third among the submitted works, demonstrating the efficacy of our proposed CAD system. The results also show that our proposed spherical shell filter in combination with conventional features can significantly reduce the number of false positives from the detected candidate nodules.
Automated detection of prostate cancer in digitized H and E whole-slide images is an important first step for computer-driven grading. Most automated grading algorithms work on preselected image patches as they are too computationally expensive to calculate on the multi-gigapixel whole-slide images. An automated multi-resolution cancer detection system could reduce the computational workload for subsequent grading and quantification in two ways: by excluding areas of definitely normal tissue within a single specimen or by excluding entire specimens which do not contain any cancer. In this work we present a multi-resolution cancer detection algorithm geared towards the latter. The algorithm methodology is as follows: at a coarse resolution the system uses superpixels, color histograms and local binary patterns in combination with a random forest classifier to assess the likelihood of cancer. The five most suspicious superpixels are identified and at a higher resolution more computationally expensive graph and gland features are added to refine classification for these superpixels. Our methods were evaluated in a data set of 204 digitized whole-slide H and E stained images of MR-guided biopsy specimens from 163 patients. A pathologist exhaustively annotated the specimens for areas containing cancer. The performance of our system was evaluated using ten-fold cross-validation, stratified according to patient. Image-based receiver operating characteristic (ROC) analysis was subsequently performed where a specimen containing cancer was considered positive and specimens without cancer negative. We obtained an area under the ROC curve of 0.96 and a 0.4 specificity at a 1.0 sensitivity.
This paper presents a new algorithm for automatic detection of regions of interest in whole slide histopathological images. The proposed algorithm generates and classifies superpixels at multiple resolutions to detect regions of interest. The algorithm emulates the way the pathologist examines the whole slide histopathology image by processing the image at low magnifications and performing more sophisticated analysis only on areas requiring more detailed information. However, instead of the traditional usage of fixed sized rectangular patches for the identification of relevant areas, we use superpixels as the visual primitives to detect regions of interest. Rectangular patches can span multiple distinct structures, thus degrade the classification performance. The proposed multi-scale superpixel classification approach yields superior performance for the identification of the regions of interest. For the evaluation, a set of 10 whole slide histopathology images of breast tissue were used. Empirical evaluation of the performance of our proposed algorithm relative to expert manual annotations shows that the algorithm achieves an area under the Receiver operating characteristic (ROC) curve of 0.958, demonstrating its efficacy for the detection of regions of interest.
This paper presents data on the sources of variation of the widely used hematoxylin and eosin (H&E) histological
staining, as well as a new algorithm to reduce these variations in digitally scanned tissue sections. Experimental
results demonstrate that staining protocols in different laboratories and staining on different days of the week are
the major factors causing color variations in histopathological images. The proposed algorithm for standardizing
histology slides is based on an initial clustering of the image into two tissue components having different absorption
characteristics for different dyes. The color distribution for each tissue component is standardized by aligning
the 2D histogram of color distribution in the hue-saturation-density (HSD) model. Qualitative evaluation of the
proposed standardization algorithm shows that color constancy of the standardized images is improved. Quantitative
evaluation demonstrates that the algorithm outperforms competing methods. In conclusion, the paper
demonstrates that staining variations, which may potentially hamper usefulness of computer assisted analysis of
histopathological images, can be reduced considerably by applying the proposed algorithm.
This paper presents a novel fully automatic unsupervised framework for the segmentation of brain tissues in magnetic resonance (MR) images. The framework is a combination of our proposed Bayesian-based adaptive mean shift (BAMS), a priori spatial tissue probability maps and fuzzy c-means. BAMS is applied to cluster the tissues in the joint spatialintensity feature space and then a fuzzy c-means algorithm is employed with initialization by a priori spatial tissue probability maps to assign the clusters into three tissue types; white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF). The proposed framework is validated on multimodal synthetic as well as on real T1-weighted MR data with varying noise characteristics and spatial intensity inhomogeneity. The performance of the proposed framework is evaluated relative to our previous method BAMS and other existing adaptive mean shift framework. Both of these are based on the mode pruning and voxel weighted k-means algorithm for classifying the clusters into WM, GM and CSF tissue. The experimental results demonstrate the robustness of the proposed framework to noise and spatial intensity inhomogeneity, and that it exhibits a higher degree of segmentation accuracy in segmenting both synthetic and real MR data compared to competing methods.
This paper presents a set of novel structural texture features for quantifying nuclear chromatin patterns in cells on a conventional Pap smear. The features are derived from an initial segmentation of the chromatin into bloblike texture primitives. The results of a comprehensive feature selection experiment, including the set of proposed structural texture features and a range of different cytology features drawn from the literature, show that two of the four top ranking features are structural texture features. They also show that a combination of structural and conventional features yields a classification performance of 0.954±0.019 (AUC±SE) for the discrimination of normal (NILM) and abnormal (LSIL and HSIL) slides. The results of a second classification experiment, using only normal-appearing cells from both normal and abnormal slides, demonstrates that a single structural texture feature measuring chromatin margination yields a classification performance of 0.815±0.019. Overall the results demonstrate the efficacy of the proposed structural approach and that it is possible to detect malignancy associated changes (MACs) in Papanicoloau stain.
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