Graph run-length matrices for histopathological image segmentation

Cataloged from PDF version of article.The histopathological examination of tissue specimens is essential for cancer diagnosis and grading. However, this examination is subject to a considerable amount of observer variability as it mainly relies on visual interpretation of pathologists. To alleviate this problem, it is very important to develop computational quantitative tools, for which image segmentation constitutes the core step. In this paper, we introduce an effective and robust algorithm for the segmentation of histopathological tissue images. This algorithm incorporates the background knowledge of the tissue organization into segmentation. For this purpose, it quantifies spatial relations of cytological tissue components by constructing a graph and uses this graph to define new texture features for image segmentation. This new texture definition makes use of the idea of gray-level run-length matrices. However, it considers the runs of cytological components on a graph to form a matrix, instead of considering the runs of pixel intensities. Working with colon tissue images, our experiments demonstrate that the texture features extracted from "graph run-length matrices" lead to high segmentation accuracies, also providing a reasonable number of segmented regions. Compared with four other segmentation algorithms, the results show that the proposed algorithm is more effective in histopathological image segmentatio

Robust pedestrian detection and tracking in crowded scenes

In this paper, a robust computer vision approach to detecting and tracking pedestrians in unconstrained crowded scenes is presented. Pedestrian detection is performed via a 3D clustering process within a region-growing framework. The clustering process avoids using hard thresholds by using bio-metrically inspired constraints and a number of plan view statistics. Pedestrian tracking is achieved by formulating the track matching process as a weighted bipartite graph and using a Weighted Maximum Cardinality Matching scheme. The approach is evaluated using both indoor and outdoor sequences, captured using a variety of different camera placements and orientations, that feature significant challenges in terms of the number of pedestrians present, their interactions and scene lighting conditions. The evaluation is performed against a manually generated groundtruth for all sequences. Results point to the extremely accurate performance of the proposed approach in all cases

Automated detection of extended sources in radio maps: progress from the SCORPIO survey

Automated source extraction and parameterization represents a crucial challenge for the next-generation radio interferometer surveys, such as those performed with the Square Kilometre Array (SKA) and its precursors. In this paper we present a new algorithm, dubbed CAESAR (Compact And Extended Source Automated Recognition), to detect and parametrize extended sources in radio interferometric maps. It is based on a pre-filtering stage, allowing image denoising, compact source suppression and enhancement of diffuse emission, followed by an adaptive superpixel clustering stage for final source segmentation. A parameterization stage provides source flux information and a wide range of morphology estimators for post-processing analysis. We developed CAESAR in a modular software library, including also different methods for local background estimation and image filtering, along with alternative algorithms for both compact and diffuse source extraction. The method was applied to real radio continuum data collected at the Australian Telescope Compact Array (ATCA) within the SCORPIO project, a pathfinder of the ASKAP-EMU survey. The source reconstruction capabilities were studied over different test fields in the presence of compact sources, imaging artefacts and diffuse emission from the Galactic plane and compared with existing algorithms. When compared to a human-driven analysis, the designed algorithm was found capable of detecting known target sources and regions of diffuse emission, outperforming alternative approaches over the considered fields.Comment: 15 pages, 9 figure

Localizing Region-Based Active Contours

©2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or distribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.DOI: 10.1109/TIP.2008.2004611In this paper, we propose a natural framework that allows any region-based segmentation energy to be re-formulated in a local way. We consider local rather than global image statistics and evolve a contour based on local information. Localized contours are capable of segmenting objects with heterogeneous feature profiles that would be difficult to capture correctly using a standard global method. The presented technique is versatile enough to be used with any global region-based active contour energy and instill in it the benefits of localization. We describe this framework and demonstrate the localization of three well-known energies in order to illustrate how our framework can be applied to any energy. We then compare each localized energy to its global counterpart to show the improvements that can be achieved. Next, an in-depth study of the behaviors of these energies in response to the degree of localization is given. Finally, we show results on challenging images to illustrate the robust and accurate segmentations that are possible with this new class of active contour models

Modified JSEG algorithm for reducing over-segmentation problems in underwater coral reef images

The original JSEG algorithm has proved to be very useful and robust in variety of image segmentation case studies.However, when it is applied into the underwater coral reef images, the original JSEG algorithm produces over-segementation problem, thus making this algorithm futile in such a situation. In this paper, an approach to reduce the over-segmentation problem occurred in the underwater coral reef image segmentation is presented. The approach works by replacing the color histogram computation in region merge stage of the original JSEG algorithm with the new computation of color and texture features in the similarity measurement. Based on the perceptual observation results of the test images, the proposed modified JSEG algorithm could automatically segment the regions better than the original JSEG algorithm

Graph Refinement based Airway Extraction using Mean-Field Networks and Graph Neural Networks

Graph refinement, or the task of obtaining subgraphs of interest from over-complete graphs, can have many varied applications. In this work, we extract trees or collection of sub-trees from image data by, first deriving a graph-based representation of the volumetric data and then, posing the tree extraction as a graph refinement task. We present two methods to perform graph refinement. First, we use mean-field approximation (MFA) to approximate the posterior density over the subgraphs from which the optimal subgraph of interest can be estimated. Mean field networks (MFNs) are used for inference based on the interpretation that iterations of MFA can be seen as feed-forward operations in a neural network. This allows us to learn the model parameters using gradient descent. Second, we present a supervised learning approach using graph neural networks (GNNs) which can be seen as generalisations of MFNs. Subgraphs are obtained by training a GNN-based graph refinement model to directly predict edge probabilities. We discuss connections between the two classes of methods and compare them for the task of extracting airways from 3D, low-dose, chest CT data. We show that both the MFN and GNN models show significant improvement when compared to one baseline method, that is similar to a top performing method in the EXACT'09 Challenge, and a 3D U-Net based airway segmentation model, in detecting more branches with fewer false positives.Comment: Accepted for publication at Medical Image Analysis. 14 page

Integrating spatial and spectral information for automatic feature identification in high -resolution remotely sensed images

This research used image objects, instead of pixels, as the basic unit of analysis in high-resolution imagery. Thus, not only spectral radiance and texture were used in the analysis, but also spatial context. Furthermore, the automated identification of attributed objects is potentially useful for integrating remote sensing with a vector-based GIS.;A study area in Morgantown, WV was chosen as a site for the development and testing of automated feature extraction methods with high-resolution data. In the first stage of the analysis, edges were identified using texture. Experiments with simulated data indicated that a linear operator identified curved and sharp edges more accurately than square shaped operators. Areas with edges that formed a closed boundary were used to delineate sub-patches. In the region growing step, the similarities of all adjacent subpatches were examined using a multivariate Hotelling T2 test that draws on the classes\u27 covariance matrices. Sub-patches that were not sufficiently dissimilar were merged to form image patches.;Patches were then classified into seven classes: Building, Road, Forest, Lawn, Shadowed Vegetation, Water, and Shadow. Six classification methods were compared: the pixel-based ISODATA and maximum likelihood approaches, field-based ECHO, and region based maximum likelihood using patch means, a divergence index, and patch probability density functions (pdfs). Classification with the divergence index showed the lowest accuracy, a kappa index of 0.254. The highest accuracy, 0.783, was obtained from classification using the patch pdf. This classification also produced a visually pleasing product, with well-delineated objects and without the distracting salt-and-pepper effect of isolated misclassified pixels. The accuracies of classification with patch mean, pixel based maximum likelihood, ISODATA and ECHO were 0.735, 0.687, 0.610, and 0.605, respectively.;Spatial context was used to generate aggregate land cover information. An Urbanized Rate Index, defined based on the percentage of Building and Road area within a local window, was used to segment the image. Five summary landcover classes were identified from the Urbanized Rate segmentation and the image object classification: High Urbanized Rate and large building sizes, Intermediate Urbanized Rate and intermediate building sizes, Low urbanized rate and small building sizes, Forest, and Water