Graph Cut Segmentation Research Articles

CANFIS based glioma brain tumor classification and retrieval system for tumor diagnosis

AbstractBrain tumor classification and retrieval system plays an important role in medical field. In this paper, an efficient Glioma Brain Tumor detection and its retrieval system is proposed. The proposed methodology consists of two modules as classification and retrieval. The classification modules are designed using preprocessing, feature extraction and tumor detection techniques using Co‐Active Adaptive Neuro Fuzzy Inference System (CANFIS) classifier. The image enhancement can be achieved using Heuristic histogram equalization technique as preprocessing and further texture features as Local Ternary Pattern (LTP) features and Grey Level Co‐occurrence Matrix (GLCM) features are extracted from the enhanced image. These features are used to classify the brain image into normal and abnormal using CANFIS classifier. The tumor region in abnormal brain image is segmented using normalized graph cut segmentation algorithm. The retrieval module is used to retrieve the similar segmented tumor regions from the dataset for diagnosing the tumor region using Euclidean algorithm. The proposed Glioma Brain tumor classification methodology achieves 97.28% sensitivity, 98.16% specificity and 99.14% accuracy. The proposed retrieval system achieves 97.29% precision and 98.16% recall rate with respect to ground truth images.

A voting-based statistical cylinder detection framework applied to fallen tree mapping in terrestrial laser scanning point clouds

This paper introduces a statistical framework for detecting cylindrical shapes in dense point clouds. We target the application of mapping fallen trees in datasets obtained through terrestrial laser scanning. This is a challenging task due to the presence of ground vegetation, standing trees, DTM artifacts, as well as the fragmentation of dead trees into non-collinear segments. Our method shares the concept of voting in parameter space with the generalized Hough transform, however two of its significant drawbacks are improved upon. First, the need to generate samples on the shape’s surface is eliminated. Instead, pairs of nearby input points lying on the surface cast a vote for the cylinder’s parameters based on the intrinsic geometric properties of cylindrical shapes. Second, no discretization of the parameter space is required: the voting is carried out in continuous space by means of constructing a kernel density estimator and obtaining its local maxima, using automatic, data-driven kernel bandwidth selection. Furthermore, we show how the detected cylindrical primitives can be efficiently merged to obtain object-level (entire tree) semantic information using graph-cut segmentation and a tailored dynamic algorithm for eliminating cylinder redundancy. Experiments were performed on 3 plots from the Bavarian Forest National Park, with ground truth obtained through visual inspection of the point clouds. It was found that relative to sample consensus (SAC) cylinder fitting, the proposed voting framework can improve the detection completeness by up to 10 percentage points while maintaining the correctness rate.

Graph cuts segmentation based on multi‐dimensional features for the right ventricle in cardiac MRI

The segmentation of the right ventricle in cardiac magnetic resonance imaging is a difficult task due to the blurred border and variable shape. To overcome these problems, an approach using graph cuts (GC) segmentation based on multi-dimensional local features is proposed. The features are reduced by a principal component analysis, which are incorporated into the t-link and the n-link. Experiments are performed on 240 MR images from 16 patients. The segmentation results of the proposed algorithm are obtained using Gabor and histogram of oriented gradient (HOG) features, respectively. For Dice metric, the median value of using Gabor and HOG increases significantly compared to original GC from 0.8012 to 0.8174 and 0.8306 at end-diastole (ED), from 0.6555 to 0.7021 and 0.7124 at end-systole (ES). For Hausdorff distance, the median value of using Gabor and HOG decreases significantly compared to original GC from 12.88 to 12.33 and 11.82 mm at ED, from 17.20 to 12.75 and 13.41 mm at ES. The proposed method outperforms original GC depending on image intensity only. The segmentation errors of using HOG are slightly less than those of using Gabor.

A practical algorithm for the retrieval of floe size distribution of Arctic sea ice from high-resolution satellite Synthetic Aperture Radar imagery

In this study, we present an algorithm for summer sea ice conditions that semi-automatically produces the floe size distribution of Arctic sea ice from high-resolution satellite Synthetic Aperture Radar data. Currently, floe size distribution data from satellite images are very rare in the literature, mainly due to the lack of a reliable algorithm to produce such data. Here, we developed the algorithm by combining various image analysis methods, including Kernel Graph Cuts, distance transformation and watershed transformation, and a rule-based boundary revalidation. The developed algorithm has been validated against the ground truth that was extracted manually with the aid of 1-m resolution visible satellite data. Comprehensive validation analysis has shown both perspectives and limitations. The algorithm tends to fail to detect small floes (mostly less than 100 m in mean caliper diameter) compared to ground truth, which is mainly due to limitations in water-ice segmentation. Some variability in the power law exponent of floe size distribution is observed due to the effects of control parameters in the process of de-noising, Kernel Graph Cuts segmentation, thresholds for boundary revalidation and image resolution. Nonetheless, the algorithm, for floes larger than 100 m, has shown a reasonable agreement with ground truth under various selections of these control parameters. Considering that the coverage and spatial resolution of satellite Synthetic Aperture Radar data have increased significantly in recent years, the developed algorithm opens a new possibility to produce large volumes of floe size distribution data, which is essential for improving our understanding and prediction of the Arctic sea ice cover.

Theoretical-information quality model for image segmentation

A problem of image segmentation quality is considered. The problem is viewed as selecting the best segmentation from a set of images generated by segmentation algorithm at different parameter values. A segmentation quality model for selecting the best segmentation based on information redundancy measure is proposed. The developed technique was applied to SLIC and graph-cut segmentation algorithms. Computing experiment confirmed that the segmented image corresponding to minimum redundancy measure demonstrates suitable dissimilarity when compared with the original image. The segmented image which was selected using the proposed criterion, gives the highest similarity with the ground-truth segmentations.

Detection of Multiple Innervation Zones from Multi-Channel Surface EMG Recordings with Low Signal-to-Noise Ratio Using Graph-Cut Segmentation.

Knowledge of the location of muscle Innervation Zones (IZs) is important in many applications, e.g. for minimizing the quantity of injected botulinum toxin for the treatment of spasticity or for deciding on the type of episiotomy during child delivery. Surface EMG (sEMG) can be noninvasively recorded to assess physiological and morphological characteristics of contracting muscles. However, it is not often possible to record signals of high quality. Moreover, muscles could have multiple IZs, which should all be identified. We designed a fully-automatic algorithm based on the enhanced image Graph-Cut segmentation and morphological image processing methods to identify up to five IZs in 60-ms intervals of very-low to moderate quality sEMG signal detected with multi-channel electrodes (20 bipolar channels with Inter Electrode Distance (IED) of 5 mm). An anisotropic multilayered cylinder model was used to simulate 750 sEMG signals with signal-to-noise ratio ranging from -5 to 15 dB (using Gaussian noise) and in each 60-ms signal frame, 1 to 5 IZs were included. The micro- and macro- averaged performance indices were then reported for the proposed IZ detection algorithm. In the micro-averaging procedure, the number of True Positives, False Positives and False Negatives in each frame were summed up to generate cumulative measures. In the macro-averaging, on the other hand, precision and recall were calculated for each frame and their averages are used to determine F1-score. Overall, the micro (macro)-averaged sensitivity, precision and F1-score of the algorithm for IZ channel identification were 82.7% (87.5%), 92.9% (94.0%) and 87.5% (90.6%), respectively. For the correctly identified IZ locations, the average bias error was of 0.02±0.10 IED ratio. Also, the average absolute conduction velocity estimation error was 0.41±0.40 m/s for such frames. The sensitivity analysis including increasing IED and reducing interpolation coefficient for time samples was performed. Meanwhile, the effect of adding power-line interference and using other image interpolation methods on the deterioration of the performance of the proposed algorithm was investigated. The average running time of the proposed algorithm on each 60-ms sEMG frame was 25.5±8.9 (s) on an Intel dual-core 1.83 GHz CPU with 2 GB of RAM. The proposed algorithm correctly and precisely identified multiple IZs in each signal epoch in a wide range of signal quality and is thus a promising new offline tool for electrophysiological studies.

Automatic Segmentation of Cell Images by Improved Graph Cut-Based Approach

Cell segmentation provides an opportunity to reveal object of interest from the background of an image. In the traditional graph cut segmentation approach, the user initiates the segmentation process by selecting pixels for foreground and background. However, one of the problems of traditional graph cut is that it is time consuming, especially on a large dataset. Thus, we propose a fully automatic technique for cell segmentation on graph cut to automate the selection of sample foreground and background pixels. In order to achieve this, a combination of two methods namely Otsu thresholding and kmeans clustering algorithm is explored. The Otsu thresholding and the k-means provides an initial cell segmentation, creating a platform to automatically select sample foreground and background pixels initiating the graph cut segmentation. Experimental results on two public datasets suggest promising results.

Spectral-Spatial Classification of Hyperspectral Images Using Joint Bilateral Filter and Graph Cut Based Model

Hyperspectral image classification can be achieved by modeling an energy minimization problem on a graph of image pixels. In this paper, an effective spectral-spatial classification method for hyperspectral images based on joint bilateral filtering (JBF) and graph cut segmentation is proposed. In this method, a novel technique for labeling regions obtained by the spectral-spatial segmentation process is presented. Our method includes the following steps. First, the probabilistic support vector machines (SVM) classifier is used to estimate probabilities belonging to each information class. Second, an extended JBF is employed to perform image smoothing on the probability maps. By using our JBF process, salt-and-pepper classification noise in homogeneous regions can be effectively smoothed out while object boundaries in the original image are better preserved as well. Third, a sequence of modified bi-labeling graph cut models is constructed for each information class to extract the desirable object belonging to the corresponding class from the smoothed probability maps. Finally, a classification map is achieved by merging the segmentation maps obtained in the last step using a simple and effective rule. Experimental results based on three benchmark airborne hyperspectral datasets with different resolutions and contexts demonstrate that our method can achieve 8.56%–13.68% higher overall accuracies than the pixel-wise SVM classifier. The performance of our method was further compared to several classical hyperspectral image classification methods using objective quantitative measures and a visual qualitative evaluation.

A probabilistic framework based on SLIC-superpixel and Gaussian processes for segmenting nerves in ultrasound images.

We deal with an important problem in the field of anesthesiology known as automatic segmentation of nerve structures depicted in ultrasound images. This is important to aid the experts in anesthesiology, in order to carry out Peripheral Nerve Blocking (PNB). Ultrasound imaging has gained recent interest for performing PNB procedures since it offers a non-invasive visualization of the nerve and the anatomical structures around it. However, the location of these nerves in ultrasound images is a difficult task for the specialist due to the artifacts (i.e. speckle noise) that affect the intelligibility of a given image. In this paper, we present a probabilistic approach based on Simple Linear Iterative Clustering (SLIC-superpixels) and Gaussian processes for automatic segmentation of peripheral nerves. First, we use Graph cuts segmentation to define a region of interest (ROI). Such a ROI is divided into several correlated regions using SLIC-superpixels, then, a nonlinear Wavelet transform is applied as feature extraction stage. Finally, we use a classification scheme based on Gaussian Processes in order to predict the label of each parametrized superpixel (the label can be "nerve" or "background"). The accuracy of the proposed method is measured in terms of the Dice coefficient. Results obtained show performances with a Dice coefficient of 0.6524±0.0085 which brings accurate performances in nerve segmentation processes.

Intensity and Compactness Enabled Saliency Estimation for Leakage Detection in Diabetic and Malarial Retinopathy.

Leakage in retinal angiography currently is a key feature for confirming the activities of lesions in the management of a wide range of retinal diseases, such as diabetic maculopathy and paediatric malarial retinopathy. This paper proposes a new saliency-based method for the detection of leakage in fluorescein angiography. A superpixel approach is firstly employed to divide the image into meaningful patches (or superpixels) at different levels. Two saliency cues, intensity and compactness, are then proposed for the estimation of the saliency map of each individual superpixel at each level. The saliency maps at different levels over the same cues are fused using an averaging operator. The two saliency maps over different cues are fused using a pixel-wise multiplication operator. Leaking regions are finally detected by thresholding the saliency map followed by a graph-cut segmentation. The proposed method has been validated using the only two publicly available datasets: one for malarial retinopathy and the other for diabetic retinopathy. The experimental results show that it outperforms one of the latest competitors and performs as well as a human expert for leakage detection and outperforms several state-of-the-art methods for saliency detection.

Interactive graph-cut segmentation for fast creation of finite element models from clinical ct data for hip fracture prediction

In this study, we propose interactive graph cut image segmentation for fast creation of femur finite element (FE) models from clinical computed tomography scans for hip fracture prediction. Using a sample of N = 48 bone scans representing normal, osteopenic and osteoporotic subjects, the proximal femur was segmented using manual (gold standard) and graph cut segmentation. Segmentations were subsequently used to generate FE models to calculate overall stiffness and peak force in a sideways fall simulations. Results show that, comparable FE results can be obtained with the graph cut method, with a reduction from 20 to 2–5 min interaction time. Average differences between segmentation methods of 0.22 mm were not significantly correlated with differences in FE derived stiffness (R2 = 0.08, p = 0.05) and weakly correlated to differences in FE derived peak force (R2 = 0.16, p = 0.01). We further found that changes in automatically assigned boundary conditions as a consequence of small segmentation differences were significantly correlated with FE derived results. The proposed interactive graph cut segmentation software MITK-GEM is freely available online at https://simtk.org/home/mitk-gem.

ADAPTIVE PARAMETER SELECTION FOR GRAPH CUT-BASED SEGMENTATION ON CELL IMAGES

Graph cut segmentation approach provides a platform for segmenting images in a globally optimised fashion. The graph cut energy function includes a parameter that adjusts its data term and smoothness term relative to each other. However, one of the key challenges in graph cut segmentation is finding a suitable parameter value that suits a given segmentation. A suitable parameter value is desirable in order to avoid image oversegmentation or under-segmentation. To address the problem of trial and error in manual parameter selection, we propose an intuitive and adaptive parameter selection for cell segmentation using graph cut. The greyscale image of the cell is logarithmically transformed to shrink the dynamic range of foreground pixels in order to extract the boundaries of cells. The extracted cell boundary dynamically adjusts and contextualises the parameter value of the graph cut, countering its shrink bias. Experiments suggest that the proposed model outperforms previous cell segmentation approaches.

Segmentation of Lung Structures with Fuzzy Clustering Algorithm

Tuberculosis are considered to be the chief health threat in many regions of the world. Nextto HIV, it is the foremost infectious disease in worldwide causing death. When it is left untreated and undiagnosed, patients‘ mortality rates are high. The methods of diagnosisare slow and yet complex to detect. This method includes automatic methodology for recognizing tuberculosis to reduce the problematic disease. At first, the extraction of the lung region is performed by using a graph cut segmentation method. In this lung region, we work out a set of features like texture, shape, etc. It permits to classify the X-rays as normal or abnormal by using the SVM. This work proposes a shortened methodology using fuzzy logic segmentation from the normal image processing to lung segmentation tasks over GC segmentation. The proposed systematic system for examining TB segmentation attains an improved performance than the approaches of graph cut segmentation.

3D automatic liver segmentation using feature-constrained Mahalanobis distance in CT images.

Automatic 3D liver segmentation is a fundamental step in the liver disease diagnosis and surgery planning. This paper presents a novel fully automatic algorithm for 3D liver segmentation in clinical 3D computed tomography (CT) images. Based on image features, we propose a new Mahalanobis distance cost function using an active shape model (ASM). We call our method MD-ASM. Unlike the standard active shape model (ST-ASM), the proposed method introduces a new feature-constrained Mahalanobis distance cost function to measure the distance between the generated shape during the iterative step and the mean shape model. The proposed Mahalanobis distance function is learned from a public database of liver segmentation challenge (MICCAI-SLiver07). As a refinement step, we propose the use of a 3D graph-cut segmentation. Foreground and background labels are automatically selected using texture features of the learned Mahalanobis distance. Quantitatively, the proposed method is evaluated using two clinical 3D CT scan databases (MICCAI-SLiver07 and MIDAS). The evaluation of the MICCAI-SLiver07 database is obtained by the challenge organizers using five different metric scores. The experimental results demonstrate the availability of the proposed method by achieving an accurate liver segmentation compared to the state-of-the-art methods.

Random Walk and Graph Cut for Co-Segmentation of Lung Tumor on PET-CT Images.

Accurate lung tumor delineation plays an important role in radiotherapy treatment planning. Since the lung tumor has poor boundary in positron emission tomography (PET) images and low contrast in computed tomography (CT) images, segmentation of tumor in the PET and CT images is a challenging task. In this paper, we effectively integrate the two modalities by making fully use of the superior contrast of PET images and superior spatial resolution of CT images. Random walk and graph cut method is integrated to solve the segmentation problem, in which random walk is utilized as an initialization tool to provide object seeds for graph cut segmentation on the PET and CT images. The co-segmentation problem is formulated as an energy minimization problem which is solved by max-flow/min-cut method. A graph, including two sub-graphs and a special link, is constructed, in which one sub-graph is for the PET and another is for CT, and the special link encodes a context term which penalizes the difference of the tumor segmentation on the two modalities. To fully utilize the characteristics of PET and CT images, a novel energy representation is devised. For the PET, a downhill cost and a 3D derivative cost are proposed. For the CT, a shape penalty cost is integrated into the energy function which helps to constrain the tumor region during the segmentation. We validate our algorithm on a data set which consists of 18 PET-CT images. The experimental results indicate that the proposed method is superior to the graph cut method solely using the PET or CT is more accurate compared with the random walk method, random walk co-segmentation method, and non-improved graph cut method.

Automated cerebellar lobule segmentation with application to cerebellar structural analysis in cerebellar disease

The cerebellum plays an important role in both motor control and cognitive function. Cerebellar function is topographically organized and diseases that affect specific parts of the cerebellum are associated with specific patterns of symptoms. Accordingly, delineation and quantification of cerebellar sub-regions from magnetic resonance images are important in the study of cerebellar atrophy and associated functional losses. This paper describes an automated cerebellar lobule segmentation method based on a graph cut segmentation framework. Results from multi-atlas labeling and tissue classification contribute to the region terms in the graph cut energy function and boundary classification contributes to the boundary term in the energy function. A cerebellar parcellation is achieved by minimizing the energy function using the α-expansion technique. The proposed method was evaluated using a leave-one-out cross-validation on 15 subjects including both healthy controls and patients with cerebellar diseases. Based on reported Dice coefficients, the proposed method outperforms two state-of-the-art methods. The proposed method was then applied to 77 subjects to study the region-specific cerebellar structural differences in three spinocerebellar ataxia (SCA) genetic subtypes. Quantitative analysis of the lobule volumes shows distinct patterns of volume changes associated with different SCA subtypes consistent with known patterns of atrophy in these genetic subtypes.

MODEL-BASED BUILDING DETECTION FROM LOW-COST OPTICAL SENSORS ONBOARD UNMANNED AERIAL VEHICLES

Abstract. The automated and cost-effective building detection in ultra high spatial resolution is of major importance for various engineering and smart city applications. To this end, in this paper, a model-based building detection technique has been developed able to extract and reconstruct buildings from UAV aerial imagery and low-cost imaging sensors. In particular, the developed approach through advanced structure from motion, bundle adjustment and dense image matching computes a DSM and a true orthomosaic from the numerous GoPro images which are characterised by important geometric distortions and fish-eye effect. An unsupervised multi-region, graphcut segmentation and a rule-based classification is responsible for delivering the initial multi-class classification map. The DTM is then calculated based on inpaininting and mathematical morphology process. A data fusion process between the detected building from the DSM/DTM and the classification map feeds a grammar-based building reconstruction and scene building are extracted and reconstructed. Preliminary experimental results appear quite promising with the quantitative evaluation indicating detection rates at object level of 88% regarding the correctness and above 75% regarding the detection completeness.

Severity quantification of pediatric viral respiratory illnesses in chest X-ray images.

Accurate assessment of severity of viral respiratory illnesses (VRIs) allows early interventions to prevent morbidity and mortality in young children. This paper proposes a novel imaging biomarker framework with chest X-ray image for assessing VRI's severity in infants, developed specifically to meet the distinct challenges for pediatric population. The proposed framework integrates three novel technical contributions: a) lung segmentation using weighted partitioned active shape model, b) obtrusive object removal using graph cut segmentation with asymmetry constraint, and c) severity quantification using information-theoretic heterogeneity measures. This paper presents our pilot experimental results with a dataset of 148 images and the ground-truth severity scores given by a board-certified pediatric pulmonologist, demonstrating the effectiveness and clinical relevance of the presented framework.

Automatic segmentation of nerve structures in ultrasound images using Graph Cuts and Gaussian processes.

Peripheral Nerve Blocking (PNB), is a procedure used for performing regional anesthesia, that comprises the administration of anesthetic in the proximity of a nerve. Several techniques have been used with the purpose of locating nerve structures when the PNB procedure is performed: anatomical surface landmarks, elicitation of paresthesia, nerve stimulation and ultrasound imaging. Among those, ultrasound imaging has gained great attention because it is not invasive and offers an accurate location of the nerve and the structures around it. However, the segmentation of nerve structures in ultrasound images is a difficult task for the specialist, since such images are affected by echo perturbations and speckle noise. The development of systems for the automatic segmentation of nerve structures can aid the specialist for locating nerve structures accurately. In this paper we present a methodology for the automatic segmentation of nerve structures in ultrasound images. An initial step is carried out using Graph Cut segmentation in order to generate regions of interest; we then use machine learning techniques with the aim of segmenting the nerve structure; here, a specific non-linear Wavelet transform is used for the feature extraction stage, and Gaussian processes for the classification step. The methodology performance is measured in terms of accuracy and the dice coefficient. Results show that the implemented methodology can be used for automatically segmenting nerve structures.

GRAPH CUT SEGMENTATION METHOD AND ITS APPLICATION IN MEDICAL IMAGES

Graph cut is an interactive segmentation method. It works based on preparing graph from image and finds the minimum cut for the graph. The edges value is calculated based on belonging a pixel to object or background. The advantage of this method is using the cost function. If the cost function is clearly described, graph cut is presents a generally optimum result. In this paper graph concepts and preparing graph according to image pixels is described. Preparing different edges and performing min cut/max flow is explained. Finally, the method is applied on some medical images.