A Bayesian approach to DNA sequence segmentation

Many deoxyribonucleic acid (DNA) sequences display compositional heterogeneity in the form of segments of similar structure. This article describes a Bayesian method that identifies such segments by using a Markov chain governed by a hidden Markov model. Markov chain Monte Carlo (MCMC) techniques are employed to compute all posterior quantities of interest and, in particular, allow inferences to be made regarding the number of segment types and the order of Markov dependence in the DNA sequence. The method is applied to the segmentation of the bacteriophage lambda genome, a common benchmark sequence used for the comparison of statistical segmentation algorithms.     

A novel intensity-based multi-level classification approach for coronary plaque characterization in intravascular ultrasound images

Background

Intravascular ultrasound (IVUS) is a commonly used diagnostic imaging method for coronary artery disease. Virtual histology (VH) characterizes the plaque components into fibrous tissue (FT), fibro-fatty tissue (FFT), necrotic core (NC), or dense calcium (DC). However, VH can obtain only a single-frame image in one cardiac cycle, and specific software is needed to obtain the radio frequency data. This study proposed a novel intensity-based multi-level classification model for plaque characterization.

Methods

The plaque-containing regions between the intima and the media-adventitia were segmented manually for all IVUS frames. A total of 54 features including first order statistics, grey level co-occurrence matrix, Law’s energy measures, extended grey level run length matrix, intensity, and local binary pattern were estimated from the plaque-containing regions. After feature extraction, optimal features were selected using principle component analysis (PCA), and these were utilized as the input for the classification models. Plaque components were classified into FT, FFT, NC, or DC using an intensity-based multi-level classification model consisting of three different nets. Net 1 differentiated low-intensity components into FT/FFT and NC/DC groups. Then, net 2 subsequently divided FT/FFT into FT or FFT, whereas the remainder and high-intensity components were classified into NC or DC via net 3. To improve classification accuracy, each net utilized three different input features obtained by PCA. Classification performance was evaluated in terms of sensitivity, specificity, accuracy, and receiver operating characteristic curve.

Results

Quantitative results indicated that the proposed method showed significantly high classification accuracy for all tissue types. The classifiers had classification accuracies of 85.1%, 71.9%, and 77.2%, respectively, and the areas under the curve were 0.845, 0.704, and 0.783. In particular, the proposed method achieved relatively high sensitivity (82.0%) and specificity (87.1%) for differentiating between the FT/FFT and NC/DC groups.

Conclusions

These results confirmed the clinical applicability of the proposed approach for IVUS-based tissue characterization.

     

An improved approach for the segmentation of starch granules in microscopic images

Background

Starches are the main storage polysaccharides in plants and are distributed widely throughout plants including seeds, roots, tubers, leaves, stems and so on. Currently, microscopic observation is one of the most important ways to investigate and analyze the structure of starches. The position, shape, and size of the starch granules are the main measurements for quantitative analysis. In order to obtain these measurements, segmentation of starch granules from the background is very important. However, automatic segmentation of starch granules is still a challenging task because of the limitation of imaging condition and the complex scenarios of overlapping granules.

Results

We propose a novel method to segment starch granules in microscopic images. In the proposed method, we first separate starch granules from background using automatic thresholding and then roughly segment the image using watershed algorithm. In order to reduce the oversegmentation in watershed algorithm, we use the roundness of each segment, and analyze the gradient vector field to find the critical points so as to identify oversegments. After oversegments are found, we extract the features, such as the position and intensity of the oversegments, and use fuzzy c-means clustering to merge the oversegments to the objects with similar features. Experimental results demonstrate that the proposed method can alleviate oversegmentation of watershed segmentation algorithm successfully.

Conclusions

We present a new scheme for starch granules segmentation. The proposed scheme aims to alleviate the oversegmentation in watershed algorithm. We use the shape information and critical points of gradient vector flow (GVF) of starch granules to identify oversegments, and use fuzzy c-mean clustering based on prior knowledge to merge these oversegments to the objects. Experimental results on twenty microscopic starch images demonstrate the effectiveness of the proposed scheme.

     

A differential structure approach to membrane segmentation in electron tomography

Electron tomography allows three-dimensional visualization of cellular landscapes in molecular detail. Segmentation is a paramount stage for the interpretation of the reconstructed tomograms. Although several computational approaches have been proposed, none has prevailed as a generic method and thus segmentation through manual annotation is still a common choice. In this work we introduce a segmentation method targeted at membranes, which define the natural limits of compartments within biological specimens. Our method is based on local differential structure and on a Gaussian-like membrane model. First, it isolates information through scale-space and finds potential membrane-like points at a local scale. Then, the structural information is integrated at a global scale to yield the definite segmentation. We show and validate the performance of the algorithm on a number of tomograms under different experimental conditions.     

A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images.

Automated segmentation and morphometry of fluorescently labeled cell nuclei in batches of 3D confocal stacks is essential for quantitative studies. Model-based segmentation algorithms are attractive due to their robustness. Previous methods incorporated a single nuclear model. This is a limitation for tissues containing multiple cell types with different nuclear features. Improved segmentation for such tissues requires algorithms that permit multiple models to be used simultaneously. This requires a tight integration of classification and segmentation algorithms. Two or more nuclear models are constructed semiautomatically from user-provided training examples. Starting with an initial over-segmentation produced by a gradient-weighted watershed algorithm, a hierarchical fragment merging tree rooted at each object is built. Linear discriminant analysis is used to classify each candidate using multiple object models. On the basis of the selected class, a Bayesian score is computed. Fragment merging decisions are made by comparing the score with that of other candidates, and the scores of constituent fragments of each candidate. The overall segmentation accuracy was 93.7% and classification accuracy was 93.5%, respectively, on a diverse collection of images drawn from five different regions of the rat brain. The multi-model method was found to achieve high accuracy on nuclear segmentation and classification by correctly resolving ambiguities in clustered regions containing heterogeneous cell populations.     

A segmentation approach to long duration surface EMG recordings.

The purpose of this study was to develop an automatic segmentation method in order to identify postural surface EMG segments in long-duration recordings. Surface EMG signals were collected from the cervical erector spinae (CES), erector spinae (ES), external oblique (EO), and tibialis anterior (TA) muscles of 11 subjects using a bipolar electrode configuration. Subjects remained seated in a car seat over the 150-min data-collection period. The modified dynamic cumulative sum (MDCS) algorithm was used to automatically segment the surface EMG signals. Signals were rejected by comparison with an exponential mathematical model of the spectrum of a surface EMG signal. The average power ratio computed between two successive retained segments was used to classify segments as postural or surface EMG. The presence of a negative slope of a regression line fitted to the median frequency values of postural surface EMG segments was taken as an indication of fatigue. Alpha level was set at 0.05. The overall classification error rate was 8%, and could be performed in 25 min for a 150-min signal using a custom-built software program written in C (Borland Software Corporation, CA, USA). This error rate could be enhanced by concentrating on the rejection method, which caused most of the misclassification (6%). Furthermore, the elimination of non-postural surface EMG segments by the use of a segmentation approach enabled muscular fatigue to be identified in signals that contained no evidence of fatigue when analysed using traditional methods.     

A two-stage adaptive thresholding segmentation for noisy low-contrast images

Image recognition is the process of recognizing and classifying objects with machine learning algorithms. Image binarization is the first and most challenging step in image recognition, in which foreground objects are separated from their background. When foreground objects have complex morphological structure and background noise is strong, foreground objects are often being fractured into subcomponents. To address the over-segmentation issue of organisms with complex structures, we propose a 2-stage adaptive binarization approach based on Sauvola's binarization algorithm. We tested the effectiveness of the new approach on a set of underwater images with jellyfish collected in nearshore waters using a shadowgraph underwater plankton imaging system, PlanktonScope, because jellyfish have relatively complex structure and are often over-segemented. The results showed that the 2-stage approach improved the integrity of extracted jellyfish compared to traditional binarization methods, including Sauvola's algorithm. The analysis of local entropy values showed that the first stage effectively suppresses redundant information in the image and reduces the number of Region of Interests (ROIs), and the second stage preserves relatively weak and low-intensity signals to ensure the integrity of the extracted targets. The 2-stage approach improves hardware resource utilization and computational efficiency. It is robust for images acquired in sub-optimal conditions and enhances the accuracy of analytical results in the study of marine organisms using imaging systems.     

Simple low-cost approaches to semantic segmentation in radiation therapy planning for prostate cancer using deep learning with non-contrast planning CT images

PurposeDeep learning has shown great efficacy for semantic segmentation. However, there are difficulties in the collection, labeling and management of medical imaging data, because of ethical complications and the limited number of imaging studies available at a single facility.This study aimed to find a simple and low-cost method to increase the accuracy of deep learning semantic segmentation for radiation therapy of prostate cancer.MethodsIn total, 556 cases with non-contrast CT images for prostate cancer radiation therapy were examined using a two-dimensional U-Net. Initially, all slices were used for the input data. Then, we removed slices of the cranial portions, which were beyond the margins of the bladder and rectum. Finally, the ground truth labels for the bladder and rectum were added as channels to the input for the prostate training dataset.ResultsThe highest mean dice similarity coefficients (DSCs) for each organ in the test dataset of 56 cases were 0.85 ± 0.05, 0.94 ± 0.04 and 0.85 ± 0.07 for the prostate, bladder and rectum, respectively. Removal of the cranial slices from the original images significantly increased the DSC of the rectum from 0.83 ± 0.09 to 0.85 ± 0.07 (p < 0.05). Adding bladder and rectum information to prostate training without removing the slices significantly increased the DSC of the prostate from 0.79 ± 0.05 to 0.85 ± 0.05 (p < 0.05).ConclusionsThese cost-free approaches may be useful for new applications, which may include updated models and datasets. They may be applicable to other organs at risk (OARs) and clinical targets such as elective nodal irradiation.     

Rotationally resliced 3D prostate segmentation of MR images using Bhattacharyya similarity and active band theory

PurposeIn this article, we propose a novel, semi-automatic segmentation method to process 3D MR images of the prostate using the Bhattacharyya coefficient and active band theory with the goal of providing technical support for computer-aided diagnosis and surgery of the prostate.MethodsOur method consecutively segments a stack of rotationally resectioned 2D slices of a prostate MR image by assessing the similarity of the shape and intensity distribution in neighboring slices. 2D segmentation is first performed on an initial slice by manually selecting several points on the prostate boundary, after which the segmentation results are propagated consecutively to neighboring slices. A framework of iterative graph cuts is used to optimize the energy function, which contains a global term for the Bhattacharyya coefficient with the help of an auxiliary function. Our method does not require previously segmented data for training or for building statistical models, and manual intervention can be applied flexibly and intuitively, indicating the potential utility of this method in the clinic.ResultsWe tested our method on 3D T2-weighted MR images from the ISBI dataset and PROMISE12 dataset of 129 patients, and the Dice similarity coefficients were 90.34 ± 2.21% and 89.32 ± 3.08%, respectively. The comparison was performed with several state-of-the-art methods, and the results demonstrate that the proposed method is robust and accurate, achieving similar or higher accuracy than other methods without requiring training.ConclusionThe proposed algorithm for segmenting 3D MR images of the prostate is accurate, robust, and readily applicable to a clinical environment for computer-aided surgery or diagnosis.     

An information-theoretic approach to interactions in images.

In this paper it will be argued that the notion of interactions in images is closely related to that of entropy associated with an image, and it will be shown that interactions make processing of the information coming from the retina computationally less expensive. A procedure will be presented, based on the evolution of joint entropy across different scales, to gauge the contributions of different types of interactions to the structure of the images.     

Graph ranking based butterfly segmentation in ecological images

An accurate cultural insect detection and recognition relies mainly on a proper automatic segmentation. This paper deals with butterfly segmentation in ecological images characterized by several artifacts like the complexity of environmental decors and cluttered backgrounds. The distractors contained in the rich ecological environment and the huge difference between butterfly species complicate severely the segmentation and make it a challenging task. As butterflies appears to be well contrasted from their surrounding, we suggest to explore the saliency property to delineate accurately the butterfly boundaries. In this vein, we perform a graph ranking process with high level guidance according to foreground and background cues to improve the quality of segmentation. The ranking accuracy is improved through a weighting scheme that combines accurately color, texture and spatial information. The contribution of each used feature is controlled according to its relevance in highlighting butterfly regions. After that, we initialize foreground seeds from most salient pixels and background seeds from less salient pixels as an input for a Graph-cut algorithm to extract the butterfly from the background. Comparative evaluation has shown that our segmentation scheme outperforms some existing segmentation methods that provide high segmentation scores.     

A watershed approach for improving medical image segmentation

In this paper, a novel watershed approach based on seed region growing and image entropy is presented which could improve the medical image segmentation. The proposed algorithm enables the prior information of seed region growing and image entropy in its calculation. The algorithm starts by partitioning the image into several levels of intensity using watershed multi-degree immersion process. The levels of intensity are the input to a computationally efficient seed region segmentation process which produces the initial partitioning of the image regions. These regions are fed to entropy procedure to carry out a suitable merging which produces the final segmentation. The latter process uses a region-based similarity representation of the image regions to decide whether regions can be merged. The region is isolated from the level and the residual pixels are uploaded to the next level and so on, we recall this process as multi-level process and the watershed is called multi-level watershed. The proposed algorithm is applied to challenging applications: grey matter–white matter segmentation in magnetic resonance images (MRIs). The established methods and the proposed approach are experimented by these applications to a variety of simulating immersion, multi-degree, multi-level seed region growing and multi-level seed region growing with entropy. It is shown that the proposed method achieves more accurate results for medical image oversegmentation.     

A multidisciplinary approach to the management of hormone-refractory prostate cancer

The patient with hormone-refractory prostate cancer (HRPC) presents unique management challenges for both the urologist and the medical oncologist. Because of a lack of effective treatment options, the management of patients with HRPC has historically been palliative. Over the past 10 years, the advent of relatively efficacious chemotherapeutic regimens, particularly taxane-based chemotherapy, has resulted in a desire to treat patients with HRPC more aggressively. The complex needs of these patients have made a multidisciplinary approach, inclusive of specialists with expertise in disease processes directly affecting the patient, the optimal means of treating HRPC. An understanding of the natural history and complications of HRPC, combined with a systemic evaluative process, can allow the multidisciplinary team to comprehensively address the needs of the individual patient with HRPC.