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1.  Mass segmentation using a combined method for cancer detection 
BMC Systems Biology  2011;5(Suppl 3):S6.
Background
Breast cancer is one of the leading causes of cancer death for women all over the world and mammography is thought of as one of the main tools for early detection of breast cancer. In order to detect the breast cancer, computer aided technology has been introduced. In computer aided cancer detection, the detection and segmentation of mass are very important. The shape of mass can be used as one of the factors to determine whether the mass is malignant or benign. However, many of the current methods are semi-automatic. In this paper, we investigate fully automatic segmentation method.
Results
In this paper, a new mass segmentation algorithm is proposed. In the proposed algorithm, a fully automatic marker-controlled watershed transform is proposed to segment the mass region roughly, and then a level set is used to refine the segmentation. For over-segmentation caused by watershed, we also investigated different noise reduction technologies. Images from DDSM were used in the experiments and the results show that the new algorithm can improve the accuracy of mass segmentation.
Conclusions
The new algorithm combines the advantages of both methods. The combination of the watershed based segmentation and level set method can improve the efficiency of the segmentation. Besides, the introduction of noise reduction technologies can reduce over-segmentation.
doi:10.1186/1752-0509-5-S3-S6
PMCID: PMC3287574  PMID: 22784625
2.  Volumetric quantification of fibrous caps using intravascular optical coherence tomography 
Biomedical Optics Express  2012;3(6):1413-1426.
The rupture of thin-cap fibroatheroma accounts for most acute coronary events. Optical Coherence Tomography (OCT) allows quantification of fibrous cap (FC) thickness in vivo. Conventional manual analysis, by visually determining the thinnest part of the FC is subject to inter-observer variability and does not capture the 3-D morphology of the FC. We propose and validate a computer-aided method that allows volumetric analysis of FC. The radial FC boundary is semi-automatically segmented using a dynamic programming algorithm. The thickness at every point of the FC boundary, along with 3-D morphology of the FC, can be quantified. The method was validated against three experienced OCT image analysts in 14 lipid-rich lesions. The proposed method may advance our understanding of the mechanisms behind plaque rupture and improve disease management.
doi:10.1364/BOE.3.001413
PMCID: PMC3370980  PMID: 22741086
(100.0100) Image processing; (110.4500) Optical coherence tomography
3.  3D Axon Structure Extraction and Analysis in Confocal Fluorescence Microscopy Images 
Neural computation  2008;20(8):1899-1927.
The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects.
doi:10.1162/neco.2008.05-07-519
PMCID: PMC2587013  PMID: 18336075
4.  Modified Watershed Technique and Post-Processing for Segmentation of Skin Lesions in Dermoscopy Images 
In previous research, a watershed-based algorithm was shown to be useful for automatic lesion segmentation in dermoscopy images, and was tested on a set of 100 benign and malignant melanoma images with the average of three sets of dermatologist-drawn borders used as the ground truth, resulting in an overall error of 15.98%. In this study, to reduce the border detection errors, a neural network classifier was utilized to improve the first-pass watershed segmentation; a novel “Edge Object Value (EOV) Threshold” method was used to remove large light blobs near the lesion boundary; and a noise removal procedure was applied to reduce the peninsula-shaped false-positive areas. As a result, an overall error of 11.09% was achieved.
doi:10.1016/j.compmedimag.2010.09.006
PMCID: PMC3183575  PMID: 20970307
Malignant Melanoma; Watershed; Image Processing; Segmentation; Neural Network
5.  Watershed segmentation of dermoscopy images using a watershed technique 
Background/purpose
Automatic lesion segmentation is an important part of computer-based image analysis of pigmented skin lesions. In this research, a watershed algorithm is developed and investigated for adequacy of skin lesion segmentation in dermoscopy images.
Methods
Hair, black border and vignette removal methods are introduced as preprocessing steps. The flooding variant of the watershed segmentation algorithm was implemented with novel features adapted to this domain. An outer bounding box, determined by a difference function derived from horizontal and vertical projection functions, is added to estimate the lesion area, and the lesion area error is reduced by a linear estimation function. As a post-processing step, a second-order B-Spline smoothing method is introduced to smooth the watershed border.
Results
Using the average of three sets of dermatologist-drawn borders as the ground truth, an overall error of 15.98% was obtained using the watershed technique.
Conclusion
The implementation of the flooding variant of the watershed algorithm presented here allows satisfactory automatic segmentation of pigmented skin lesions.
doi:10.1111/j.1600-0846.2010.00445.x
PMCID: PMC3160671  PMID: 20637008
malignant melanoma; watershed; image processing; segmentation
6.  Automatic Estimation of Orientation and Position of Spine in Digitized X-rays using Mathematical Morphology 
Journal of Digital Imaging  2005;18(3):234-241.
In this paper, we propose a method for automatic determination of position and orientation of spine in digitized spine X-rays using mathematical morphology. As the X-ray images are usually highly smeared, vertebrae segmentation is a complex process. The image is first coarsely segmented to obtain the location and orientation information of the spine. The state-of-the-art technique is based on the deformation model of a template, and as the vertebrae shape usually shows variation from case to case, accurate representation using a template is a difficult process. The proposed method makes use of the vertebrae morphometry and gray-scale profile of the spine. The top-hat transformation-based method is proposed to enhance the ridge points in the posterior boundary of the spine. For cases containing external objects such as ornaments, H-Maxima transform is used for segmentation and removal of these objects. The Radon transform is then used to estimate the location and orientation of the line joining the ridge point clusters appearing on the boundary of the vertebra body. The method was validated for 100 cervical spine X-ray images, and in all cases, the error in orientation was within the accepted tolerable limit of 15°. The average error was found to be 4.6°. A point on the posterior boundary was located with an accuracy of ±5.2 mm. The accurate information about location and orientation of thespine is necessary for fine-grained segmentation of the vertebrae using techniques such as active shape modeling. Accurate vertebrae segmentation is needed in successful feature extraction for applications such as content-based image retrieval of biomedical images.
doi:10.1007/s10278-005-5150-4
PMCID: PMC3046718  PMID: 15924275
Vertebrae segmentation; spine X-ray; content-based image retrieval; mathematical morphology
7.  Semi-automatic algorithm for construction of the left ventricular area variation curve over a complete cardiac cycle 
Background
Two-dimensional echocardiography (2D-echo) allows the evaluation of cardiac structures and their movements. A wide range of clinical diagnoses are based on the performance of the left ventricle. The evaluation of myocardial function is typically performed by manual segmentation of the ventricular cavity in a series of dynamic images. This process is laborious and operator dependent. The automatic segmentation of the left ventricle in 4-chamber long-axis images during diastole is troublesome, because of the opening of the mitral valve.
Methods
This work presents a method for segmentation of the left ventricle in dynamic 2D-echo 4-chamber long-axis images over the complete cardiac cycle. The proposed algorithm is based on classic image processing techniques, including time-averaging and wavelet-based denoising, edge enhancement filtering, morphological operations, homotopy modification, and watershed segmentation. The proposed method is semi-automatic, requiring a single user intervention for identification of the position of the mitral valve in the first temporal frame of the video sequence. Image segmentation is performed on a set of dynamic 2D-echo images collected from an examination covering two consecutive cardiac cycles.
Results
The proposed method is demonstrated and evaluated on twelve healthy volunteers. The results are quantitatively evaluated using four different metrics, in a comparison with contours manually segmented by a specialist, and with four alternative methods from the literature. The method's intra- and inter-operator variabilities are also evaluated.
Conclusions
The proposed method allows the automatic construction of the area variation curve of the left ventricle corresponding to a complete cardiac cycle. This may potentially be used for the identification of several clinical parameters, including the area variation fraction. This parameter could potentially be used for evaluating the global systolic function of the left ventricle.
doi:10.1186/1475-925X-9-5
PMCID: PMC3224979  PMID: 20078864
8.  A Probabilistic Approach for Breast Boundary Extraction in Mammograms 
The extraction of the breast boundary is crucial to perform further analysis of mammogram. Methods to extract the breast boundary can be classified into two categories: methods based on image processing techniques and those based on models. The former use image transformation techniques such as thresholding, morphological operations, and region growing. In the second category, the boundary is extracted using more advanced techniques, such as the active contour model. The problem with thresholding methods is that it is a hard to automatically find the optimal threshold value by using histogram information. On the other hand, active contour models require defining a starting point close to the actual boundary to be able to successfully extract the boundary. In this paper, we propose a probabilistic approach to address the aforementioned problems. In our approach we use local binary patterns to describe the texture around each pixel. In addition, the smoothness of the boundary is handled by using a new probability model. Experimental results show that the proposed method reaches 38% and 50% improvement with respect to the results obtained by the active contour model and threshold-based methods respectively, and it increases the stability of the boundary extraction process up to 86%.
doi:10.1155/2013/408595
PMCID: PMC3842063  PMID: 24324523
9.  Automatic Detection and Classification of Breast Tumors in Ultrasonic Images Using Texture and Morphological Features 
Due to severe presence of speckle noise, poor image contrast and irregular lesion shape, it is challenging to build a fully automatic detection and classification system for breast ultrasonic images. In this paper, a novel and effective computer-aided method including generation of a region of interest (ROI), segmentation and classification of breast tumor is proposed without any manual intervention. By incorporating local features of texture and position, a ROI is firstly detected using a self-organizing map neural network. Then a modified Normalized Cut approach considering the weighted neighborhood gray values is proposed to partition the ROI into clusters and get the initial boundary. In addition, a regional-fitting active contour model is used to adjust the few inaccurate initial boundaries for the final segmentation. Finally, three textures and five morphologic features are extracted from each breast tumor; whereby a highly efficient Affinity Propagation clustering is used to fulfill the malignancy and benign classification for an existing database without any training process. The proposed system is validated by 132 cases (67 benignancies and 65 malignancies) with its performance compared to traditional methods such as level set segmentation, artificial neural network classifiers, and so forth. Experiment results show that the proposed system, which needs no training procedure or manual interference, performs best in detection and classification of ultrasonic breast tumors, while having the lowest computation complexity.
doi:10.2174/1874431101105010026
PMCID: PMC3158436  PMID: 21892371
Breast ultrasonic images; fully automatic; region of interest; Normalized Cut; Affinity Propagation clustering.
10.  Vascular Tree Segmentation in Medical Images Using Hessian-Based Multiscale Filtering and Level Set Method 
Vascular segmentation plays an important role in medical image analysis. A novel technique for the automatic extraction of vascular trees from 2D medical images is presented, which combines Hessian-based multiscale filtering and a modified level set method. In the proposed algorithm, the morphological top-hat transformation is firstly adopted to attenuate background. Then Hessian-based multiscale filtering is used to enhance vascular structures by combining Hessian matrix with Gaussian convolution to tune the filtering response to the specific scales. Because Gaussian convolution tends to blur vessel boundaries, which makes scale selection inaccurate, an improved level set method is finally proposed to extract vascular structures by introducing an external constrained term related to the standard deviation of Gaussian function into the traditional level set. Our approach was tested on synthetic images with vascular-like structures and 2D slices extracted from real 3D abdomen magnetic resonance angiography (MRA) images along the coronal plane. The segmentation rates for synthetic images are above 95%. The results for MRA images demonstrate that the proposed method can extract most of the vascular structures successfully and accurately in visualization. Therefore, the proposed method is effective for the vascular tree extraction in medical images.
doi:10.1155/2013/502013
PMCID: PMC3852584  PMID: 24348738
11.  A Knowledge-Based Approach for Carpal Tunnel Segmentation from Magnetic Resonance Images 
Journal of Digital Imaging  2012;26(3):510-520.
Carpal tunnel syndrome (CTS) has been reported as one of the most common peripheral neuropathies. Carpal tunnel segmentation from magnetic resonance (MR) images is important for the evaluation of CTS. To date, manual segmentation, which is time-consuming and operator dependent, remains the most common approach for the analysis of the carpal tunnel structure. Therefore, we propose a new knowledge-based method for automatic segmentation of the carpal tunnel from MR images. The proposed method first requires the segmentation of the carpal tunnel from the most proximally cross-sectional image. Three anatomical features of the carpal tunnel are detected by watershed and polygonal curve fitting algorithms to automatically initialize a deformable model as close to the carpal tunnel in the given image as possible. The model subsequently deforms toward the tunnel boundary based on image intensity information, shape bending degree, and the geometry constraints of the carpal tunnel. After the deformation process, the carpal tunnel in the most proximal image is segmented and subsequently applied to a contour propagation step to extract the tunnel contours sequentially from the remaining cross-sectional images. MR volumes from 15 subjects were included in the validation experiments. Compared with the ground truth of two experts, our method showed good agreement on tunnel segmentations by an average margin of error within 1 mm and dice similarity coefficient above 0.9.
doi:10.1007/s10278-012-9530-2
PMCID: PMC3649045  PMID: 23053905
Carpal tunnel; Knowledge-based segmentation; MR; Deformable model; Watershed; Polygonal curve
12.  SIMPLE PARADIGM FOR EXTRA-CEREBRAL TISSUE REMOVAL: ALGORITHM AND ANALYSIS 
NeuroImage  2011;56(4):1982-1992.
Extraction of the brain — i.e. cerebrum, cerebellum, and brain stem — from T1-weighted structural magnetic resonance images is an important initial step in neuroimage analysis. Although automatic algorithms are available, their inconsistent handling of the cortical mantle often requires manual interaction, thereby reducing their effectiveness. This paper presents a fully automated brain extraction algorithm that incorporates elastic registration, tissue segmentation, and morphological techniques which are combined by a watershed principle, while paying special attention to the preservation of the boundary between the gray matter and the cerebrospinal fluid. The approach was evaluated by comparison to a manual rater, and compared to several other leading algorithms on a publically available data set of brain images using the Dice coefficient and containment index as performance metrics. The qualitative and quantitative impact of this initial step on subsequent cortical surface generation is also presented. Our experiments demonstrate that our approach is quantitatively better than six other leading algorithms (with statistical significance on modern T1-weighted MR data). We also validated the robustness of the algorithm on a very large data set of over one thousand subjects, and showed that it can replace an experienced manual rater as preprocessing for a cortical surface extraction algorithm with statistically insignificant differences in cortical surface position.
doi:10.1016/j.neuroimage.2011.03.045
PMCID: PMC3105165  PMID: 21458576
Brain extraction; skull stripping; watershed principle; segmentation; medical image processing
13.  Multi-Feature Contour Evolution for Automatic Live Cell Segmentation in Time Lapse Imagery 
Cell boundary segmentation in live cell image sequences is the first step towards quantitative analysis of cell motion and behavior. The time lapse microscopy imaging produces large volumes of image sequence collections which requires fast and robust automatic segmentation of cell boundaries to utilize further automated tools such as cell tracking to quantify and classify cell behavior. This paper presents a methodology that is based on utilizing the temporal context of the cell image sequences to accurately delineate the boundaries of non-homogeneous cells. A novel flux tensor-based detection of moving cells provides initial localization that is further refined by a multi-feature level set-based method using an efficient additive operator splitting scheme. The segmentation result is processed by a watershed-based algorithm to avoid merging boundaries of neighboring cells. By utilizing robust features, the level-set algorithm produces accurate segmentation for non-homogeneous cells with concave shapes and varying intensities.
PMCID: PMC2632969  PMID: 19162670
14.  Computerized nipple identification for multiple image analysis in computer-aided diagnosis 
Medical physics  2004;31(10):2871-2882.
Correlation of information from multiple-view mammograms (e.g., MLO and CC views, bilateral views, or current and prior mammograms) can improve the performance of breast cancer diagnosis by radiologists or by computer. The nipple is a reliable and stable landmark on mammograms for the registration of multiple mammograms. However, accurate identification of nipple location on mammograms is challenging because of the variations in image quality and in the nipple projections, resulting in some nipples being nearly invisible on the mammograms. In this study, we developed a computerized method to automatically identify the nipple location on digitized mammograms. First, the breast boundary was obtained using a gradient-based boundary tracking algorithm, and then the gray level profiles along the inside and outside of the boundary were identified. A geometric convergence analysis was used to limit the nipple search to a region of the breast boundary. A two-stage nipple detection method was developed to identify the nipple location using the gray level information around the nipple, the geometric characteristics of nipple shapes, and the texture features of glandular tissue or ducts which converge toward the nipple. At the first stage, a rule-based method was designed to identify the nipple location by detecting significant changes of intensity along the gray level profiles inside and outside the breast boundary and the changes in the boundary direction. At the second stage, a texture orientation-field analysis was developed to estimate the nipple location based on the convergence of the texture pattern of glandular tissue or ducts towards the nipple. The nipple location was finally determined from the detected nipple candidates by a rule-based confidence analysis. In this study, 377 and 367 randomly selected digitized mammograms were used for training and testing the nipple detection algorithm, respectively. Two experienced radiologists identified the nipple locations which were used as the gold standard. In the training data set, 301 nipples were positively identified and were referred to as visible nipples. Seventy six nipples could not be positively identified and were referred to as invisible nipples. The radiologists provided their estimation of the nipple locations in the latter group for comparison with the computer estimates. The computerized method could detect 89.37% (269/301) of the visible nipples and 69.74% (53/76) of the invisible nipples within 1 cm of the gold standard. In the test data set, 298 and 69 of the nipples were classified as visible and invisible, respectively. 92.28% (275/298) of the visible nipples and 53.62% (37/69) of the invisible nipples were identified within 1 cm of the gold standard. The results demonstrate that the nipple locations on digitized mammograms can be accurately detected if they are visible and can be reasonably estimated if they are invisible. Automated nipple detection will be an important step towards multiple image analysis for CAD.
PMCID: PMC2898150  PMID: 15543797
computer-aided detection; mammography; nipple detection; texture orientation field analysis
15.  Automatic Initialization Active Contour Model for the Segmentation of the Chest Wall on Chest CT 
Objectives
Snake or active contours are extensively used in computer vision and medical image processing applications, and particularly to locate object boundaries. Yet problems associated with initialization and the poor convergence to boundary concavities have limited their utility. The new method of external force for active contours, which is called gradient vector flow (GVF), was recently introduced to address the problems.
Methods
This paper presents an automatic initialization value of the snake algorithm for the segmentation of the chest wall. Snake algorithms are required to have manually drawn initial contours, so this needs automatic initialization. In this paper, our proposed algorithm is the mean shape for automatic initialization in the GVF.
Results
The GVF is calculated as a diffusion of the gradient vectors of a gray-level or binary edge map derived from the medical images. Finally, the mean shape coordinates are used to automatic initialize thepoint of the snake. The proposed algorithm is composed of three phases: the landmark phase, the procrustes shape distance metric phase and aligning a set of shapes phase. The experiments showed the good performance of our algorithm in segmenting the chest wall by chest computed tomography.
Conclusions
An error analysis for the active contours results on simulated test medical images is also presented. We showed that GVF has a large capture range and it is able to move a snake into boundary concavities. Therefore, the suggested algorithm is better than the traditional potential forces of image segmentation.
doi:10.4258/hir.2010.16.1.36
PMCID: PMC3089843  PMID: 21818422
Active Contour Model; Automatic Initialization; Mean Shape; Gradient Vector Flow; Computed Tomography
16.  Automatic Segmentation of Right Ventricle on Ultrasound Images Using Sparse Matrix Transform and Level Set 
Proceedings of SPIE  2013;8669:10.1117/12.2006490.
An automatic framework is proposed to segment right ventricle on ultrasound images. This method can automatically segment both epicardial and endocardial boundaries from a continuous echocardiography series by combining sparse matrix transform (SMT), a training model, and a localized region based level set. First, the sparse matrix transform extracts main motion regions of myocardium as eigenimages by analyzing statistical information of these images. Second, a training model of right ventricle is registered to the extracted eigenimages in order to automatically detect the main location of the right ventricle and the corresponding transform relationship between the training model and the SMT-extracted results in the series. Third, the training model is then adjusted as an adapted initialization for the segmentation of each image in the series. Finally, based on the adapted initializations, a localized region based level set algorithm is applied to segment both epicardial and endocardial boundaries of the right ventricle from the whole series. Experimental results from real subject data validated the performance of the proposed framework in segmenting right ventricle from echocardiography. The mean Dice scores for both epicardial and endocardial boundaries are 89.1%±2.3% and 83.6±7.3%, respectively. The automatic segmentation method based on sparse matrix transform and level set can provide a useful tool for quantitative cardiac imaging.
doi:10.1117/12.2006490
PMCID: PMC3824270  PMID: 24236228
Image segmentation; ultrasound imaging; sparse matrix transform; level set; right ventricle; cardiac imaging; heart; myocardium; genetic algorithm; functional imaging
17.  A Confident Scale-Space Shape Representation Framework for Cell Migration Detection 
Journal of microscopy  2008;231(3):395-407.
SUMMARY
Automated segmentation of time-lapse images is a method to facilitate the understanding of the intricate biological progression, e.g., cancer cell migration. To address this problem, we introduce a shape representation enhancement over popular snake models in the context of confident scale-space such that a higher level of interpretation can hopefully be achieved. Our proposed system consists of a hierarchical analytic framework including feedback loops, self-adaptive and demand-adaptive adjustment, incorporating a steerable boundary detail term constraint based on multiscale B-spline interpolation. To minimize the noise interference inherited from microscopy acquisition, the coarse boundary derived from the initial segmentation with refined watershed line is coupled with microscopy compensation using the mean shift filtering. A progressive approximation is applied to achieve represented as a balance between a relief function of watershed algorithm and local minima concerning multi-scale optimality, convergence, and robust constraints. Experimental results show that the proposed method overcomes problems with spurious branches, arbitrary gaps, low contrast boundaries and low signal-to-noise ratio. The proposed system has the potential to serve as an automated data processing tool for cell migration applications.
doi:10.1111/j.1365-2818.2008.02050.x
PMCID: PMC2896032  PMID: 18754994
cellular image segmentation; 3T3 cell; time-lapse microscopy; snake model; multiscale detail detection; mean shift filtering
18.  An improved approach for the segmentation of starch granules in microscopic images 
BMC Genomics  2010;11(Suppl 2):S13.
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.
doi:10.1186/1471-2164-11-S2-S13
PMCID: PMC2975413  PMID: 21047380
19.  Extraction of microcalcifications in digital mammograms using regional watershed 
Journal of Digital Imaging  2000;13(Suppl 1):127-129.
In this report, a novel technique is proposed for computer-aided automatic extraction of microcalcifications in a digital mammogram. First, the microcalcifications are detected by morphological filtering, followed by entropy-based thresholding. Next, the microcalcifications are segmented by computing regional watershed. The proposed automatic technique is designed to serve as a visual aid to radiologists. Its efficacy is demonstrated through experimental results.
doi:10.1007/BF03167642
PMCID: PMC3453277  PMID: 10847380
20.  A Novel Cell Segmentation Method and Cell Phase Identification Using Markov Model 
Optical microscopy is becoming an important technique in drug discovery and life science research. The approaches used to analyze optical microscopy images are generally classified into two categories: automatic and manual approaches. However, the existing automatic systems are rather limited in dealing with large volume of time-lapse microscopy images because of the complexity of cell behaviors and morphological variance. On the other hand, manual approaches are very time-consuming. In this paper, we propose an effective automated, quantitative analysis system that can be used to segment, track, and quantize cell cycle behaviors of a large population of cells nuclei effectively and efficiently. We use adaptive thresholding and watershed algorithm for cell nuclei segmentation followed by a fragment merging method that combines two scoring models based on trend and no trend features. Using the context information of time-lapse data, the phases of cell nuclei are identified accurately via a Markov model. Experimental results show that the proposed system is effective for nuclei segmentation and phase identification.
doi:10.1109/TITB.2008.2007098
PMCID: PMC2846548  PMID: 19272857
Cell phase identification; continuous Markov model; nuclei segmentation; time-lapse fluorescence microscopy; tracking
21.  Simultaneous Nonrigid Registration, Segmentation, and Tumor Detection in MRI Guided Cervical Cancer Radiation Therapy 
IEEE transactions on medical imaging  2012;31(6):1213-1227.
External beam radiation therapy (EBRT) for the treatment of cancer enables accurate placement of radiation dose on the cancerous region. However, the deformation of soft tissue during the course of treatment, such as in cervical cancer, presents significant challenges for the delineation of the target volume and other structures of interest. Furthermore, the presence and regression of pathologies such as tumors may violate registration constraints and cause registration errors. In this paper, automatic segmentation, nonrigid registration and tumor detection in cervical magnetic resonance (MR) data are addressed simultaneously using a unified Bayesian framework. The proposed novel method can generate a tumor probability map while progressively identifying the boundary of an organ of interest based on the achieved nonrigid transformation. The method is able to handle the challenges of significant tumor regression and its effect on surrounding tissues. The new method was compared to various currently existing algorithms on a set of 36 MR data from six patients, each patient has six T2-weighted MR cervical images. The results show that the proposed approach achieves an accuracy comparable to manual segmentation and it significantly outperforms the existing registration algorithms. In addition, the tumor detection result generated by the proposed method has a high agreement with manual delineation by a qualified clinician.
doi:10.1109/TMI.2012.2186976
PMCID: PMC3889159  PMID: 22328178
Cervical cancer; external beam radiation therapy; image segmentation; nonrigid registration; tumor detection
22.  SEGMENTATION OF ELASTOGRAPHIC IMAGES USING A COARSE-TO-FINE ACTIVE CONTOUR MODEL 
Ultrasound in medicine & biology  2006;32(3):397-408.
Delineation of radiofrequency-ablation-induced coagulation (thermal lesion) boundaries is an important clinical problem that is not well addressed by conventional imaging modalities. Elastography, which produces images of the local strain after small, externally applied compressions, can be used for visualization of thermal coagulations. This paper presents an automated segmentation approach for thermal coagulations on 3-D elastographic data to obtain both area and volume information rapidly. The approach consists of a coarse-to-fine method for active contour initialization and a gradient vector flow, active contour model for deformable contour optimization with the help of prior knowledge of the geometry of general thermal coagulations. The performance of the algorithm has been shown to be comparable to manual delineation of coagulations on elastograms by medical physicists (r = 0.99 for volumes of 36 radiofrequency-induced coagulations). Furthermore, the automatic algorithm applied to elastograms yielded results that agreed with manual delineation of coagulations on pathology images (r = 0.96 for the same 36 lesions). This algorithm has also been successfully applied on in vivo elastograms.
doi:10.1016/j.ultrasmedbio.2005.11.011
PMCID: PMC1764611  PMID: 16530098
Ablation; Active contour models; Breast tumor; Elasticity imaging; Elastography; Gradient vector flow; Image segmentation; Multiresolution; Snakes; Strain; 3-D ultrasound
23.  Semi-Automatic Integrated Segmentation Approaches and Contour Extraction Applied to Computed Tomography Scan Images 
We propose to segment two-dimensional CT scans traumatic brain injuries with various methods. These methods are hybrid, feature extraction, level sets, region growing, and watershed which are analysed based upon their parametric and nonparametric arguments. The pixel intensities, gradient magnitude, affinity map, and catchment basins of these methods are validated based upon various constraints evaluations. In this article, we also develop a new methodology for a computational pipeline that uses bilateral filtering, diffusion properties, watershed, and filtering with mathematical morphology operators for the contour extraction of the lesion in the feature available based mainly on the gradient function. The evaluations of the classification of these lesions are very briefly outlined in this context and are being undertaken by pattern recognition in another paper work.
doi:10.1155/2008/759354
PMCID: PMC2579322  PMID: 19002262
24.  Automatic Image Analysis of Histopathology Specimens Using Concave Vertex Graph 
Automatic image analysis of histopathology specimens would help the early detection of blood cancer. The first step for automatic image analysis is segmentation. However, touching cells bring the difficulty for traditional segmentation algorithms. In this paper, we propose a novel algorithm which can reliably handle touching cells segmentation. Robust estimation and color active contour models are used to delineate the outer boundary. Concave points on the boundary and inner edges are automatically detected. A concave vertex graph is constructed from these points and edges. By minimizing a cost function based on morphological characteristics, we recursively calculate the optimal path in the graph to separate the touching cells. The algorithm is computationally efficient and has been tested on two large clinical dataset which contain 207 images and 3898 images respectively. Our algorithm provides better results than other studies reported in the recent literature.
PMCID: PMC3683135  PMID: 18979823
25.  Improving the clinical correlation of multiple sclerosis black hole volume change by paired-scan analysis☆ 
NeuroImage : Clinical  2012;1(1):29-36.
The change in T1-hypointense lesion (“black hole”) volume is an important marker of pathological progression in multiple sclerosis (MS). Black hole boundaries often have low contrast and are difficult to determine accurately and most (semi‐)automated segmentation methods first compute the T2-hyperintense lesions, which are a superset of the black holes and are typically more distinct, to form a search space for the T1w lesions. Two main potential sources of measurement noise in longitudinal black hole volume computation are partial volume and variability in the T2w lesion segmentation. A paired analysis approach is proposed herein that uses registration to equalize partial volume and lesion mask processing to combine T2w lesion segmentations across time. The scans of 247 MS patients are used to compare a selected black hole computation method with an enhanced version incorporating paired analysis, using rank correlation to a clinical variable (MS functional composite) as the primary outcome measure. The comparison is done at nine different levels of intensity as a previous study suggests that darker black holes may yield stronger correlations. The results demonstrate that paired analysis can strongly improve longitudinal correlation (from -0.148 to -0.303 in this sample) and may produce segmentations that are more sensitive to clinically relevant changes.
doi:10.1016/j.nicl.2012.08.004
PMCID: PMC3757731  PMID: 24179734
Multiple sclerosis; Black holes; Image segmentation; Longitudinal analysis; Volume change; Clinical correlation

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