Topology adaptive deformable surfaces for medical image volume segmentation

Methods of Brain Extraction from Magnetic Resonance Images of Human Head: A Review

Medical images are providing vital information to aid physicians in diagnosing a disease afflicting the organ of a human body. Magnetic resonance imaging is an important imaging modality in capturing the soft tissues of the brain. Segmenting and extracting the brain is essential in studying the structure and pathological condition of brain. There are several methods that are developed for this purpose. Researchers in brain extraction or segmentation need to know the current status of the work that have been done. Such an information is also important for improving the existing method to get more accurate results or to reduce the complexity of the algorithm. In this paper we review the classical methods and convolutional neural network-based deep learning brain extraction methods.

Application of the Maximum Flow-Minimum Cut Algorithm to Segmentation and Clustering of Materials Datasets

Problems involving image segmentation, atomic cluster identification, segmentation of microstructure constituents in images and austenite reconstruction have seen various approaches attempt to solve them with mixed results. No single computational technique has been able to effectively tackle these problems due to the vast differences between them. We propose the application of graph cutting as a versatile technique that can provide solutions to numerous materials data analysis problems. This can be attributed to its configuration flexibility coupled with the ability to handle noisy experimental data. Implementation of a Bayesian statistical approach allows for the prior information, based on experimental results and already ingrained within nodes, to drive the expected solutions. This way, nodes within the graph can be grouped together with similar, neighboring nodes that are then assigned to a specific system with respect to calculated likelihoods. Associating probabilities with potential solutions and states of the system allows for quantitative, stochastic analysis. The promising, robust results for each problem indicate the potential usefulness of the technique so long as a network of nodes can be effectively established within the model system.

Quantitative image analysis for evaluation of tumor response in clinical oncology

The objective, accurate, and standardized evaluation of tumor response to treatment is an indispensable procedure in clinical oncology. Compared to manual measurement, computer-assisted linear measurement can significantly improve the accuracy and reproducibility of tumor burden quantification. For irregular-shaped and infiltrating or diffuse tumors, which are difficult to quantify by linear measurement, computer-assisted volumetric measurement may provide a more objective and sensitive quantification to evaluate tumor response to treatment than linear measurement does. In the evaluation of tumor response to novel oncologic treatments such as targeted therapy, changes in overall tumor size do not necessarily reflect tumor response to therapy due to the presence of internal necrosis or hemorrhages. This leads to a new generation of imaging biomarkers to evaluate tumor response by using texture analysis methods, also called radiomics. Computer-assisted texture analysis technology offers a more comprehensive and in-depth imaging biomarker to evaluate tumor response. The application of computer-assisted quantitative imaging analysis techniques not only reduces the inaccuracy and improves the reliability in tumor burden quantification, but facilitates the development of more comprehensive and intelligent approaches to evaluate treatment response, and hence promotes precision imaging in the evaluation of tumor response in clinical oncology. This article summarizes the state-of-the-art technical developments and clinical applications of quantitative imaging analysis in evaluation of tumor response in clinical oncology.

Objective breast tissue image classification using Quantitative Transmission ultrasound tomography

Quantitative Transmission Ultrasound (QT) is a powerful and emerging imaging paradigm which has the potential to perform true three-dimensional image reconstruction of biological tissue. Breast imaging is an important application of QT and allows non-invasive, non-ionizing imaging of whole breasts in vivo. Here, we report the first demonstration of breast tissue image classification in QT imaging. We systematically assess the ability of the QT images’ features to differentiate between normal breast tissue types. The three QT features were used in Support Vector Machines (SVM) classifiers, and classification of breast tissue as either skin, fat, glands, ducts or connective tissue was demonstrated with an overall accuracy of greater than 90%. Finally, the classifier was validated on whole breast image volumes to provide a color-coded breast tissue volume. This study serves as a first step towards a computer-aided detection/diagnosis platform for QT.

Detection and tracking of overlapping cell nuclei for large scale mitosis analyses

Background

Cell culture on printed micropatterns slides combined with automated fluorescent microscopy allows for extraction of tens of thousands of videos of small isolated growing cell clusters. The analysis of such large dataset in space and time is of great interest to the community in order to identify factors involved in cell growth, cell division or tissue formation by testing multiples conditions. However, cells growing on a micropattern tend to be tightly packed and to overlap with each other. Consequently, image analysis of those large dynamic datasets with no possible human intervention has proven impossible using state of the art automated cell detection methods.

Results

Here, we propose a fully automated image analysis approach to estimate the number, the location and the shape of each cell nucleus, in clusters at high throughput. The method is based on a robust fit of Gaussian mixture models with two and three components on each frame followed by an analysis over time of the fitting residual and two other relevant features. We use it to identify with high precision the very first frame containing three cells. This allows in our case to measure a cell division angle on each video and to construct division angle distributions for each tested condition. We demonstrate the accuracy of our method by validating it against manual annotation on about 4000 videos of cell clusters.

Conclusions

The proposed approach enables the high throughput analysis of video sequences of isolated cell clusters obtained using micropatterns. It relies only on two parameters that can be set robustly as they reduce to the average cell size and intensity.

Energy minimization in medical image analysis: Methodologies and applications

Energy minimization is of particular interest in medical image analysis. In the past two decades, a variety of optimization schemes have been developed. In this paper, we present a comprehensive survey of the state-of-the-art optimization approaches. These algorithms are mainly classified into two categories: continuous method and discrete method. The former includes Newton-Raphson method, gradient descent method, conjugate gradient method, proximal gradient method, coordinate descent method, and genetic algorithm-based method, while the latter covers graph cuts method, belief propagation method, tree-reweighted message passing method, linear programming method, maximum margin learning method, simulated annealing method, and iterated conditional modes method. We also discuss the minimal surface method, primal-dual method, and the multi-objective optimization method. In addition, we review several comparative studies that evaluate the performance of different minimization techniques in terms of accuracy, efficiency, or complexity. These optimization techniques are widely used in many medical applications, for example, image segmentation, registration, reconstruction, motion tracking, and compressed sensing. We thus give an overview on those applications as well.

Iterative mesh transformation for 3D segmentation of livers with cancers in CT images

Segmentation of diseased liver remains a challenging task in clinical applications due to the high inter-patient variability in liver shapes, sizes and pathologies caused by cancers or other liver diseases. In this paper, we present a multi-resolution mesh segmentation algorithm for 3D segmentation of livers, called iterative mesh transformation that deforms the mesh of a region-of-interest (ROI) in a progressive manner by iterations between mesh transformation and contour optimization. Mesh transformation deforms the 3D mesh based on the deformation transfer model that searches the optimal mesh based on the affine transformation subjected to a set of constraints of targeting vertices. Besides, contour optimization searches the optimal transversal contours of the ROI by applying the dynamic-programming algorithm to the intersection polylines of the 3D mesh on 2D transversal image planes. The initial constraint set for mesh transformation can be defined by a very small number of targeting vertices, namely landmarks, and progressively updated by adding the targeting vertices selected from the optimal transversal contours calculated in contour optimization. This iterative 3D mesh transformation constrained by 2D optimal transversal contours provides an efficient solution to a progressive approximation of the mesh of the targeting ROI. Based on this iterative mesh transformation algorithm, we developed a semi-automated scheme for segmentation of diseased livers with cancers using as little as five user-identified landmarks. The evaluation study demonstrates that this semi-automated liver segmentation scheme can achieve accurate and reliable segmentation results with significant reduction of interaction time and efforts when dealing with diseased liver cases.

A 3D active model framework for segmentation of proximal femur in MR images

PURPOSE

Segmentation of osseous structures from clinical MR images is difficult due to acquisition artifacts and variable signal intensity of bones. Segmentation of femoral head is required for evaluation of hip joint abnormalities such as cam- type femoroacetabular impingement. A parametric deformable model (PDM) framework was developed for segmentation of 3D magnetic resonance (MR) images of the hip.

METHOD

A two-phase segmentation scheme was implemented: (i) Radial basis function interpolation was performed for semi-automatic piecewise registration of a proximal femur atlas model to an MRI scan region of interest. User-defined control points on the mesh model were registered to the corresponding landmarks on the image. (ii) An active PDM was then used for coarse-to-fine level segmentation. The segmentation technique was tested using 3D synthetic image data and clinical MR scans of the hip with varying resolution.

RESULTS

The segmentation method provided a mean target overlap of 0.95 and misclassification error of 0.035 for the synthetic data. The average target overlap was 0.88, and misclassification error rate was 0.12 for the clinical MRI data sets.

CONCLUSION

A framework for segmentation of proximal femur in hip MRI scans was developed and tested. This method is robust to artifacts and intensity inhomogeneity and resistant to leakage into adjacent tissues. In comparison with slicewise segmentation techniques, this method features inter-slice consistency, which results in a smooth model of the proximal femur in hip MRI scans.

Detection and Reconstruction of an Implicit Boundary Surface by Adaptively Expanding A Small Surface Patch in a 3D Image

In this paper we propose a novel and easy to use 3D reconstruction method. With the method, users only need to specify a small boundary surface patch in a 2D section image, and then an entire continuous implicit boundary surface (CIBS) can be automatically reconstructed from a 3D image. In the method, a hierarchical tracing strategy is used to grow the known boundary surface patch gradually in the 3D image. An adaptive detection technique is applied to detect boundary surface patches from different local regions. The technique is based on both context dependence and adaptive contrast detection as in the human vision system. A recognition technique is used to distinguish true boundary surface patches from the false ones in different cubes. By integrating these different approaches, a high-resolution CIBS model can be automatically reconstructed by adaptively expanding the small boundary surface patch in the 3D image. The effectiveness of our method is demonstrated by its applications to a variety of real 3D images, where the CIBS with complex shapes/branches and with varying gray values/gradient magnitudes can be well reconstructed. Our method is easy to use, which provides a valuable tool for 3D image visualization and analysis as needed in many applications.

Fitting C² continuous parametric surfaces to frontiers delimiting physiologic structures

We present a technique to fit C(2) continuous parametric surfaces to scattered geometric data points forming frontiers delimiting physiologic structures in segmented images. Such mathematical representation is interesting because it facilitates a large number of operations in modeling. While the fitting of C(2) continuous parametric curves to scattered geometric data points is quite trivial, the fitting of C(2) continuous parametric surfaces is not. The difficulty comes from the fact that each scattered data point should be assigned a unique parametric coordinate, and the fit is quite sensitive to their distribution on the parametric plane. We present a new approach where a polygonal (quadrilateral or triangular) surface is extracted from the segmented image. This surface is subsequently projected onto a parametric plane in a manner to ensure a one-to-one mapping. The resulting polygonal mesh is then regularized for area and edge length. Finally, from this point, surface fitting is relatively trivial. The novelty of our approach lies in the regularization of the polygonal mesh. Process performance is assessed with the reconstruction of a geometric model of mouse heart ventricles from a computerized tomography scan. Our results show an excellent reproduction of the geometric data with surfaces that are C(2) continuous.

Automatic rectum limit detection by anatomical markers correlation

Several diseases take place at the end of the digestive system. Many of them can be diagnosed by means of different medical imaging modalities together with computer aided detection (CAD) systems. These CAD systems mainly focus on the complete segmentation of the digestive tube. However, the detection of limits between different sections could provide important information to these systems. In this paper we present an automatic method for detecting the rectum and sigmoid colon limit using a novel global curvature analysis over the centerline of the segmented digestive tube in different imaging modalities. The results are compared with the gold standard rectum upper limit through a validation scheme comprising two different anatomical markers: the third sacral vertebra and the average rectum length. Experimental results in both magnetic resonance imaging (MRI) and computed tomography colonography (CTC) acquisitions show the efficacy of the proposed strategy in automatic detection of rectum limits. The method is intended for application to the rectum segmentation in MRI for geometrical modeling and as contextual information source in virtual colonoscopies and CAD systems.

D-Snake: Image Registration by As-Similar-As-Possible Template Deformation

We describe a snake-type method for shape registration in 2D and 3D, by fitting a given polygonal template to an acquired image or volume data. The snake aspires to fit itself to the data in a shape which is locally As-Similar-As-Possible (ASAP) to the template. Our ASAP regulating force is based on the Moving Least Squares (MLS) similarity deformation. Combining this force with the traditional internal and external forces associated with a snake leads to a powerful and robust registration algorithm, capable of extracting precise shape information from image data.

Learning and Prediction of Complex Molecular Structure-Property Relationships

The problem of modeling and predicting complex structure-property relationships, such as the absorption, distribution, metabolism, and excretion of putative drug molecules is a fundamental one in contemporary drug discovery. An accurate model can not only be used to predict the behavior of a molecule and understand how structural variations may influence molecular property, but also to identify regions of molecular space that hold promise in context of a specific investigation. However, a variety of factors contribute to the difficulty of constructing robust structure activity models for such complex properties. These include conceptual issues related to how well the true bio-chemical property is accounted for by formulation of the specific learning strategy, algorithmic issues associated with determining the proper molecular descriptors, access to small quantities of data, possibly on tens of molecules only, due to the high cost and complexity of the experimental process, and the complex nature of bio-chemical phenomena underlying the data. This chapter attempts to address this problem from the rudiments: the authors first identify and discuss the salient computational issues that span (and complicate) structure-property modeling formulations and present a brief review of the state-of-the-art. The authors then consider a specific problem: that of modeling intestinal drug absorption, where many of the aforementioned factors play a role. In addressing them, their solution uses a novel characterization of molecular space based on the notion of surface-based molecular similarity. This is followed by identifying a statistically relevant set of molecular descriptors, which along with an appropriate machine learning technique, is used to build the structure-property model. The authors propose simultaneous use of both ratio and ordinal error-measures for model construction and validation. The applicability of the approach is demonstrated in a real world case study.

SEGMENTATION OF BREAST THERMOGRAM: IMPROVED BOUNDARY DETECTION WITH MODIFIED SNAKE ALGORITHM

Background: Breast cancer is a common and dreadful disease in women. One in five cancers in Singaporean women is due to breast cancer. Breast health is every woman's right and responsibility. In average, every $100 spent on breast mammogram screening, an additional $33 was spent on evaluating possible false-positive results. Thermography, with its non-radiation, non-contact and low-cost basis has been demonstrated to be a valuable and safe early risk marker of breast pathology, and an excellent case management tool available today in the ongoing monitoring and treatment of breast disease. The surface temperature and the vascularization pattern of the breast could indicate breast diseases and early detection saves lives. To establish the surface isotherm pattern of the breast and the normal range of cyclic variations of temperature distribution can assist in identifying the abnormal infrared images of diseased breasts. Before these thermograms can be analyzed objectively via computer algorithm, they must be digitized and segmented. The authors present a method to segment thermograms and extract useful region from the background. Thermography could detect the presence of tumors much earlier and of much smaller size than mammography. This paper thus aims to develop an intelligent diagnostic system based on thermography for the detection of tumors in breast. Methods: We have examined about 50 normal, healthy female volunteers in Nanyang Technological University and 130 patients in Singapore General Hospital. We did the examinations for some of them continuously for two months. From these examinations, we obtained about 1000 thermograms for contact and 800 thermograms for non-contact approaches. Standard ambient conditions were observed for all examinations. The thermograms obtained were analyzed. The first step in processing these thermograms is image segmentation. Its aim is to discern the useful region from the background. In general, autonomous segmentation is one of the most difficult tasks in image processing. This step in the process determines the eventual success or failure of the analysis. In this work, two different techniques have been presented to extract the objects from the background. Results: After analyzing these thermograms and with reference to some relevant well-documented papers, we were able to classify the thermograms. The step is very useful in identifying the normal or suspected (abnormal) thermograms. A series of thermograms was studied with the help of the in-house developed computer software. On the basis of the anatomic and vascular symmetry, the surface temperature distributions of both left and right breasts were compared. The surface isotherm pattern of breasts can indicate the local metabolism and vascularity of the underlying tissues, and the change in local blood or glandular activities can be reflected in the surface temperature of breast. We evaluated the temperature distribution pattern and the menstrual cyclic variation of temperature with time. All these results can be used to detect breast cancer. Conclusion: Automatic identification of object and surface boundary of breast thermal images is a difficult and challenging task. Both the traditional snake and gradient vector flow snake failed to detect the boundary of these images successfully. In this work, a new method is proposed in conjunction with image pre-processing, image transition, image derivative, filtering and gradient vector flow snake. This novel method can easily detect the boundary of the breast thermal image with good agreement.

Geometrically induced force interaction for three-dimensional deformable models

In this paper, we propose a novel 3-D deformable model that is based upon a geometrically induced external force field which can be conveniently generalized to arbitrary dimensions. This external force field is based upon hypothesized interactions between the relative geometries of the deformable model and the object boundary characterized by image gradient. The evolution of the deformable model is solved using the level set method so that topological changes are handled automatically. The relative geometrical configurations between the deformable model and the object boundaries contribute to a dynamic vector force field that changes accordingly as the deformable model evolves. The geometrically induced dynamic interaction force has been shown to greatly improve the deformable model performance in acquiring complex geometries and highly concave boundaries, and it gives the deformable model a high invariancy in initialization configurations. The voxel interactions across the whole image domain provide a global view of the object boundary representation, giving the external force a long attraction range. The bidirectionality of the external force field allows the new deformable model to deal with arbitrary cross-boundary initializations, and facilitates the handling of weak edges and broken boundaries. In addition, we show that by enhancing the geometrical interaction field with a nonlocal edge-preserving algorithm, the new deformable model can effectively overcome image noise. We provide a comparative study on the segmentation of various geometries with different topologies from both synthetic and real images, and show that the proposed method achieves significant improvements against existing image gradient techniques.

Quantitative characterization of preneoplastic progression using single-cell computed tomography and three-dimensional karyometry

The development of morphological biosignatures to precisely characterize preneoplastic progression necessitates high-resolution three-dimensional (3D) cell imagery and robust image processing algorithms. We report on the quantitative characterization of nuclear structure alterations associated with preneoplastic progression in human esophageal epithelial cells using single-cell optical tomography and fully automated 3D karyometry. We stained cultured cells with hematoxylin and generated 3D images of individual cells by mathematically reconstructing 500 projection images acquired using optical absorption tomographic imaging. For 3D karyometry, we developed novel, fully automated algorithms to robustly segment the cellular, nuclear, and subnuclear components in the acquired cell images, and computed 41 quantitative morphological descriptors from these segmented volumes. In addition, we developed algorithms to quantify the spatial distribution and texture of the nuclear DNA. We applied our methods to normal, metaplastic, and dysplastic human esophageal epithelial cell lines, analyzing 100 cells per line. The 3D karyometric descriptors elucidated quantitative differences in morphology and enabled robust discrimination between cell lines on the basis of extracted morphological features. The morphometric hallmarks of cancer progression such as increased nuclear size, elevated nuclear content, and anomalous chromatin texture and distribution correlated with this preneoplastic progression model, pointing to the clinical use of our method for early cancer detection.

A segmentation framework for abdominal organs from CT scans

OBJECTIVE

Computed tomography images are becoming an invaluable mean for abdominal organ investigation. In the field of medical image processing, some of the current interests are the automatic diagnosis of liver, spleen, and kidney pathologies, and the 3D volume rendering of these abdominal organs. Their automatic segmentation is the first and fundamental step in all these studies, but it is still an open problem.

METHODS

In this paper we propose a fully automatic, gray-level based segmentation framework based on a multiplanar fast marching method. The proposed segmentation scheme is general, and employs only established and not critical anatomical knowledge. For this reason, it can be easily adapted to segment different abdominal organs, by overcoming problems due to the high inter- and intra-patient gray-level, and shape variabilities; the extracted volumes are then combined to produce the final results.

RESULTS

The system has been evaluated by computing the symmetric volume overlap (SVO) between the automatically segmented (liver and spleen) volumes and the volumes manually traced by radiological experts. The test dataset is composed of 60 images, where 40 images belong to a private dataset, and 20 images to a public one. Liver segmentation has achieved an average SVO congruent with94, which is comparable to the mean intra- and inter-personal variation (96). Spleen segmentation achieves similar, promising results (SVO congruent with93). The comparison of these results with those achieved by active contour models (SVO congruent with90), and topology adaptive snakes (SVO congruent with92) proves the efficacy of our system.

CONCLUSIONS

The described segmentation method is a general framework that can be adapted to segment different abdominal organs, achieving promising segmentation results. It has to be noted that its performance could be further improved by incorporating shape based rules.

Topology-corrected segmentation and local intensity estimates for improved partial volume classification of brain cortex in MRI

In magnetic resonance imaging (MRI), accuracy and precision with which brain structures may be quantified are frequently affected by the partial volume (PV) effect. PV is due to the limited spatial resolution of MRI compared to the size of anatomical structures. Accurate classification of mixed voxels and correct estimation of the proportion of each pure tissue (fractional content) may help to increase the precision of cortical thickness estimation in regions where this measure is particularly difficult, such as deep sulci. The contribution of this work is twofold: on the one hand, we propose a new method to label voxels and compute tissue fractional content, integrating a mechanism for detecting sulci with topology preserving operators. On the other hand, we improve the computation of the fractional content of mixed voxels using local estimation of pure tissue intensity means. Accuracy and precision were assessed using simulated and real MR data and comparison with other existing approaches demonstrated the benefits of our method. Significant improvements in gray matter (GM) classification and cortical thickness estimation were brought by the topology correction. The fractional content root mean squared error diminished by 6.3% (p<0.01) on simulated data. The reproducibility error decreased by 8.8% (p<0.001) and the Jaccard similarity measure increased by 3.5% on real data. Furthermore, compared with manually guided expert segmentations, the similarity measure was improved by 12.0% (p<0.001). Thickness estimation with the proposed method showed a higher reproducibility compared with the measure performed after partial volume classification using other methods.

Coronary artery segmentation using geometric moments based tracking and snake-driven refinement

Automatic or semi-automatic segmentation and tracking of artery trees from computed tomography angiography (CTA) is an important step to improve the diagnosis and treatment of artery diseases, but it still remains a significant challenging problem. In this paper, we present an artery extraction method to address the challenge. The proposed method consists of two steps: (1) a geometric moments based tracking to secure a rough centerline, and (2) a fully automatic generalized cylinder structure-based snake method to refine the centerlines and estimate the radii of the arteries. In this method, a new line direction based on first and second order geometric moments is adopted while both gradient and intensity information are used in the snake model to improve the accuracy. The approach has been evaluated on synthetic images as well as 8 clinical coronary CTA images with 32 coronary arteries. Our method achieves 94.7% overlap tracking ability within an average distance inside the vessel of 0.36 mm.

Algorithm-based method for detection of blood vessels in breast MRI for development of computer-aided diagnosis

PURPOSE

To develop a computer-based algorithm for detecting blood vessels that appear in breast dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI), and to evaluate the improvement in reducing the number of vascular pixels that are labeled by computer-aided diagnosis (CAD) systems as being suspicious of malignancy.

MATERIALS AND METHODS

The analysis was performed in 34 cases. The algorithm applied a filter bank based on wavelet transform and the Hessian matrix to detect linear structures as blood vessels on a two-dimensional maximum intensity projection (MIP). The vessels running perpendicular to the MIP plane were then detected based on the connectivity of enhanced pixels above a threshold. The nonvessel enhancements were determined and excluded based on their morphological properties, including those showing scattered small segment enhancements or nodular or planar clusters. The detected vessels were first converted to a vasculature skeleton by thinning and subsequently compared to the vascular track manually drawn by a radiologist.

RESULTS

When evaluating the performance of the algorithm in identifying vascular tissue, the correct-detection rate refers to pixels identified by both the algorithm and radiologist, while the incorrect-detection rate refers to pixels identified by only the algorithm, and the missed-detection rate refers to pixels identified only by the radiologist. From 34 analyzed cases the median correct-detection rate was 85.6% (mean 84.9% +/- 7.8%), the incorrect-detection rate was 13.1% (mean 15.1% +/- 7.8%), and the missed-detection rate was 19.2% (mean 21.3% +/- 12.8%). When detected vessels were excluded in the hot-spot color-coding of the CAD system, they could reduce the labeling of vascular vessels in 2.6%-68.6% of hot-spot pixels (mean 16.6% +/- 15.9%).

CONCLUSION

The computer algorithm-based method can detect most large vessels and provide an effective means in reducing the labeling of vascular pixels as suspicious on a DCE-MRI CAD system. This algorithm may improve the workflow of radiologists using CAD for image display, but will be particularly useful for development of automated CAD that gives diagnostic impression.

An automatic integrated approach for stained neuron detection in studying neuron migration

Neurons that come to populate the six-layered cerebral cortex are born deep within the developing brain in the surface of the embryonic cerebral ventricles. It is very important to detect these neurons for studying histogenesis of the brain and abnormal migration that had been linked to cognitive deficits, mental retardation, and motor disorders. The visualization of labeled cells in brain sections was performed by immunocytochemical examination and its image data were documented to microscopic pictures. Based on the fact, automatic accurate neurons labeling is prerequisite instead of time-consuming manual labeling. In this article, a fully automated image processing approach is proposed to detect all the stained neurons in microscopic images. First of all, dark stained neurons are achieved by thresholding in blue channel of image. And then a modified fuzzy c-means clustering method, called alternative fuzzy c-means is applied to achieve higher classification accuracy in extracting constraint factor. Finally, watershed based on gradient vector flow is employed to the constraint factor image to segment all the neurons, including clustered neurons. The results demonstrate that the proposed method can be a useful tool in neuron image analysis.

A combined region growing and deformable model method for extraction of closed surfaces in 3D CT and MRI scans

Image segmentation of 3D medical images is a challenging problem with several still not totally solved practical issues, such as noise interference, variable object structures and image artifacts. This paper describes a hybrid 3D image segmentation method which combines region growing and deformable models to obtain accurate and topologically preserving surface structures of anatomical objects of interest. The proposed strategy starts by determining a rough but robust approximation of the objects using a region-growing algorithm. Then, the closed surface mesh that encloses the region is constructed and used as the initial geometry of a deformable model for the final refinement. This integrated strategy provides an alternative solution to one of the flaws of traditional deformable models, achieving good refinements of internal surfaces in few steps. Experimental segmentation results of complex anatomical structures on both simulated and real data from MRI scans are presented, and the method is assessed by comparing with standard reference segmentations of head MRI. The evaluation was mainly based on the average overlap measure, which was tested on the segmentation of white matter, corresponding to a simulated brain data set, showing excellent performance exceeding 90% accuracy. In addition, the algorithm was applied to the detection of anatomical head structures on two real MRI and one CT data set. The final reconstructions resulting from the deformable models produce high quality meshes suitable for 3D visualization and further numerical analysis. The obtained results show that the approach achieves high quality segmentations with low computational complexity.

Training models of anatomic shape variability

Learning probability distributions of the shape of anatomic structures requires fitting shape representations to human expert segmentations from training sets of medical images. The quality of statistical segmentation and registration methods is directly related to the quality of this initial shape fitting, yet the subject is largely overlooked or described in an ad hoc way. This article presents a set of general principles to guide such training. Our novel method is to jointly estimate both the best geometric model for any given image and the shape distribution for the entire population of training images by iteratively relaxing purely geometric constraints in favor of the converging shape probabilities as the fitted objects converge to their target segmentations. The geometric constraints are carefully crafted both to obtain legal, nonself-interpenetrating shapes and to impose the model-to-model correspondences required for useful statistical analysis. The paper closes with example applications of the method to synthetic and real patient CT image sets, including same patient male pelvis and head and neck images, and cross patient kidney and brain images. Finally, we outline how this shape training serves as the basis for our approach to IGRT/ART.

Computer aided evaluation of ankylosing spondylitis using high-resolution CT

Ankylosing Spondylitis is a disease characterized by abnormal bone structures (syndesmophytes) growing at intervertebral disk spaces. Because this growth is so slow as to be undetectable on plain radiographs taken over years, it is desirable to resort to computerized techniques to complement qualitative human judgment with precise quantitative measures. We developed an algorithm with minimal user intervention that provides such measures using high-resolution computed tomography (CT) images. To the best of our knowledge it is the first time that determination of the disease's status is attempted by direct measurement of the syndesmophytes. The first part of our algorithm segments the whole vertebral body using a 3-D multiscale cascade of successive level sets. The second part extracts the continuous ridgeline of the vertebral body where syndesmophytes are located. For that we designed a novel level set implementation capable of evolving on the isosurface of an object represented by a triangular mesh using curvature features. The third part of the algorithm segments the syndesmophytes from the vertebral body using local cutting planes and quantitates them. We present experimental work done with 10 patients from each of which we processed five vertebrae. The results of our algorithm were validated by comparison with a semi-quantitative evaluation made by a medical expert who visually inspected the CT scans. Correlation between the two evaluations was found to be 0.936 ( p < 10(-18)) .

Automatic active model initialization via Poisson inverse gradient

Active models have been widely used in image processing applications. A crucial stage that affects the ultimate active model performance is initialization. This paper proposes a novel automatic initialization approach for parametric active models in both 2-D and 3-D. The PIG initialization method exploits a novel technique that essentially estimates the external energy field from the external force field and determines the most likely initial segmentation. Examples and comparisons with two state-of-the- art automatic initialization methods are presented to illustrate the advantages of this innovation, including the ability to choose the number of active models deployed, rapid convergence, accommodation of broken edges, superior noise robustness, and segmentation accuracy.

Self-repelling snakes for topology-preserving segmentation models

The implicit framework of the level-set method has several advantages when tracking propagating fronts. Indeed, the evolving contour is embedded in a higher dimensional level-set function and its evolution can be phrased in terms of a Eulerian formulation. The ability of this intrinsic method to handle topological changes (merging and breaking) makes it useful in a wide range of applications (fluid mechanics, computer vision) and particularly in image segmentation, the main subject of this paper. Nevertheless, in some applications, this topological flexibility turns out to be undesirable: for instance, when the shape to be detected has a known topology, or when the resulting shape must be homeomorphic to the initial one. The necessity of designing topology-preserving processes arises in medical imaging, for example, in the human cortex reconstruction. It is known that the human cortex has a spherical topology so throughout the reconstruction process this topological feature must be preserved. Therefore, we propose in this paper a segmentation model based on an implicit level-set formulation and on the geodesic active contours, in which a topological constraint is enforced.

Multiscale vascular surface model generation from medical imaging data using hierarchical features

Computational fluid dynamics (CFD) modeling of blood flow from image-based patient specific models can provide useful physiologic information for guiding clinical decision making. A novel method for the generation of image-based, 3-D, multiscale vascular surface models for CFD is presented. The method generates multiscale surfaces based on either a linear triangulated or a globally smooth nonuniform rational B-spline (NURB) representation. A robust local curvature analysis is combined with a novel global feature analysis to set mesh element size. The method is particularly useful for CFD modeling of complex vascular geometries that have a wide range of vasculature size scales, in conditions where 1) initial surface mesh density is an important consideration for balancing surface accuracy with manageable size volumetric meshes, 2) adaptive mesh refinement based on flow features makes an underlying explicit smooth surface representation desirable, and 3) semi-automated detection and trimming of a large number of inlet and outlet vessels expedites model construction.

A computational framework for approximating boundary surfaces in 3-D biomedical images

We propose a new method for detecting and approximating the boundary surfaces in three-dimensional (3-D) biomedical images. Using this method, each boundary surface in the original 3-D image is normalized as a zero-value isosurface of a new 3-D image transformed from the original 3-D image. A novel computational framework is proposed to perform such an image transformation. According to this framework, we first detect boundary surfaces from the original 3-D image and compute discrete samplings of the boundary surfaces. Based on these discrete samplings, a new 3-D image is constructed for each boundary surface such that the boundary surface can be well approximated by a zero-value isosurface in the new 3-D image. In this way, the complex problem of reconstructing boundary surfaces in the original 3-D image is converted into a task to extract a zero-value isosurface from the new 3-D image. The proposed technique is not only capable of adequately reconstructing complex boundary surfaces in 3-D biomedical images, but it also overcomes vital limitations encountered by the isosurface-extracting method when the method is used to reconstruct boundary surfaces from 3-D images. The performances and advantages of the proposed computational framework are illustrated by many examples from different 3-D biomedical images.

Weighted local variance-based edge detection and its application to vascular segmentation in magnetic resonance angiography

Accurate detection of vessel boundaries is particularly important for a precise extraction of vasculatures in magnetic resonance angiography (MRA). In this paper, we propose the use of weighted local variance (WLV)-based edge detection scheme for vessel boundary detection in MRA. The proposed method is robust against changes of intensity contrast of edges and capable of giving high detection responses on low contrast edges. These robustness and capabilities are essential for detecting the boundaries of vessels in low contrast regions of images, which can contain intensity inhomogeneity, such as bias field, interferences induced from other tissues, or fluctuation of the speed related vessel intensity. The performance of the WLV-based edge detection scheme is studied and shown to be able to return strong and consistent detection responses on low contrast edges in the experiments. The proposed edge detection scheme can be embedded naturally in the active contour models for vascular segmentation. The WLV-based vascular segmentation method is tested using MRA image volumes. It is experimentally shown that the WLV-based edge detection approach can achieve high-quality segmentation of vasculatures in MRA images.

Active contour external force using vector field convolution for image segmentation

Snakes, or active contours, have been widely used in image processing applications. Typical roadblocks to consistent performance include limited capture range, noise sensitivity, and poor convergence to concavities. This paper proposes a new external force for active contours, called vector field convolution (VFC), to address these problems. VFC is calculated by convolving the edge map generated from the image with the user-defined vector field kernel. We propose two structures for the magnitude function of the vector field kernel, and we provide an analytical method to estimate the parameter of the magnitude function. Mixed VFC is introduced to alleviate the possible leakage problem caused by choosing inappropriate parameters. We also demonstrate that the standard external force and the gradient vector flow (GVF) external force are special cases of VFC in certain scenarios. Examples and comparisons with GVF are presented in this paper to show the advantages of this innovation, including superior noise robustness, reduced computational cost, and the flexibility of tailoring the force field.

Application of a new segmentation tool based on interactive simplex meshes to cardiac images and pulmonary MRI data

RATIONALE AND OBJECTIVES

Medical image segmentation is still very time consuming and is therefore seldom integrated into clinical routine. Various three-dimensional (3D) segmentation approaches could facilitate the work, but they are rarely used in clinical setups because of complex initialization and parametrization of such models.

MATERIALS AND METHODS

We developed a new semiautomatic 3D-segmentation tool based on deformable simplex meshes. The user can define attracting points in the original image data. The new deformation algorithm guarantees that the surface model will pass through these interactively set points. The user can directly influence the evolution of the deformable model and gets direct feedback during the segmentation process.

RESULTS

The segmentation tool was evaluated for cardiac image data and magnetic resonance imaging lung images. Comparison with manual segmentation showed high accuracy. Time needed for delineation of the various structures could be reduced in some cases. The model was not sensitive to noise in the input data and model initialization.

CONCLUSIONS

The tool is suitable for fast interactive segmentation of any kind of 3D or 3D time-resolved medical image data. It enables the clinician to influence a complex 3D-segmentation algorithm and makes this algorithm controllable. The better the quality of the data, the less interaction is required. The tool still works when the processed images have low quality.

Coronary vessel trees from 3D imagery: a topological approach

We propose a simple method for reconstructing vascular trees from 3D images. Our algorithm extracts persistent maxima of the intensity on all axis-aligned 2D slices of the input image. The maxima concentrate along 1D intensity ridges, in particular along blood vessels. We build a forest connecting the persistent maxima with short edges. The forest tends to approximate the blood vessels present in the image, but also contains numerous spurious features and often fails to connect segments belonging to one vessel in low contrast areas. We improve the forest by applying simple geometric filters that trim short branches, fill gaps in blood vessels and remove spurious branches from the vascular tree to be extracted. Experiments show that our technique can be applied to extract coronary trees from heart CT scans.

Augmented vessels for quantitative analysis of vascular abnormalities and endovascular treatment planning

Endovascular treatment plays an important role in the minimally invasive treatment of patients with vascular diseases, a major cause of morbidity and mortality worldwide. Given a segmentation of an angiography, quantitative analysis of abnormal structures can aid radiologists in choosing appropriate treatments and apparatuses. However, effective quantitation is only attainable if the abnormalities are identified from the vasculature. To achieve this, a novel method is developed, which works on the simpler shape of normal vessels to identify different vascular abnormalities (viz. stenotic atherosclerotic plaque, and saccular and fusiform aneurysmal lumens) in an indirect fashion, instead of directly manipulating the complex-shaped abnormalities. The proposed method has been tested on three synthetic and 17 clinical data sets. Comparisons with two related works are also conducted. Experimental results show that our method can produce satisfactory identification of the abnormalities and approximations of the ideal post-treatment vessel lumens. In addition, it can help increase the repeatability of the measurement of clinical parameters significantly.

Segmentation of thin structures in volumetric medical images

We present a new segmentation method for extracting thin structures embedded in three-dimensional medical images based on modern variational principles. We demonstrate the importance of the edge alignment and homogeneity terms in the segmentation of blood vessels and vascular trees. For that goal, the Chan-Vese minimal variance method is combined with the boundary alignment, and the geodesic active surface models. An efficient numerical scheme is proposed. In order to simultaneously detect a number of different objects in the image, a hierarchal approach is applied.

A Multiresolution PDE-Based Deformable Surface for Medical Imaging Applications

We recently developed a multiresolution PDE-based deformable surface whose deformation behavior is governed by partial differential equations (PDEs) such as the weighted minimal surface flow. Comparing with the level-set approach, our new model has better control of the mesh quality and model resolution, and is much simpler to implement since all the computations are local. The new deformable model is very useful for a variety of medical imaging applications including boundary reconstruction, surface visualization, data segmentation, and topology discovery. In this paper, we demonstrate both the accuracy and robustness of our model on areas such as medical image segmentation through a number of experiments on both real (MRI/CT) and synthetic volumetric datasets.

Brain Structure Segmentation from MRI by Geometric Surface Flow

We present a method for semiautomatic segmentation of brain structures such as thalamus from MRI images based on the concept of geometric surface flow. Given an MRI image, the user can interactively initialize a seed model within region of interest. The model will then start to evolve by incorporating both boundary and region information following the principle of variational analysis. The deformation will stop when an equilibrium state is achieved. To overcome the low contrast of the original image data, a nonparametric kernel-based method is applied to simultaneously update the interior probability distribution during the model evolution. Our experiments on both 2D and 3D image data demonstrate that the new method is robust to image noise and inhomogeneity and will not leak from spurious edge gaps.

Bayesian image segmentation using local iso-intensity structural orientation

Image segmentation is a fundamental problem in early computer vision. In segmentation of flat shaded, nontextured objects in real-world images, objects are usually assumed to be piecewise homogeneous. This assumption, however, is not always valid with images such as medical images. As a result, any techniques based on this assumption may produce less-than-satisfactory image segmentation. In this work, we relax the piecewise homogeneous assumption. By assuming that the intensity nonuniformity is smooth in the imaged objects, a novel algorithm that exploits the coherence in the intensity profile to segment objects is proposed. The algorithm uses a novel smoothness prior to improve the quality of image segmentation. The formulation of the prior is based on the coherence of the local structural orientation in the image. The segmentation process is performed in a Bayesian framework. Local structural orientation estimation is obtained with an orientation tensor. Comparisons between the conventional Hessian matrix and the orientation tensor have been conducted. The experimental results on the synthetic images and the real-world images have indicated that our novel segmentation algorithm produces better segmentations than both the global thresholding with the maximum likelihood estimation and the algorithm with the multilevel logistic MRF model.

CPM: a deformable model for shape recovery and segmentation based on charged particles

A novel, physically motivated deformable model for shape recovery and segmentation is presented. The model, referred to as the charged-particle model (CPM), is inspired by classical electrodynamics and is based on a simulation of charged particles moving in an electrostatic field. The charges are attracted towards the contours of the objects of interest by an electrostatic field, whose sources are computed based on the gradient-magnitude image. The electric field plays the same role as the potential forces in the snake model, while internal interactions are modeled by repulsive Coulomb forces. We demonstrate the flexibility and potential of the model in a wide variety of settings: shape recovery using manual initialization, automatic segmentation, and skeleton computation. We perform a comparative analysis of the proposed model with the active contour model and show that specific problems of the latter are surmounted by our model. The model is easily extendable to 3D and copes well with noisy images.