Improved interactive medical image segmentation using Enhanced Intelligent Scissors (EIS)

Efficient Johnson-SB Mixture Model for Segmentation of CT Liver Image

To overcome the problem that the traditional Gaussian mixture model (GMM) cannot well describe the skewness distribution of the gray-level histogram of a liver CT slice, we propose a novel segmentation method for liver CT images by introducing the Johnson-SB mixture model (J_SBMM). The Johnson-SB model not only has a flexible asymmetrical distribution but also covers a variety of other distributions as well. In this article, the parameter optimization formulas for J_SBMM were derived by employing the expectation-maximization (EM) algorithm and maximum likelihood. The implementation process of the J_SBMM-based segmentation algorithm is provided in detail. To make better use of the skewness of Johnson-SB and improve the segmentation accuracy, we devise an idea to divide the histogram into two parts and calculate the segmentation threshold for each part, respectively, which is called J_SBMM-TDH. By analyzing and comparing the segmentation thresholds with different cluster numbers, it is illustrated that the segmentation threshold of J_SBMM-TDH will tend to be stable with the increasing of cluster number, while that of GMM is sensitive to different cluster numbers. The proposed J_SBMM-TDH is applied to segment four randomly obtained abdominal CT image sequences, and the segmentation results and robustness have been compared between J_SBMM-TDH and GMM. It is verified that J_SBMM-TDH has preferable segmentation results and better robustness than GMM for the segmentation of liver CT images.

The CellBorderTracker, a novel tool to quantitatively analyze spatiotemporal endothelial junction dynamics at the subcellular level

Endothelial junctions are dynamic structures organized by multi-protein complexes that control monolayer integrity, homeostasis, inflammation, cell migration and angiogenesis. Newly developed methods for both the genetic manipulation of endothelium and microscopy permit time-lapse recordings of fluorescent proteins over long periods of time. Quantitative data analyses require automated methods. We developed a software package, the CellBorderTracker, allowing quantitative analysis of fluorescent-tagged cell junction protein dynamics in time-lapse sequences. The CellBorderTracker consists of the CellBorderExtractor that segments cells and identifies cell boundaries and mapping tools for data extraction. The tool is illustrated by analyzing fluorescent-tagged VE-cadherin the backbone of adherence junctions in endothelium. VE-cadherin displays high dynamics that is forced by junction-associated intermittent lamellipodia (JAIL) that are actin driven and WASP/ARP2/3 complex controlled. The manual segmentation and the automatic one agree to 90 %, a value that indicates high reliability. Based on segmentations, different maps were generated allowing more detailed data extraction. This includes the quantification of protein distribution pattern, the generation of regions of interest, junction displacements, cell shape changes, migration velocities and the visualization of junction dynamics over many hours. Furthermore, we demonstrate an advanced kymograph, the J-kymograph that steadily follows irregular cell junction dynamics in time-lapse sequences for individual junctions at the subcellular level. By using the CellBorderTracker, we demonstrate that VE-cadherin dynamics is quickly arrested upon thrombin stimulation, a phenomenon that was largely due to transient inhibition of JAIL and display a very heterogeneous subcellular and divers VE-cadherin dynamics during intercellular gap formation and resealing.

A technique for semiautomatic segmentation of echogenic structures in 3D ultrasound, applied to infant hip dysplasia

PURPOSE

Automatic segmentation of anatomical structures and lesions from medical ultrasound images is a formidable challenge in medical imaging due to image noise, blur and artifacts. In this paper we present a segmentation technique with features highly suited to use in noisy 3D ultrasound volumes and demonstrate its use in modeling bone, specifically the acetabulum in infant hips. Quantification of the acetabular shape is crucial in diagnosing developmental dysplasia of the hip (DDH), a common condition associated with hip dislocation and premature osteoarthritis if not treated. The well-established Graf technique for DDH diagnosis has been criticized for high inter-observer and inter-scan variability. In our earlier work we have introduced a more reliable instability metric based on 3D ultrasound data. Visualizing and interpreting the acetabular shape from noisy 3D ultrasound volumes has been one of the major roadblocks in using 3D ultrasound as diagnostic tool for DDH. For this study we developed a semiautomated segmentation technique to rapidly generate 3D acetabular surface models and classified the acetabulum based on acetabular contact angle (ACA) derived from the models. We tested the feasibility and reliability of the technique compared with manual segmentation.

METHODS

The proposed segmentation algorithm is based on graph search. We formulate segmentation of the acetabulum as an optimal path finding problem on an undirected weighted graph. Slice contours are defined as the optimal path passing through a set of user-defined seed points in the graph, and it can be found using dynamic programming techniques (in this case Dijkstra's algorithm). Slice contours are then interpolated over the 3D volume to generate the surface model. A three-dimensional ACA was calculated using normal vectors of the surface model.

RESULTS

The algorithm was tested over an extensive dataset of 51 infant ultrasound hip volumes obtained from 42 subjects with normal to dysplastic hips. The contours generated by the segmentation algorithm closely matched with those obtained from manual segmentation. The average RMS errors between the semiautomated and manual segmentation for the 51 volumes were 0.28 mm/1.1 voxel (with 2 node points) and 0.24 mm/0.9 voxel (with 3 node points). The semiautomatic algorithm gave visually acceptable results on images with moderate levels of noise and was able to trace the boundary of the acetabulum even in the presence of significant shadowing. Semiautomatic contouring was also faster than manual segmentation at 37 versus 56 s per scan. It also improved the repeatability of the ACA calculation with inter-observer and intra-observer variability of 1.4 ± 0.9 degree and 1.4 ± 1.0 degree.

CONCLUSION

The semiautomatic segmentation technique proposed in this work offers a fast and reliable method to delineate the contours of the acetabulum from 3D ultrasound volumes of the hip. Since the technique does not rely upon contour evolution, it is less susceptible than other methods to the frequent missing or incomplete boundaries and noise artifacts common in ultrasound images. ACA derived from the segmented 3D surface was able to accurately classify the acetabulum under the categories normal, borderline and dysplastic. The semiautomatic technique makes it easier to segment the volume and reduces the inter-observer and intra-observer variation in ACA calculation compared with manual segmentation. The method can be applied to any structure with an echogenic boundary on ultrasound (such as a ventricle, blood vessel, organ or tumor), or even to structures with a bright border on computed tomography or magnetic resonance imaging.

Homotopic non-local regularized reconstruction from sparse positron emission tomography measurements

Background

Positron emission tomography scanners collect measurements of a patient’s in vivo radiotracer distribution. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule, and the tomograms must be reconstructed from projections. The reconstruction of tomograms from the acquired PET data is an inverse problem that requires regularization. The use of tightly packed discrete detector rings, although improves signal-to-noise ratio, are often associated with high costs of positron emission tomography systems. Thus a sparse reconstruction, which would be capable of overcoming the noise effect while allowing for a reduced number of detectors, would have a great deal to offer.

Methods

In this study, we introduce and investigate the potential of a homotopic non-local regularization reconstruction framework for effectively reconstructing positron emission tomograms from such sparse measurements.

Results

Results obtained using the proposed approach are compared with traditional filtered back-projection as well as expectation maximization reconstruction with total variation regularization.

Conclusions

A new reconstruction method was developed for the purpose of improving the quality of positron emission tomography reconstruction from sparse measurements. We illustrate that promising reconstruction performance can be achieved for the proposed approach even at low sampling fractions, which allows for the use of significantly fewer detectors and have the potential to reduce scanner costs.

Semi-automatic Fisher-Tippett guided active contour for lumbar multifidus muscle segmentation

Rehabilitative Ultrasound Imaging or diagnostic ultrasound is used to measure geometric properties of the lumbar multifidus muscle to infer muscle strength or degeneration for back pain therapy. For this purpose, a novel semi-automatic approach (FTS: Fisher-Tippett Segmentation) based upon the Decoupled Active Contour is proposed to reliably and quickly segment the lumbar multifidus muscle in diagnostic ultrasound. To overcome speckle or hardly visible region boundaries in ultrasound images, we first propose a novel external energy functional to explicitly consider the underlying Fisher-Tippett distribution of ultrasound data. We then introduce a user-guided Hidden Markov Model trellis formation for improved segmentation of weakly-defined regions. Extensive experiments have shown that our approach not only improves the segmentation performance when compared to existing methods, but also does not rely on sub-specialized knowledge for segmentation.

Semi-automatic segmentation of brain tumors using population and individual information

Efficient segmentation of tumors in medical images is of great practical importance in early diagnosis and radiation plan. This paper proposes a novel semi-automatic segmentation method based on population and individual statistical information to segment brain tumors in magnetic resonance (MR) images. First, high-dimensional image features are extracted. Neighborhood components analysis is proposed to learn two optimal distance metrics, which contain population and patient-specific information, respectively. The probability of each pixel belonging to the foreground (tumor) and the background is estimated by the k-nearest neighborhood classifier under the learned optimal distance metrics. A cost function for segmentation is constructed through these probabilities and is optimized using graph cuts. Finally, some morphological operations are performed to improve the achieved segmentation results. Our dataset consists of 137 brain MR images, including 68 for training and 69 for testing. The proposed method overcomes segmentation difficulties caused by the uneven gray level distribution of the tumors and even can get satisfactory results if the tumors have fuzzy edges. Experimental results demonstrate that the proposed method is robust to brain tumor segmentation.

Enhanced Decoupled Active Contour Using Structural and Textural Variation Energy Functionals

Active contours are a popular approach for object segmentation that uses an energy minimizing spline to extract an object's boundary. Nonparametric approaches can be computationally complex, whereas parametric approaches can be impacted by parameter sensitivity. A decoupled active contour (DAC) overcomes these problems by decoupling the external and internal energies and optimizing them separately. However a drawback of this approach is its reliance on the edge gradient as the external energy. This can lead to poor convergence toward the object boundary in the presence of weak object and strong background edges. To overcome these issues with convergence, a novel approach is proposed that takes advantage of a sparse texture model, which explicitly considers texture for boundary detection. The approach then defines the external energy as a weighted combination of textural and structural variation maps and feeds it into a multifunctional hidden Markov model for more robust object boundary detection. The enhanced DAC (EDAC) is qualitatively and visually analyzed on two natural image data sets as well as Brodatz images. The results demonstrate that EDAC effectively combines texture and structural information to extract the object boundary without impact on computation time and a reliance on color.

ACTIVE LEARNING GUIDED INTERACTIONS FOR CONSISTENT IMAGE SEGMENTATION WITH REDUCED USER INTERACTIONS

Interactive techniques leverage the expert knowledge of users to produce accurate image segmentations. However, the segmentation accuracy varies with the users. Additionally, users may also require training with the algorithm and its exposed parameters to obtain the best segmentation with minimal effort. Our work combines active learning with interactive segmentation and (i) achieves as good accuracy compared to a fully user guided segmentation but with significantly lower number of user interactions (on average 50%), and (ii) achieves robust segmentation by reducing segmantation variability with user inputs. Our approach interacts with user to suggest gestures or seed point placements. We present extensive experimental evaluation of our results on two different publicly available datasets.

Decoupled active contour (DAC) for boundary detection

The accurate detection of object boundaries via active contours is an ongoing research topic in computer vision. Most active contours converge toward some desired contour by minimizing a sum of internal (prior) and external (image measurement) energy terms. Such an approach is elegant, but suffers from a slow convergence rate and frequently misconverges in the presence of noise or complex contours. To address these limitations, a decoupled active contour (DAC) is developed which applies the two energy terms separately. Essentially, the DAC consists of a measurement update step, employing a Hidden Markov Model (HMM) and Viterbi search, and then a separate prior step, which modifies the updated curve based on the relative strengths of the measurement uncertainty and the nonstationary prior. By separating the measurement and prior steps, the algorithm is less likely to misconverge; furthermore, the use of a Viterbi optimizer allows the method to converge far more rapidly than energy-based iterative solvers. The results clearly demonstrate that the proposed approach is robust to noise, can capture regions of very high curvature, and exhibits limited dependence on contour initialization or parameter settings. Compared to five other published methods and across many image sets, the DAC is found to be faster with better or comparable segmentation accuracy.