Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. Conclusions: By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. There is a pressing need for visualization and analysis tools for 5-D live cell image data. We combine accurate unsupervised processes with an intuitive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Level-Set Based Artery-Vein Separation in Blood Pool Agent CE-MR Angiograms

Blood pool agents (BPAs) for contrast-enhanced (CE) magnetic-resonance angiography (MRA) allow prolonged imaging times for higher contrast and resolution. Imaging is performed during the steady state when the contrast agent is distributed through the complete vascular system. However, simultaneous venous and arterial enhancement in this steady state hampers interpretation. In order to improve visualization of the arteries and veins from steady-state BPA data, a semiautomated method for artery-vein separation is presented. In this method, the central arterial axis and central venous axis are used as initializations for two surfaces that simultaneously evolve in order to capture the arterial and venous parts of the vasculature using the level-set framework. Since arteries and veins can be in close proximity of each other, leakage from the evolving arterial (venous) surface into the venous (arterial) part of the vasculature is inevitable. In these situations, voxels are labeled arterial or venous based on the arrival time of the respective surface. The evolution is steered by external forces related to feature images derived from the image data and by internal forces related to the geometry of the level sets. In this paper, the robustness and accuracy of three external forces (based on image intensity, image gradient, and vessel-enhancement filtering) and combinations of them are investigated and tested on seven patient datasets. To this end, results with the level-set-based segmentation are compared to the reference-standard manually obtained segmentations. Best results are achieved by applying a combination of intensity- and gradient-based forces and a smoothness constraint based on the curvature of the surface. By applying this combination to the seven datasets, it is shown that, with minimal user interaction, artery-vein separation for improved arterial and venous visualization in BPA CE-MRA can be achieved

Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

Unsupervised Multi Class Segmentation of 3D Images with Intensity Inhomogeneities

Intensity inhomogeneities in images constitute a considerable challenge in image segmentation. In this paper we propose a novel biconvex variational model to tackle this task. We combine a total variation approach for multi class segmentation with a multiplicative model to handle the inhomogeneities. Our method assumes that the image intensity is the product of a smoothly varying part and a component which resembles important image structures such as edges. Therefore, we penalize in addition to the total variation of the label assignment matrix a quadratic difference term to cope with the smoothly varying factor. A critical point of our biconvex functional is computed by a modified proximal alternating linearized minimization method (PALM). We show that the assumptions for the convergence of the algorithm are fulfilled by our model. Various numerical examples demonstrate the very good performance of our method. Particular attention is paid to the segmentation of 3D FIB tomographical images which was indeed the motivation of our work

Shape-driven segmentation of the arterial wall in intravascular ultrasound images

Segmentation of arterial wall boundaries from intravascular images is an important problem for many applications in the study of plaque characteristics, mechanical properties of the arterial wall, its 3D reconstruction, and its measurements such as lumen size, lumen radius, and wall radius. We present a shape-driven approach to segmentation of the arterial wall from intravascular ultrasound images in the rectangular domain. In a properly built shape space using training data, we constrain the lumen and media-adventitia contours to a smooth, closed geometry, which increases the segmentation quality without any tradeoff with a regularizer term. In addition to a shape prior, we utilize an intensity prior through a non-parametric probability density based image energy, with global image measurements rather than pointwise measurements used in previous methods. Furthermore, a detection step is included to address the challenges introduced to the segmentation process by side branches and calcifications. All these features greatly enhance our segmentation method. The tests of our algorithm on a large dataset demonstrate the effectiveness of our approach

Retinal vessel segmentation:An efficient graph cut approach with Retinex and local phase

Our application concerns the automated detection of vessels in retinal images to improve understanding of the disease mechanism, diagnosis and treatment of retinal and a number of systemic diseases. We propose a new framework for segmenting retinal vasculatures with much improved accuracy and efficiency. The proposed framework consists of three technical components: Retinex-based image inhomogeneity correction, local phase-based vessel enhancement and graph cut-based active contour segmentation. These procedures are applied in the following order. Underpinned by the Retinex theory, the inhomogeneity correction step aims to address challenges presented by the image intensity inhomogeneities, and the relatively low contrast of thin vessels compared to the background. The local phase enhancement technique is employed to enhance vessels for its superiority in preserving the vessel edges. The graph cut-based active contour method is used for its efficiency and effectiveness in segmenting the vessels from the enhanced images using the local phase filter. We have demonstrated its performance by applying it to four public retinal image datasets (3 datasets of color fundus photography and 1 of fluorescein angiography). Statistical analysis demonstrates that each component of the framework can provide the level of performance expected. The proposed framework is compared with widely used unsupervised and supervised methods, showing that the overall framework outperforms its competitors. For example, the achieved sensitivity (0:744), specificity (0:978) and accuracy (0:953) for the DRIVE dataset are very close to those of the manual annotations obtained by the second observer