A novel framework for cellular tracking and mitosis detection in dense phase contrast microscopy images

The aim of this paper is to detail the development of a novel tracking framework that is able to extract the cell motility indicators and to determine the cellular division (mitosis) events in large time-lapse phase-contrast image sequences. To address the challenges induced by non-structured (random) motion, cellular agglomeration, and cellular mitosis, the process of automatic (unsupervised) cell tracking is carried out in a sequential manner, where the inter-frame cell association is achieved by assessing the variation in the local cellular structures in consecutive frames of the image sequence. In our study a strong emphasis has been placed on the robust use of the topological information in the cellular tracking process and in the development of targeted pattern recognition techniques that were designed to redress the problems caused by segmentation errors, and to precisely identify mitosis using a backward (reversed) tracking strategy. The proposed algorithm has been evaluated on dense phase contrast cellular data and the experimental results indicate that the proposed algorithm is able to accurately track epithelial and endothelial cells in time-lapse image sequences that are characterized by low contrast and high level of noise. Our algorithm achieved 86.10% overall tracking accuracy and 90.12% mitosis detection accuracy

Accelerated gravity testing of aquitard core permeability and implications at formation and regional scale

Evaluating the possibility of leakage through low-permeability geological strata is critically important for sustainable water supplies, the extraction of fuels from coal and other strata, and the confinement of waste within the earth. The current work demonstrates that relatively rapid and realistic vertical hydraulic conductivity (Kv) measurements of aquitard cores using accelerated gravity can constrain and compliment larger-scale assessments of hydraulic connectivity. Steady-state fluid velocity through a low-K porous sample is linearly related to accelerated gravity (g level) in a centrifuge permeameter (CP) unless consolidation or geochemical reactions occur. A CP module was custom designed to fit a standard 2 m diameter geotechnical centrifuge (550 g maximum) with a capacity for sample dimensions up to 100 mm diameter and 200 mm length, and a total stress of  ∼  2 MPa at the base of the core. Formation fluids were used as influent to limit any shrink–swell phenomena, which may alter the permeability. Kv results from CP testing of minimally disturbed cores from three sites within a clayey-silt formation varied from 10−10 to 10−7  m s−1 (number of samples, n = 18). Additional tests were focussed on the Cattle Lane (CL) site, where Kv within the 99 % confidence interval (n = 9) was 1.1 × 10−9 to 2.0 × 10−9 m s−1. These Kv results were very similar to an independent in situ Kv method based on pore pressure propagation though the sequence. However, there was less certainty at two other core sites due to limited and variable Kv data. Blind standard 1 g column tests underestimated Kv compared to CP and in situ Kv data, possibly due to deionised water interactions with clay, and were more time-consuming than CP tests. Our Kv results were compared with the set-up of a flow model for the region, and considered in the context of heterogeneity and preferential flow paths at site and formation scale. Reasonable assessments of leakage and solute transport through aquitards over multi-decadal timescales can be achieved by accelerated core testing together with complimentary hydrogeological monitoring, analysis, and modelling

Two chemically similar stellar overdensities on opposite sides of the plane of the Galaxy

Our Galaxy is thought to have undergone an active evolutionary history dominated by star formation, the accretion of cold gas, and, in particular, mergers up to 10 gigayear ago. The stellar halo reveals rich fossil evidence of these interactions in the form of stellar streams, substructures, and chemically distinct stellar components. The impact of dwarf galaxy mergers on the content and morphology of the Galactic disk is still being explored. Recent studies have identified kinematically distinct stellar substructures and moving groups, which may have extragalactic origin. However, there is mounting evidence that stellar overdensities at the outer disk/halo interface could have been caused by the interaction of a dwarf galaxy with the disk. Here we report detailed spectroscopic analysis of 14 stars drawn from two stellar overdensities, each lying about 5 kiloparsecs above and below the Galactic plane - locations suggestive of association with the stellar halo. However, we find that the chemical compositions of these stars are almost identical, both within and between these groups, and closely match the abundance patterns of the Milky Way disk stars. This study hence provides compelling evidence that these stars originate from the disk and the overdensities they are part of were created by tidal interactions of the disk with passing or merging dwarf galaxies.Comment: accepted for publication in Natur

The definitions of three-dimensional landmarks on the human face: an interdisciplinary view

The analysis of shape is a key part of anatomical research and in the large majority of cases landmarks provide a standard starting point. However, while the technology of image capture has developed rapidly and in particular three-dimensional imaging is widely available, the de nitions of anatomical landmarks remain rooted in their two-dimensional origins. In the important case of the human face, standard de nitions often require careful orientation of the subject. This paper considers the de nitions of facial landmarks from an interdis- ciplinary perspective, including biological and clinical motivations, issues associated with imaging and subsequent analysis, and the mathematical definition of surface shape using differential geometry. This last perspective provides a route to de nitions of landmarks based on surface curvature, often making use of ridge and valley curves, which is genuinely three-dimensional and is independent of orientation. Specific definitions based on curvature are proposed. These are evaluated, along with traditional definitions, in a study which uses a hierarchical (random e ects) model to estimate the error variation which is present at several different levels within the image capture process. The estimates of variation at these different levels are of interest in their own right but, in addition, evidence is provided that variation is reduced at the observer level when the new landmark definitions are used

Internet Image Viewer (iiV)

<p>Abstract</p> <p>Background</p> <p>Visualizing 3-dimensional (3-D) datasets is an important part of modern neuroimaging research. Many tools address this problem; however, they often fail to address specific needs and flexibility, such as the ability to work with different data formats, to control how and what data are displayed, to interact with values, and to undo mistakes.</p> <p>Results</p> <p>iiV, an interactive software program for displaying 3-D brain images, is described. This tool was programmed to solve basic problems in 3-D data visualization. It is written in Java so it is extensible, is platform independent, and can display images within web pages.</p> <p>iiV displays 3-D images as 2-dimensional (2-D) slices with each slice being an independent object with independent features such as location, zoom, colors, labels, etc. Feature manipulation becomes easier by having a full set of editing capabilities including the following: undo or redo changes; drag, copy, delete and paste objects; and save objects with their features to a file for future editing. It can read multiple standard positron emission tomography (PET) and magnetic resonance imaging (MRI) file formats like ECAT, ECAT7, ANALYZE, NIfTI-1 and DICOM. We present sample applications to illustrate some of the features and capabilities.</p> <p>Conclusion</p> <p>iiV is an image display tool with many useful features. It is highly extensible, platform independent, and web-compatible. This report summarizes its features and applications, while illustrating iiV's usefulness to the biomedical imaging community.</p

Assessing the information desire of patients with advanced cancer by providing information with a decision aid, which is evaluated in a randomized trial: a study protocol

Contains fulltext : 95653.pdf (publisher's version ) (Open Access)BACKGROUND: There is a continuing debate on the desirability of informing patients with cancer and thereby involving them in treatment decisions. On the one hand, information uptake may be hampered, and additional stress could be inflicted by involving these patients. On the other hand, even patients with advanced cancer desire information on risks and prognosis. To settle the debate, a decision aid will be developed and presented to patients with advanced disease at the point of decision making. The aid is used to assess the amount of information desired. Factors related to information desire are explored, as well as the ability of the medical oncologist to judge the patient's information desire. The effects of the information on patient well-being are assessed by comparing the decision aid group with a usual care group. METHODS/DESIGN: This study is a randomized controlled trial of patients with advanced colorectal, breast, or ovarian cancer who have started treatment with first-line palliative chemotherapy. The trial will consist of 100 patients in the decision aid group and 70 patients in the usual care group. To collect complete data of 170 patients, 246 patients will be approached for the study. Patients will complete a baseline questionnaire on sociodemographic data, well-being measures, and psychological measures, believed to predict information desire. The medical oncologist will judge the patient's information desire. After disease progression is diagnosed, the medical oncologist offers the choice between second-line palliative chemotherapy plus best supportive care (BSC) and BSC alone. Randomization will take place to determine whether patients will receive usual care (n = 70) or usual care and the decision aid (n = 100). The aid offers information about the potential risks and benefits of both treatment options, in terms of adverse events, tumour response, and survival. Patients decide for each item whether they desire the information or not. Two follow-up questionnaires will evaluate the effect of the decision aid. DISCUSSION: This study attempts to settle the debate on the desirability of informing patients with cancer. In contrast to several earlier studies, we will actually deliver information on treatment options to patients at the point of decision making

The relationship between fertility and lifespan in humans

Evolutionary theories of aging predict a trade-off between fertility and lifespan, where increased lifespan comes at the cost of reduced fertility. Support for this prediction has been obtained from various sources. However, which genes underlie this relationship is unknown. To assess it, we first analyzed the association of fertility with age at menarche and menopause, and with mortality in 3,575 married female participants of the Rotterdam Study. In addition, we conducted a candidate gene study where 1,664 single nucleotide polymorphisms (SNPs) in 25 candidate genes were analyzed in relation to number of children as a measure of fertility. SNPs that associated with fertility were analyzed for association with mortality. We observed no associations between fertility and age at menarche (p = 0.38) and menopause (p = 0.07). In contrast, fertility was associated with mortality. Women with two to three children had significantly lower mortality (hazard ratio (HR), 0.82; 95% confidence interval (95% CI), 0.69–0.97) compared to women with no children. No such benefit was observed for women with four or more children, who had a similar mortality risk (HR, 0.93; 95% CI, 0.76–1.13) as women with no children. The analysis of candidate genes revealed four genes that influence fertility after correction for multiple testing: CGB/LHB gene cluster (p = 0.0036), FSHR (p = 0.023), FST (p = 0.023), and INHBA (p = 0.021). However, none of the independent SNPs in these genes predicted mortality. In conclusion, women who bear two to three children live longer than those who bear none or many children, but this relationship was not mediated by the candidate genes analyzed in this study

RGB-D Odometry and SLAM

The emergence of modern RGB-D sensors had a significant impact in many application fields, including robotics, augmented reality (AR) and 3D scanning. They are low-cost, low-power and low-size alternatives to traditional range sensors such as LiDAR. Moreover, unlike RGB cameras, RGB-D sensors provide the additional depth information that removes the need of frame-by-frame triangulation for 3D scene reconstruction. These merits have made them very popular in mobile robotics and AR, where it is of great interest to estimate ego-motion and 3D scene structure. Such spatial understanding can enable robots to navigate autonomously without collisions and allow users to insert virtual entities consistent with the image stream. In this chapter, we review common formulations of odometry and Simultaneous Localization and Mapping (known by its acronym SLAM) using RGB-D stream input. The two topics are closely related, as the former aims to track the incremental camera motion with respect to a local map of the scene, and the latter to jointly estimate the camera trajectory and the global map with consistency. In both cases, the standard approaches minimize a cost function using nonlinear optimization techniques. This chapter consists of three main parts: In the first part, we introduce the basic concept of odometry and SLAM and motivate the use of RGB-D sensors. We also give mathematical preliminaries relevant to most odometry and SLAM algorithms. In the second part, we detail the three main components of SLAM systems: camera pose tracking, scene mapping and loop closing. For each component, we describe different approaches proposed in the literature. In the final part, we provide a brief discussion on advanced research topics with the references to the state-of-the-art.Comment: This is the pre-submission version of the manuscript that was later edited and published as a chapter in RGB-D Image Analysis and Processin

Ischemia-Reperfusion Injury Leads to Distinct Temporal Cardiac Remodeling in Normal versus Diabetic Mice

Diabetes is associated with higher incidence of myocardial infarction (MI) and increased propensity for subsequent events post-MI. Here we conducted a temporal analysis of the influence of diabetes on cardiac dysfunction and remodeling after ischemia reperfusion (IR) injury in mice. Diabetes was induced using streptozotocin and IR performed by ligating the left anterior descending coronary artery for 30 min followed by reperfusion for up to 42 days. We first evaluated changes in cardiac function using echocardiography after 24 hours reperfusion and observed IR injury significantly decreased the systolic function, such as ejection fraction, fractional shortening and end systolic left ventricular volume (LVESV) in both control and diabetic mice. The longitudinal systolic and diastolic strain rate were altered after IR, but there were no significant differences between diabetic mice and controls. However, a reduced ability to metabolize glucose was observed in the diabetic animals as determined by PET-CT scanning using 2-deoxy-2-(18F)fluoro-D-glucose. Interestingly, after 24 hours reperfusion diabetic mice showed a reduced infarct size and less apoptosis indicated by TUNEL analysis in heart sections. This may be explained by increased levels of autophagy detected in diabetic mice hearts. Similar increases in IR-induced macrophage infiltration detected by CD68 staining indicated no change in inflammation between control and diabetic mice. Over time, control mice subjected to IR developed mild left ventricular dilation whereas diabetic mice exhibited a decrease in both end diastolic left ventricular volume and LVESV with a decreased intraventricular space and thicker left ventricular wall, indicating concentric hypertrophy. This was associated with marked increases in fibrosis, indicted by Masson trichrome staining, of heart sections in diabetic IR group. In summary, we demonstrate that diabetes principally influences distinct IR-induced chronic changes in cardiac function and remodeling, while a smaller infarct size and elevated levels of autophagy with similar cardiac function are observed in acute phase