Automatic Segmentation of the Left Ventricle in Cardiac CT Angiography Using Convolutional Neural Network

Accurate delineation of the left ventricle (LV) is an important step in evaluation of cardiac function. In this paper, we present an automatic method for segmentation of the LV in cardiac CT angiography (CCTA) scans. Segmentation is performed in two stages. First, a bounding box around the LV is detected using a combination of three convolutional neural networks (CNNs). Subsequently, to obtain the segmentation of the LV, voxel classification is performed within the defined bounding box using a CNN. The study included CCTA scans of sixty patients, fifty scans were used to train the CNNs for the LV localization, five scans were used to train LV segmentation and the remaining five scans were used for testing the method. Automatic segmentation resulted in the average Dice coefficient of 0.85 and mean absolute surface distance of 1.1 mm. The results demonstrate that automatic segmentation of the LV in CCTA scans using voxel classification with convolutional neural networks is feasible.Comment: This work has been published as: Zreik, M., Leiner, T., de Vos, B. D., van Hamersvelt, R. W., Viergever, M. A., I\v{s}gum, I. (2016, April). Automatic segmentation of the left ventricle in cardiac CT angiography using convolutional neural networks. In Biomedical Imaging (ISBI), 2016 IEEE 13th International Symposium on (pp. 40-43). IEE

ConvNet-Based Localization of Anatomical Structures in 3D Medical Images

Localization of anatomical structures is a prerequisite for many tasks in medical image analysis. We propose a method for automatic localization of one or more anatomical structures in 3D medical images through detection of their presence in 2D image slices using a convolutional neural network (ConvNet). A single ConvNet is trained to detect presence of the anatomical structure of interest in axial, coronal, and sagittal slices extracted from a 3D image. To allow the ConvNet to analyze slices of different sizes, spatial pyramid pooling is applied. After detection, 3D bounding boxes are created by combining the output of the ConvNet in all slices. In the experiments 200 chest CT, 100 cardiac CT angiography (CTA), and 100 abdomen CT scans were used. The heart, ascending aorta, aortic arch, and descending aorta were localized in chest CT scans, the left cardiac ventricle in cardiac CTA scans, and the liver in abdomen CT scans. Localization was evaluated using the distances between automatically and manually defined reference bounding box centroids and walls. The best results were achieved in localization of structures with clearly defined boundaries (e.g. aortic arch) and the worst when the structure boundary was not clearly visible (e.g. liver). The method was more robust and accurate in localization multiple structures

Pathogenicity locus, core genome, and accessory gene contributions to Clostridium difficile virulence

Clostridium difficile is a spore-forming anaerobic bacterium that causes colitis in patients with disrupted colonic microbiota. While some individuals are asymptomatic C. difficile carriers, symptomatic disease ranges from mild diarrhea to potentially lethal toxic megacolon. The wide disease spectrum has been attributed to the infected host’s age, underlying diseases, immune status, and microbiome composition. However, strain-specific differences in C. difficile virulence have also been implicated in determining colitis severity. Because patients infected with C. difficile are unique in terms of medical history, microbiome composition, and immune competence, determining the relative contribution of C. difficile virulence to disease severity has been challenging, and conclusions regarding the virulence of specific strains have been inconsistent. To address this, we used a mouse model to test 33 clinical C. difficile strains isolated from patients with disease severities ranging from asymptomatic carriage to severe colitis, and we determined their relative in vivo virulence in genetically identical, antibiotic-pretreated mice. We found that murine infections with C. difficile clade 2 strains (including multilocus sequence type 1/ribotype 027) were associated with higher lethality and that C. difficile strains associated with greater human disease severity caused more severe disease in mice. While toxin production was not strongly correlated with in vivo colonic pathology, the ability of C. difficile strains to grow in the presence of secondary bile acids was associated with greater disease severity. Whole-genome sequencing and identification of core and accessory genes identified a subset of accessory genes that distinguish high-virulence from lower-virulence C. difficile strains

The Whole Heliosphere Interval in the Context of a Long and Structured Solar Minimum: An Overview from Sun to Earth

Throughout months of extremely low solar activity during the recent extended solar-cycle minimum, structural evolution continued to be observed from the Sun through the solar wind and to the Earth. In 2008, the presence of long-lived and large low-latitude coronal holes meant that geospace was periodically impacted by high-speed streams, even though solar irradiance, activity, and interplanetary magnetic fields had reached levels as low as, or lower than, observed in past minima. This time period, which includes the first Whole Heliosphere Interval (WHI 1: Carrington Rotation (CR) 2068), illustrates the effects of fast solar-wind streams on the Earth in an otherwise quiet heliosphere. By the end of 2008, sunspots and solar irradiance had reached their lowest levels for this minimum (e.g., WHI 2: CR 2078), and continued solar magnetic-flux evolution had led to a flattening of the heliospheric current sheet and the decay of the low-latitude coronal holes and associated Earth-intersecting high-speed solar-wind streams. As the new solar cycle slowly began, solar-wind and geospace observables stayed low or continued to decline, reaching very low levels by June – July 2009. At this point (e.g., WHI 3: CR 2085) the Sun–Earth system, taken as a whole, was at its quietest. In this article we present an overview of observations that span the period 2008 – 2009, with highlighted discussion of CRs 2068, 2078, and 2085. We show side-by-side observables from the Sun’s interior through its surface and atmosphere, through the solar wind and heliosphere and to the Earth’s space environment and upper atmosphere, and reference detailed studies of these various regimes within this topical issue and elsewhere

Radiation dose reduction in pediatric great vessel stent computed tomography using iterative reconstruction: A phantom study

Background To study dose reduction using iterative reconstruction (IR) for pediatric great vessel stent computed tomography (CT). Methods Five different great vessel stents were separately placed in a gel-containing plastic holder within an anthropomorphic chest phantom. The stent lumen was filled with diluted contrast gel. CT acquisitions were performed at routine dose, 52% and 81% reduced dose and reconstructed with filtered back projection (FBP) and IR. Objective image quality in terms of noise, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) as well as subjective image quality were evaluated. Results Noise, SNR and CNR were improved with IR at routine and 52% reduced dose, compared to FBP at routine dose. The lowest dose level resulted in decreased objective image quality with both FBP and IR. Subjective image quality was excellent at all dose levels. Conclusion IR resulted in improved objective image quality at routine dose and 52% reduced dose, while objective image quality deteriorated at 81% reduced dose. Subjective image quality was not affected by dose reduction