Quantitative 3D analysis and visualization of cardiac fibrosis by microcomputed tomography.
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ABSTRACT:
SUBMITTER: Janbandhu V
PROVIDER: S-EPMC8715218 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background[corrected] Hepatic fibrosis can lead to deformation of vessel morphology and structure. In the present feasibility study, high-resolution computed tomography (CT) using diffraction-enhanced imaging (DEI) was used to represent three-dimensional (3D) vessel microstructures of hepatic fibrosis in rats and to differentiate different stages of hepatic fibrosis using qualitative descriptions and quantitative measurement of microvessels.Material and methodsThree typical specimens at different stages, i.e., mild, moderate and severe hepatic fibrosis, were imaged using DEI at 15 keV without contrast agents. The correspondence between DEI-CT images and histopathological findings was determined. The 3D visualizations from different stages of hepatic fibrosis were presented using DEI-CT. Additionally, Qualitative descriptions and quantitative evaluation of vessel features, such as vessel trend, vascular distortion deformation, thrombus formation and texture features on the inner wall of the vessel, were performed.ResultsDEI-CT produced high-resolution images of the vessel microstructures in hepatic fibrosis that corresponded to information on actual structures observed from the histological sections. Combined with the 3D visualization technique, DEI-CT enabled the acquisition of an accurate description of the 3D vessel morphology from different stages of hepatic fibrosis. Qualitative descriptions and quantitative assessment of microvessels demonstrated clear differences between the different stages of hepatic fibrosis. The thrombus inside the vessel of severe liver fibrosis was accurately displayed, and corresponding analysis can provide an exact measurement of vessel stenosis rate.ConclusionsDEI-CT may allow morphologic descriptions and quantitative evaluation of vessel microstructures from different stages of hepatic fibrosis and can better characterize the various stages of fibrosis progression using high-resolution 3D vessel morphology.
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Project description:PremiseX-ray microcomputed tomography (microCT) can be used to measure 3D leaf internal anatomy, providing a holistic view of tissue organization. Previously, the substantial time needed for segmenting multiple tissues limited this technique to small data sets, restricting its utility for phenotyping experiments and limiting our confidence in the inferences of these studies due to low replication numbers.Methods and resultsWe present a Python codebase for random forest machine learning segmentation and 3D leaf anatomical trait quantification that dramatically reduces the time required to process single-leaf microCT scans into detailed segmentations. By training the model on each scan using six hand-segmented image slices out of >1500 in the full leaf scan, it achieves >90% accuracy in background and tissue segmentation.ConclusionsOverall, this 3D segmentation and quantification pipeline can reduce one of the major barriers to using microCT imaging in high-throughput plant phenotyping.
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Project description:We introduce Map3-2D, a freely available software to accurately project up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps. Similar to the Earth's projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally connected map. We demonstrate its applicability for visualization and quantitative analyses of spherical and uneven surfaces in fixed and dynamic live samples by using mammalian and yeast cells, and giant unilamellar vesicles. Map3-2D software is available at http://www.zmbh.uni-heidelberg.de//Central_Services/Imaging_Facility/Map3-2D.html.
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Project description:The development of the mammalian gut was first described more than a century ago. Since then, it has been believed that a series of highly orchestrated developmental processes occur before the intestine achieves its final formation. The key steps include the formation of the umbilicus, the so-called "physiological herniation" of the midgut into the umbilical cord, an intestinal "rotation", and the "return of the gut" into the abdominal cavity. However, this sequence of events is predominantly based on histological sections of dissected embryos, a 2D technique with methodological limitations. For a better understanding of spatial relationships in the embryo, we utilized microcomputed tomography (µCT), a nondestructive 3D imaging method. Here, we show the detailed processes and mechanisms of intestinal development in rat embryos, including the development of the umbilicus, the formation of loops inside the umbilical coelom, and the subsequent shift of these loops into the abdominal cavity. Our 3D datasets of developing intestines will substantially advance the understanding of normal mammalian midgut embryology and offer new possibilities to reveal unknown mechanisms in the pathogenesis of congenital disorders.
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Project description:To assess the relationship between proximal femoral cortical bone thickness and radiological hip osteoarthritis using quantitative 3D analysis of clinical computed tomography (CT) data.Image analysis was performed on clinical CT imaging data from 203 female volunteers with a technique called cortical bone mapping (CBM). Colour thickness maps were created for each proximal femur. Statistical parametric mapping was performed to identify statistically significant differences in cortical bone thickness that corresponded with the severity of radiological hip osteoarthritis. Kellgren and Lawrence (K&L) grade, minimum joint space width (JSW) and a novel CT-based osteophyte score were also blindly assessed from the CT data.For each increase in K&L grade, cortical thickness increased by up to 25 % in distinct areas of the superolateral femoral head-neck junction and superior subchondral bone plate. For increasing severity of CT osteophytes, the increase in cortical thickness was more circumferential, involving a wider portion of the head-neck junction, with up to a 7 % increase in cortical thickness per increment in score. Results were not significant for minimum JSW.These findings indicate that quantitative 3D analysis of the proximal femur can identify changes in cortical bone thickness relevant to structural hip osteoarthritis.• CT is being increasingly used to assess bony involvement in osteoarthritis • CBM provides accurate and reliable quantitative analysis of cortical bone thickness • Cortical bone is thicker at the superior femoral head-neck with worse osteoarthritis • Regions of increased thickness co-locate with impingement and osteophyte formation • Quantitative 3D bone analysis could enable clinical disease prediction and therapy development.
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Project description:A prototype small animal imaging system was created for coupling fluorescence tomography (FT) with x-ray microcomputed tomography (microCT). The FT system has the potential to provide synergistic information content resultant from using microCT images as prior spatial information and then allows overlay of the FT image onto the original microCT image. The FT system was designed to use single photon counting to provide maximal sensitivity measurements in a noncontact geometry. Five parallel detector locations are used, each allowing simultaneous sampling of the fluorescence and transmitted excitation signals through the tissue. The calibration and linearity range performance of the system are outlined in a series of basic performance tests and phantom studies. The ability to image protoporphyrin IX in mouse phantoms was assessed and the system is ready for in vivo use to study biological production of this endogenous marker of tumors. This multimodality imaging system will have a wide range of applications in preclinical cancer research ranging from studies of the tumor microenvironment and treatment efficacy for emerging cancer therapeutics.
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Project description:Root system interactions and competition for resources are active areas of research that contribute to our understanding of how roots perceive and react to environmental conditions. Recent research has shown this complex suite of processes can now be observed in a natural environment (i.e. soil) through the use of X-ray microcomputed tomography (μCT), which allows non-destructive analysis of plant root systems. Due to their similar X-ray attenuation coefficients and densities, the roots of different plants appear as similar greyscale intensity values in μCT image data. Unless they are manually and carefully traced, it has not previously been possible to automatically label and separate different root systems grown in the same soil environment. We present a technique, based on a visual tracking approach, which exploits knowledge of the shape of root cross-sections to automatically recover from X-ray μCT data three-dimensional descriptions of multiple, interacting root architectures growing in soil. The method was evaluated on both simulated root data and real images of two interacting winter wheat Cordiale (Triticumaestivum L.) plants grown in a single soil column, demonstrating that it is possible to automatically segment different root systems from within the same soil sample. This work supports the automatic exploration of supportive and competitive foraging behaviour of plant root systems in natural soil environments.
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Project description:Kawasaki disease is an acute, systemic vasculitis that affects the coronary arteries. However, the relationship between myocardial fibrosis and Kawasaki disease has been completely unknown until now. We aimed to provide quantitative information about myocardial fibrosis using cardiac integrated backscatter in Han race Kawasaki disease patients.Ninety Kawasaki disease patients and 90 healthy control subjects were recruited. Based on Kawasaki disease status, the patients were categorized into 3 groups: acute, subacute, and convalescence phase. Based on coronary artery status, the Kawasaki disease patients were categorized into 3 groups: without coronary artery lesions, with coronary artery dilation, and with coronary artery aneurysms. All subjects underwent two-dimensional and Doppler examinations to measure clinical echocardiographic parameters. Myocardial fibrosis was detected with calibrated integrated backscatter imaging.Left ventricle systolic functions were normal in both the Kawasaki disease and control participants. The myocardial calibrated integrated backscatter values of the left ventricles of the acute (p < 0.001), subacute (p < 0.001) and convalescence phase (p < 0.001) Kawasaki disease patients were significantly greater than those of the healthy controls. The left ventricle myocardial calibrated integrated backscatter values were significantly smaller in the Kawasaki disease patients without coronary artery lesions than in the Kawasaki disease patients with coronary artery dilations and coronary artery aneurysms in different phases. The left ventricle myocardial calibrated integrated backscatter results were positively correlated with coronary artery status in the acute (r = 0.331, p < 0.001), subacute (r = 0.456, p < 0.001) and convalescence phases (r = 0.407, p < 0.001) of Kawasaki disease.Our findings may suggest that myocardial fibrosis occurs during early episodes of Kawasaki disease given uncertainties that exist regarding correlations of calibrated integrated backscatter and myocardial fibrosis.
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