The micro-CT imaging of vasculature is a powerful tool for evaluation of angiogenesis,a prominent characteristic of hepatic fibrosis.The segment or bifurcation density,which is usually adopted to evaluate the degree o...The micro-CT imaging of vasculature is a powerful tool for evaluation of angiogenesis,a prominent characteristic of hepatic fibrosis.The segment or bifurcation density,which is usually adopted to evaluate the degree of hepatic fibrosis,does not always work and may lead to incorrect assessment,especially when the threedimensional vasculature obtained is imperfect in sample preparation or image collection.In this paper,we propose a new parameter to solve this problem.The experimental results demonstrate that the method is robust and reliable,and is practical for angiogenesis evaluation,despite of image data imperfections.This quantitative analysis method can be extended to investigate other kinds of diseases in which vasculature change is a key indicator.展开更多
Biogenic carbonate structures such as rhodoliths and foraminiferal-algal nodules are a significant part of marine carbonate production and are being increasingly used as paleoenvironmental indicators for predictive mo...Biogenic carbonate structures such as rhodoliths and foraminiferal-algal nodules are a significant part of marine carbonate production and are being increasingly used as paleoenvironmental indicators for predictive modeling of the global carbon cycle and ocean acidification research.However,traditional methods to characterize and quantify the carbonate production of biogenic nodules are typically limited to two-dimensional analysis using optical and electron microscopy.While micro-computed tomography(lCT)is an excellent tool for 3D analysis of inner structures of geomaterials,the trade-off between sample size and image resolution is often a limiting factor.In this study,we address these challenges by using a novel multi-scale lCT image analysis methodology combined with electron microscopy,to visualize and quantify the carbonate volumes in a biogenic calcareous nodule.We applied our methodology to a foraminiferal-algal nodule collected from the Red Sea along the coast of NEOM,Saudi Arabia.Integrated lCT and SEM image analyses revealed the main biogenic carbonate components of this nodule to be encrusting foraminifera(EF)and crustose coralline algae(CCA).We developed a multi-scale lCT analysis approach for this study,involving a hybrid thresholding and machine-learning based image segmentation.We utilized a high resolution lCT scan from the sample as a ground-truth to improve the segmentation of the lower resolution full volume lCT scan which provided reliable volumetric quantification of the EF and CCA layers.Together,the EF and CCA layers contribute to approximately 65.5%of the studied FAN volume,corresponding to 69.01 cm3 and 73.32 cm3 respectively,and the rest is comprised of sediment infill,voids and other minor components.Moreover,volumetric quantification results in conjunction with CT density values,indicate that the CCA layers are associated with the highest amount of carbonate production within this foraminiferal-algal nodule.The methodology developed for this study is suitable for analyzing biogenic carbonate structures for a wide array of applications including quantification of carbonate production and studying the impact of ocean acidification on skeletal structures of marine calcifying organisms.In particular,the hybrid lCT image analysis we adopted in this study proved to be advantageous for the analysis of biogenic structures in which the textures and components of the internal layers are distinctly visible despite having an overlap in the range of CT density values.展开更多
基金supported by the National Basic Research Program of China(No.2010CB834301)CAS-CSIRO Collaborative Research Project(GJHZ1303)+1 种基金the Shanghai Municipal Natural Science Foundation(No.11ZR1407800)the Joint Funds of the National Natural Science Foundation of China(Nos.U1232205,81430087 and81271574)
文摘The micro-CT imaging of vasculature is a powerful tool for evaluation of angiogenesis,a prominent characteristic of hepatic fibrosis.The segment or bifurcation density,which is usually adopted to evaluate the degree of hepatic fibrosis,does not always work and may lead to incorrect assessment,especially when the threedimensional vasculature obtained is imperfect in sample preparation or image collection.In this paper,we propose a new parameter to solve this problem.The experimental results demonstrate that the method is robust and reliable,and is practical for angiogenesis evaluation,despite of image data imperfections.This quantitative analysis method can be extended to investigate other kinds of diseases in which vasculature change is a key indicator.
基金ANPERC and Vahrenkamp group lab for supporting sample preparation required for petrography and SEM analysis of the FAN sample NTN0035-17A.
文摘Biogenic carbonate structures such as rhodoliths and foraminiferal-algal nodules are a significant part of marine carbonate production and are being increasingly used as paleoenvironmental indicators for predictive modeling of the global carbon cycle and ocean acidification research.However,traditional methods to characterize and quantify the carbonate production of biogenic nodules are typically limited to two-dimensional analysis using optical and electron microscopy.While micro-computed tomography(lCT)is an excellent tool for 3D analysis of inner structures of geomaterials,the trade-off between sample size and image resolution is often a limiting factor.In this study,we address these challenges by using a novel multi-scale lCT image analysis methodology combined with electron microscopy,to visualize and quantify the carbonate volumes in a biogenic calcareous nodule.We applied our methodology to a foraminiferal-algal nodule collected from the Red Sea along the coast of NEOM,Saudi Arabia.Integrated lCT and SEM image analyses revealed the main biogenic carbonate components of this nodule to be encrusting foraminifera(EF)and crustose coralline algae(CCA).We developed a multi-scale lCT analysis approach for this study,involving a hybrid thresholding and machine-learning based image segmentation.We utilized a high resolution lCT scan from the sample as a ground-truth to improve the segmentation of the lower resolution full volume lCT scan which provided reliable volumetric quantification of the EF and CCA layers.Together,the EF and CCA layers contribute to approximately 65.5%of the studied FAN volume,corresponding to 69.01 cm3 and 73.32 cm3 respectively,and the rest is comprised of sediment infill,voids and other minor components.Moreover,volumetric quantification results in conjunction with CT density values,indicate that the CCA layers are associated with the highest amount of carbonate production within this foraminiferal-algal nodule.The methodology developed for this study is suitable for analyzing biogenic carbonate structures for a wide array of applications including quantification of carbonate production and studying the impact of ocean acidification on skeletal structures of marine calcifying organisms.In particular,the hybrid lCT image analysis we adopted in this study proved to be advantageous for the analysis of biogenic structures in which the textures and components of the internal layers are distinctly visible despite having an overlap in the range of CT density values.
