| 1. |
- Andersson, Mariam, et al.
(författare)
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Axon morphology is modulated by the local environment and impacts the noninvasive investigation of its structure-function relationship
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 117:52, s. 33649-33659
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Tidskriftsartikel (refereegranskat)abstract
- Axonal conduction velocity, which ensures efficient function of the brain network, is related to axon diameter. Noninvasive, in vivo axon diameter estimates can be made with diffusion magnetic resonance imaging, but the technique requires three-dimensional (3D) validation. Here, high-resolution, 3D synchrotron X-ray nano-holotomography images of white matter samples from the corpus callosum of a monkey brain reveal that blood vessels, cells, and vacuoles affect axonal diameter and trajectory. Within single axons, we find that the variation in diameter and conduction velocity correlates with the mean diameter, contesting the value of precise diameter determination in larger axons. These complex 3D axon morphologies drive previously reported 2D trends in axon diameter and g-ratio. Furthermore, we find that these morphologies bias the estimates of axon diameter with diffusion magnetic resonance imaging and, ultimately, impact the investigation and formulation of the axon structure-function relationship.
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| 2. |
- Dahlin, Lars B., et al.
(författare)
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Three-dimensional architecture of human diabetic peripheral nerves revealed by X-ray phase contrast holographic nanotomography
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- A deeper knowledge of the architecture of the peripheral nerve with three-dimensional (3D) imaging of the nerve tissue at the sub-cellular scale may contribute to unravel the pathophysiology of neuropathy. Here we demonstrate the feasibility of X-ray phase contrast holographic nanotomography to enable 3D imaging of nerves at high resolution, while covering a relatively large tissue volume. We show various subcomponents of human peripheral nerves in biopsies from patients with type 1 and 2 diabetes and in a healthy subject. Together with well-organized, parallel myelinated nerve fibres we show regenerative clusters with twisted nerve fibres, a sprouted axon from a node of Ranvier and other specific details. A novel 3D construction (with movie created) of a node of Ranvier with end segment of a degenerated axon and sprout of a regenerated one is captured. Many of these architectural elements are not described in the literature. Thus, X-ray phase contrast holographic nanotomography enables identifying specific morphological structures in 3D in peripheral nerve biopsies from a healthy subject and from patients with type 1 and 2 diabetes.
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| 3. |
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| 4. |
- Dong, Pei, et al.
(författare)
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Quantification of the 3D Morphology of the Bone Cell Network From Synchrotron Micro-Ct Images
- 2014
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Ingår i: Image Analysis and Stereology. - : Slovenian Society for Stereology and Quantitative Image Analysis. - 1580-3139 .- 1854-5165. ; 33:2, s. 157-166
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Tidskriftsartikel (refereegranskat)abstract
- In the context of bone diseases research, recent works have highlighted the crucial role of the osteocyte system. This system, hosted in the lacuno-canalicular network (LCN), plays a key role in the bone remodeling process. However, few data are available on the LCN due to the limitations of current microscopy techniques, and have mainly only been obtained from 2D histology sections. Here we present, for the first time, an automatic method to quantify the LCN in 3D from synchrotron radiation micro-tomography images. After segmentation of the LCN, two binary images are generated, one of lacunae (hosting the cell body) and one of canaliculi (small channels linking the lacunae). The binary image of lacunae is labeled, and for each object, lacunar descriptors are extracted after calculating the second order moments and the intrinsic volumes. Furthermore, we propose a specific method to quantify the ramification of canaliculi around each lacuna. To this aim, a signature of the numbers of canaliculi at different distances from the lacunar surface is estimated through the calculation of topological parameters. The proposed method was applied to the 3D SR micro-CT image of a human femoral mid-diaphysis bone sample. Statistical results are reported on 399 lacunae and their surrounding canaliculi.
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| 5. |
- Hesse, Bernhard, et al.
(författare)
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Accessing osteocyte lacunar geometrical properties in human jaw bone on the submicron length scale using synchrotron radiation mu CT
- 2014
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 255:3, s. 158-168
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Tidskriftsartikel (refereegranskat)abstract
- The architectural properties of the osteocyte cell network provide a valuable basis for understanding the mechanisms of bone remodelling, mineral homeostasis, ageing and pathologies. Recent advances in synchrotron microtomography enable unprecedented three-dimensional imaging of both the bone lacunar network and the extracellular matrix. Here, we investigate the three-dimensional morphological properties of osteocyte lacunae in human healthy and bisphosphonate-related osteonecrotic jaw bone based on synchrotron X-ray computed tomography images, with a spatial isotropic voxel size of 300 nm. Bisphosphonate-related osteonecrosis of the jaw is a relatively new disease with increasing incidence, which remains poorly understood. A step forward in elucidating this malady is to assess whether, and how, the morphology of the osteocyte lacunar network is modified in the affected jaw tissue. We evaluate thousands of cell lacunae from five specimens of which three originate from patients diagnosed with bisphosphonate-associated osteonecrosis. In this exploratory study, we report three-dimensional quantitative results on lacunar volumes (296-502 mu m(3)), shape (approximated by an ellipsoidal shape with principal axes a > b > c, such that a = 2.2b and a = 4c) and spatial distribution (i.e., 50% of the mineralized matrix volume is located within 12 mu m to the closest lacunar boundary) at submicron resolution on such specimens. We observe that the average lacunar volumes of the bisphosphonate-related osteonecrotic jaw specimens were within the range of volumes found in the two specimens originating from healthy donors and conclude that lacunar volumes are not the key element in the course of bisphosphonate-related osteonecrotic jaw. In three out of five specimens we observe lacunar volume sizes in segmented osteons to be significantly different compared to lacunar volumes in the adjacent tissue regions. Furthermore, we quantify the number of lacunae containing small dense objects (on average 9%). In contrast to lacunar morphology we report the lacunar density (16 000-50 000 per mm(3)) to be different in jaw bone tissue compared to what has been reported in femoral sites.
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| 6. |
- Hesse, Bernhard, et al.
(författare)
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Alterations of Mass Density and 3D Osteocyte Lacunar Properties in Bisphosphonate- Related Osteonecrotic Human Jaw Bone, a Synchrotron mu CT Study
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2, s. e88481-
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Tidskriftsartikel (refereegranskat)abstract
- Osteonecrosis of the jaw, in association with bisphosphonates (BRONJ) used for treating osteoporosis or cancer, is a severe and most often irreversible side effect whose underlying pathophysiological mechanisms remain largely unknown. Osteocytes are involved in bone remodeling and mineralization where they orchestrate the delicate equilibrium between osteoclast and osteoblast activity and through the active process called osteocytic osteolysis. Here, we hypothesized that (i) changes of the mineralized tissue matrix play a substantial role in the pathogenesis of BRONJ, and (ii) the osteocyte lacunar morphology is altered in BRONJ. Synchrotron mu CT with phase contrast is an appropriate tool for assessing both the 3D morphology of the osteocyte lacunae and the bone matrix mass density. Here, we used this technique to investigate the mass density distribution and 3D osteocyte lacunar properties at the sub-micrometer scale in human bone samples from the jaw, femur and tibia. First, we compared healthy human jaw bone to human tibia and femur in order to assess the specific differences and address potential explanations of why the jaw bone is exclusively targeted by the necrosis as a side effect of BP treatment. Second, we investigated the differences between BRONJ and control jaw bone samples to detect potential differences which could aid an improved understanding of the course of BRONJ. We found that the apparent mass density of jaw bone was significantly smaller compared to that of tibia, consistent with a higher bone turnover in the jaw bone. The variance of the lacunar volume distribution was significantly different depending on the anatomical site. The comparison between BRONJ and control jaw specimens revealed no significant increase in mineralization after BP. We found a significant decrease in osteocyte-lacunar density in the BRONJ group compared to the control jaw. Interestingly, the osteocyte-lacunar volume distribution was not altered after BP treatment.
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| 7. |
- Hesse, Bernhard, et al.
(författare)
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Canalicular Network Morphology is the Major Determinant of the Spatial Distribution of Mass Density in Human Bone Tissue : Evidence by Means of Synchrotron Radiation Phase-Contrast nano-CT
- 2015
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Ingår i: Journal of Bone and Mineral Research. - : Wiley. - 0884-0431 .- 1523-4681. ; 30:2, s. 346-356
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Tidskriftsartikel (refereegranskat)abstract
- In bone remodeling, maturation of the newly formed osteonal tissue is associated with a rapid primary increase followed by a slower secondary increase of mineralization. This requires supply and precipitation of mineral into the bone matrix. Mineral delivery can occur only from the extracellular fluid via interfaces such as the Haversian system and the osteocyte pore network. We hypothesized that in mineralization, mineral exchange is achieved by the diffusion of mineral from the lacunar-canalicular network (LCN) to the bone matrix, resulting in a gradual change in tissue mineralization with respect to the distance from the pore-matrix interface. We expected to observe alterations in the mass density distribution with tissue age. We further hypothesized that mineral exchange occurs not only at the lacunar but also at the canalicular boundaries. The aim of this study was, therefore, to investigate the spatial distribution of mass density in the perilacunar and pericanalicular bone matrix and to explore how these densities are influenced by tissue aging. This is achieved by analyzing human jawbone specimens originating from four healthy donors and four treated with high-dosage bisphosphonate using synchrotron radiation phase-contrast nano-CT with a 50-nm voxel size. Our results provide the first experimental evidence that mass density in the direct vicinity of both lacunae (p<0.001) and canaliculi (p<0.001) is different from the mean matrix mass density, resulting in gradients with respect to the distance from both pore-matrix interfaces, which diminish with increasing tissue age. Though limited by the sample size, these findings support our hypotheses. Moreover, the density gradients are more pronounced around the lacunae than around the canaliculi, which are explained by geometrical considerations in the LCN morphology. In addition, we speculate that mineral exchange occurs at all interfaces of the LCN, not only in mineralization but also in mineral homeostasis.
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| 8. |
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| 9. |
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| 10. |
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| 11. |
- Ishaq, Omer, 1979-, et al.
(författare)
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Light Tomography
- 2013
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 12. |
- Ke, Rongqin, et al.
(författare)
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In situ sequencing for RNA analysis in preserved tissue and cells
- 2013
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 10:9, s. 857-860
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Tidskriftsartikel (refereegranskat)abstract
- Tissue gene expression profiling is performed on homogenates or on populations of isolated single cells to resolve molecular states of different cell types. In both approaches, histological context is lost. We have developed an in situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved cells and tissue. We demonstrate in situ sequencing of point mutations and multiplexed gene expression profiling in human breast cancer tissue sections.
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| 13. |
- Langer, Max, et al.
(författare)
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Priors for X-ray in-line phase tomography of heterogeneous objects
- 2014
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Ingår i: Philosophical Transactions. Series A. - : The Royal Society. - 1364-503X .- 1471-2962. ; 372:2010, s. 20130129:1-9
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Tidskriftsartikel (refereegranskat)abstract
- We present a new prior for phase retrieval from X-ray Fresnel diffraction patterns. Fresnel diffraction patterns are achieved by letting a highly coherent X-ray beam propagate in free space after interaction with an object. Previously, either homogeneous or multi-material object assumptions have been used. The advantage of the homogeneous object assumption is that the prior can be introduced in the Radon domain. Heterogeneous object priors, on the other hand, have to be applied in the object domain. Here, we let the relationship between attenuation and refractive index vary as a function of the measured attenuation index. The method is evaluated using images acquired at beamline ID19 (ESRF, Grenoble, France) of a phantom where the prior is calculated by linear interpolation and of a healing bone obtained from a rat osteotomy model. It is shown that the ratio between attenuation and refractive index in bone for different levels of mineralization follows a power law. Reconstruction was performed using the mixed approach but is compatible with other, more advanced models. We achieve more precise reconstructions than previously reported in literature. We believe that the proposed method will find application in biomedical imaging problems where the object is strongly heterogeneous, such as bone healing and biomaterials engineering.
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| 14. |
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| 15. |
- Pacureanu, Alexandra, et al.
(författare)
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Adaptive filtering for enhancement of the osteocyte cell network in 3D microtomography images
- 2013
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Ingår i: IRBM. - : Elsevier BV. - 1959-0318. ; 34:1-SI, s. 48-52
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Tidskriftsartikel (refereegranskat)abstract
- The osteocyte cell network in bone tissue is thought to orchestrate tissue adaptation and remodeling, thus holding responsibility for tissue quality. Previously, this structure has been studied mainly in 2D and its architecture and functions are not fully elucidated. The assessment of the osteocyte system is prerequisite for deeper understanding of bone remodeling and for advances in management of bone diseases. Our goal is to enable 3D isotropic imaging of bone at cellular level and to develop algorithms for quantitative image analysis of the cell network. We recently demonstrated accurate 3D imaging of this cell structure with synchrotron radiation tomography at submicrometric scale. Due to the limited spatial resolution of the imaging system and the constraints in terms of radiation dose, the images suffer from low signal to noise ratio and the detection of the cell dendrites is challenging. Here we detail a method for enhancement of the osteocyte network in human bone from 3D microtomography images. The approach combines Hessian-based 3D line enhancement and bilateral filtering. Our method enables extraction of the interconnected cells from noisy images, preserving the integrity of the cells and of their slender dendrites. Qualitative and quantitative results are presented.
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| 16. |
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| 17. |
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| 18. |
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| 19. |
- Peyrin, Francoise, et al.
(författare)
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Synchrotron radiation CT from the micro to nanoscale for the investigation of bone tissue
- 2012
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Ingår i: Proceedings of SPIE. - : SPIE. - 9780819492234 ; , s. 85060L-
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Konferensbidrag (refereegranskat)abstract
- During the last decade, X-ray micro Computerized Tomography (CT) has become a conventional technique for the threedimensional (3D) investigation of trabecular bone micro-architecture. Coupling micro-CT to synchrotron sources possesses significant advantages in terms of image quality and gives access to information on bone mineralization which is an important factor of bone quality. We present an overview of the investigation of bone using Synchrotron Radiation (SR) CT from the micro to the nano scale. We introduce two synchrotron CT systems developed at the ESRF based on SR parallel-beam micro-CT and magnified phase CT respectively, achieving down to submicrometric and nanometric spatial resolution. In the latter, by using phase retrieval prior to tomographic reconstruction, the system provides maps of the 3D refractive index distribution. Parallel-beam SR micro-CT has extensively been used for the analysis of trabecular or cortical bone in human or small animals with spatial resolution in the range [3-10] μm. However, the characterization of the bone properties at the cellular scale is also of major interest. At the micrometric scale, the shape, density and morphology of osteocyte lacunae can be studied on statistically representative volumes. At the nanometric scale, unprecedented 3D displays of the canaliculi network have been obtained on fields of views including a large number of interconnected osteocyte lacunae. Finally SR magnified phase CT provides a detailed analysis of the lacuno-canalicular network and in addition information on the organization of the collagen fibers. These findings open new perspectives for three-dimensional quantitative assessment of bone tissue at the cellular scale.
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| 20. |
- Ranefall, Petter, 1968-, et al.
(författare)
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The Giga-pixel Challenge: Full Resolution Image Analysis – Without Losing the Big Picture : An open-source approach for multi-scale analysis and visualization of slide-scanner data
- 2014
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The amount of image data in a slide scanner image is usually in the giga-pixel range, inducing challenges for image analysis and visualization. At the same time, in order to maximize the information gained in these experi-ments and integrate expert knowledge with quantitative measurements, it is crucial to maintain the connection be-tween high-resolution per-cell and per-region metrics with lower resolution relational metrics. We present a free and open-source framework for full resolution image analysis of large images, e.g. slide scanner data, with the possibility of visual examination and interaction at multiple resolutions. The interface enables seamless zooming and panning, with the option to toggle multiple layers, such as segmentation masks and classification results, on or off. We make use of the strength and flexibility of existing state-of-the-art open-source software for visualization, creating resolution pyra-mids, image registration and image analysis.
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| 21. |
- Ranefall, Petter, 1968-, et al.
(författare)
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Viewing and analyzing slide scanner data using CellProfiler (work in progress)
- 2013
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Ingår i: European BioImage Analysis Symposium 2013. ; , s. 58-
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Viewing and analyzing slide scanner data using CellProfiler (work in progress)Petter Ranefall1, Alexandra Pacureanu1, and Carolina Wählby1,21Centre for Image Analysis, Department of Information Technology, Uppsala University, and Science for Life Laboratory, Sweden2Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA The amount of image data in a slide scanner image is usually very large, inducing challenges for image analysis and visualization. We would like to use the strengths and flexibility of CellProfiler for the image analysis, but performing high-resolution image analysis on large slide scanner images is unfortunately not possible due to memory limitations. At the same time, we would like to visualize the results of the analysis in the context of the full tissue slide so that for example phenotypic variations at the sub-cellular level can be related to lower-resolution structures such as vessels, ducts, or tumors in the tissue. To approach this problem we split the image into smaller tiles that are more suitable for CellProfiler to handle. By keeping track of the coordinates of the tiles we can display the results on the original, full-size image. Our aim is to enable visual examination at multiple resolutions and with the option to toggle results such as segmentation masks and classification results on or off using a “Google Maps” type of view. In particular, we work with tissue profiling by in situ sequencing of RNA molecules. The tissue samples have to be removed from the microscope for each new sequencing cycle. In this case, and in other applications dealing with repeated staining, there are often differences in the alignment between the imaging rounds. We assume that these misalignments are rigid (only translation and rotation), and we have added an image registration step in order to align the different channels before partitioning the images into tiles suitable for analysis in CellProfiler.
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| 22. |
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| 23. |
- Varga, Peter, et al.
(författare)
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Investigation of the three-dimensional orientation of mineralized collagen fibrils in human lamellar bone using synchrotron X-ray phase nano-tomography
- 2013
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Ingår i: Acta Biomaterialia. - : Elsevier BV. - 1742-7061 .- 1878-7568. ; 9:9, s. 8118-8127
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the three-dimensional (3-D) organization of mineralized collagen fibrils in human cortical bone based on synchrotron X-ray phase nano-tomography images. In lamellar bone the collagen fibrils are assumed to have a plywood-like arrangement, but due to experimental limitations the 3-D fibril structure has only been deduced from section surfaces so far and the findings have been controversial. Breakthroughs in synchrotron tomographic imaging have given access to direct 3-D information on the bone structure at the nanoscale level. Using an autocorrelation-based orientation measure we confirm that the fibrils are unidirectional in quasi-planes of sub-lamellae and find two specific dominant patterns, oscillating and twisted plywoods coexisting in a single osteon. Both patterns exhibit smooth orientation changes between adjacent quasi-planes. Moreover, we find that the periodic changes in collagen fibril orientation are independent of fluctuations in local mass density. These data improve our understanding of the lamellar arrangement in bone and allow more detailed investigations of structure-function relationships at this scale, providing templates for bio-inspired materials. The presented methodology can be applied to non-destructive 3-D characterization of the sub-micron scale structure of other natural and artificial mineralized biomaterials.
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| 24. |
- Varga, Peter, et al.
(författare)
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Synchrotron X-ray phase nano-tomography-based analysis of the lacunar-canalicular network morphology and its relation to the strains experienced by osteocytes in situ as predicted by case-specific finite element analysis
- 2015
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Ingår i: Biomechanics and Modeling in Mechanobiology. - : Springer Science and Business Media LLC. - 1617-7959 .- 1617-7940. ; 14:2, s. 267-282
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Tidskriftsartikel (refereegranskat)abstract
- Osteocytes are hypothesized to regulate bone remodeling guided by both biological and mechanical stimuli. Morphology of the lacunar-canalicular network of osteocytes has been hypothesized to be strongly related to the level of mechanical loading and to various bone diseases. Finite element modeling could help to better understand the mechanosensation process by predicting the physiological strain environment. The aims of this study were to (i) quantify the lacunar-canalicular morphology in the cortex of the human femur; (ii) predict the in situ local deformations around and in osteocytes by means of case-specific finite element models; and (iii) investigate the potential relationship between morphology and deformations. Human femoral cortical bone samples were imaged using synchrotron X-ray phase nano-tomography with 50 nm voxel size. Rectangular volumes of interest were selected to contain single osteocyte lacunae and the surrounding matrix. Lacunar-canalicular morphology was quantified and the cell geometry was artificially reconstructed based on a priori assumptions. Finite element models of the volumes of interest were generated, containing the extracellular matrix, osteocyte and peri-cellular matrix, and subjected to uniaxial compression. The morphological analysis revealed that canalicular number was dictated by lacunar size, that the spacing of canaliculi fell within a narrow range, suggesting that these pores are well distributed throughout the bone matrix and indicated the trend that lacunae at the outer osteon boundary were less elongated than others. No apparent relationship was found between the morphological parameters and the predicted strains. The globally applied strain was amplified locally by factors up to 10 and up to 70 in the extracellular matrix and the in cells, respectively. Cell deformations were localized mainly at the body-dendrite junctions, with magnitudes reaching the in vitro stimulatory threshold reported for osteocytes.
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| 25. |
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| 26. |
- Zhou, Tunhe, et al.
(författare)
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Bumblebee compound eye 3D imaging with x-ray holotomography
- 2023
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Ingår i: AIP Conference Proceedings. - : AIP Publishing.
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Konferensbidrag (refereegranskat)abstract
- Bumblebees are important pollinators, that are declining rapidly in number and need urgent protection. Visual cues are extremely important for bumblebee activities and survival so a full understanding of the micro-and nano-structure of their eyes will help us to better understand their vision and how it is affected by rapid habitat changes. Here, we present the first report on imaging of 3D structures with sub-100 nm resolution of an unstained bumblebee compound eye using X-ray holographic tomography. This study demonstrates the potential of using X-ray nano-tomography for bulk samples for zoological studies on insects. Compared to the other commonly used methods, such as TEM and FIB-SEM, X-ray nanoCT is non-destructive and relatively fast, and has the potential for providing a better understanding of a broad range of biological materials.
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| 27. |
- Zuluaga, Maria A., et al.
(författare)
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Bone canalicular network segmentation in 3D nano-CT images through geodesic voting and image tessellation
- 2014
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Ingår i: Physics in Medicine and Biology. - : IOP Publishing. - 0031-9155 .- 1361-6560. ; 59:9, s. 2155-2171
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies emphasized the role of the bone lacuno-canalicular network (LCN) in the understanding of bone diseases such as osteoporosis. However, suitable methods to investigate this structure are lacking. The aim of this paper is to introduce a methodology to segment the LCN from three-dimensional (3D) synchrotron radiation nano-CT images. Segmentation of such structures is challenging due to several factors such as limited contrast and signal-to-noise ratio, partial volume effects and huge number of data that needs to be processed, which restrains user interaction. We use an approach based on minimum-cost paths and geodesic voting, for which we propose a fully automatic initialization scheme based on a tessellation of the image domain. The centroids of pre-segmented lacunae are used as Voronoi-tessellation seeds and as start-points of a fast-marching front propagation, whereas the end-points are distributed in the vicinity of each Voronoi-region boundary. This initialization scheme was devised to cope with complex biological structures involving cells interconnected by multiple thread-like, branching processes, while the seminal geodesic-voting method only copes with tree-like structures. Our method has been assessed quantitatively on phantom data and qualitatively on real datasets, demonstrating its feasibility. To the best of our knowledge, presented 3D renderings of lacunae interconnected by their canaliculi were achieved for the first time.
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