| 1. |
- 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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| 2. |
- 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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| 3. |
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| 4. |
- 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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| 5. |
- 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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| 6. |
- 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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| 7. |
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| 8. |
- 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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| 9. |
- 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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