Four-dimensional tomographic reconstruction by time domain decomposition

Since the beginnings of tomography, the requirement that the sample does not change during the acquisition of one tomographic rotation is unchanged. We derived and successfully implemented a tomographic reconstruction method which relaxes this decades-old requirement of static samples. In the presented method, dynamic tomographic data sets are decomposed in the temporal domain using basis functions and deploying an L1 regularization technique where the penalty factor is taken for spatial and temporal derivatives. We implemented the iterative algorithm for solving the regularization problem on modern GPU systems to demonstrate its practical use

Synchrotron-based tomographic microscopy (SbTM) of wood: development of a testing device and observation of plastic deformation of uniaxially compressed Norway spruce samples

To understand better the structure-property relationships of wood in situ, nondestructive synchrotron-based tomographic microscopy (SbTM) with subcellular resolution is useful. In this context, an in situ testing device was developed to determine the cellular response of wood to mechanical loading. Different rotationally symmetric specimens were tested to synchronize the failure areas to the given scanning areas. Norway spruce samples were uniaxially compressed in the longitudinal direction and scanned in situ at several increasing relative forces ending up in the plastic deformation regime. A sufficiently high quality in situ tomography was demonstrated. The reconstructed data allowed the observation of the load-dependent development of failure regions: cracks and buckling on the microstructure were clearly visible. Future investigations with SbTM on different wood species, loading directions, and different moisture contents are promising in terms of the micromechanical behavior of woo

A comparative study of X-ray tomographic microscopy on shales at different synchrotron facilities: ALS, APS and SLS.

Synchrotron radiation X-ray tomographic microscopy (SRXTM) was used to characterize the three-dimensional microstructure, geometry and distribution of different phases in two shale samples obtained from the North Sea (sample N1) and the Upper Barnett Formation in Texas (sample B1). Shale is a challenging material because of its multiphase composition, small grain size, low but significant amount of porosity, as well as strong shape- and lattice-preferred orientation. The goals of this round-robin project were to (i) characterize microstructures and porosity on the micrometer scale, (ii) compare results measured at three synchrotron facilities, and (iii) identify optimal experimental conditions of high-resolution SRXTM for fine-grained materials. SRXTM data of these shales were acquired under similar conditions at the Advanced Light Source (ALS) of Lawrence Berkeley National Laboratory, USA, the Advanced Photon Source (APS) of Argonne National Laboratory, USA, and the Swiss Light Source (SLS) of the Paul Scherrer Institut, Switzerland. The data reconstruction of all datasets was handled under the same procedures in order to compare the data quality and determine phase proportions and microstructures. With a 10× objective lens the spatial resolution is approximately 2 µm. The sharpness of phase boundaries in the reconstructed data collected from the APS and SLS was comparable and slightly more refined than in the data obtained from the ALS. Important internal features, such as pyrite (high-absorbing), and low-density features, including pores, fractures and organic matter or kerogen (low-absorbing), were adequately segmented on the same basis. The average volume fractions of low-density features for sample N1 and B1 were estimated at 6.3 (6)% and 4.5 (4)%, while those of pyrite were calculated to be 5.6 (6)% and 2.0 (3)%, respectively. The discrepancy of data quality and volume fractions were mainly due to different types of optical instruments and varying technical set-ups at the ALS, APS and SLS

Quantitative 3D Characterization of Cellular Materials: Segmentation and Morphology of Foam

International audienceWood, trabecular bone, coral, liquid foams, grains in polycrystals, igneous rock, and even many types of food share many structural similarities and belong to the general class called cellular materials. The visualization of these materials in 3D has been made possible in the last decades through a variety of imaging techniques including magnetic resonance imaging (MRI), micro-computed X-ray tomography ($\mu$CT), and confocal microscopy. Recent advances in synchrotron-based ultra fast tomography have enabled measurements in liquid foams with thousands of bubbles and time resolutions down to 0.5 seconds. Post-processing techniques have, however, not kept pace and extracting useful physical metrics from such measurements is far from trivial. In this manuscript we present and validate a new, fully-automated method for segmenting and labeling the void space in cellular materials where the walls between cells are not visible or present. The individual cell labeling is based on a new tool, the Gradient Guided Watershed, which, while computationally simple, can be robustly scaled to large data-sets. Specifically we demonstrate the utility of this new method on several liquid foams (with varying liquid fraction and polydispersity) composed of thousands of bubbles, and the subsequent quantitative 3D structural characterization of those foams

Automatic reconstruction of brain’s micro-vascular network based onX-ray synchrotron tomography

X-ray synchrotron tomographic microscopy enables the acquisition of large amount of images with a geometric and radiometric resolution sufficient for the morphometric and topologic analysis of vascular and even of microvascular network of different organs. In this study cylindrical shaped, NiDAB labelled brain samples of a diameter of half a millimeter were imaged and analyzed with an effective pixel size of 0.38 µm. Several thousands of tomographic slices build up each reconstructed volume meaning that an automatized analysis tool is indispensable. These big data sets are processed by the developed algorithms on commercially available PCs with an automated image analysis technology in acceptable processing time. The obtained vessel segments are stored for further topological and morphometric analyses or surface/volumetric visualization purposes. These analyses contain vessel feature distribution analysis followed by 3D reconstruction. The obtained results are in accordance to the literature data.DOI: 10.17489/biohun/2015/2/0

Experimental growth law for bubbles in a "wet" 3D liquid foam

We used X-ray tomography to characterize the geometry of all bubbles in a liquid foam of average liquid fraction $\phi_l\approx 17$ and to follow their evolution, measuring the normalized growth rate $\mathcal{G}=V^{-{1/3}}\frac{dV} {dt}$ for 7000 bubbles. While $\mathcal{G}$ does not depend only on the number of faces of a bubble, its average over $f-$faced bubbles scales as $G_f\sim f-f_0$ for large $f$s at all times. We discuss the dispersion of $\mathcal{G}$ and the influence of $V$ on $\mathcal{G}$.Comment: 10 pages, submitted to PR

Structural formation during bread baking in a combined microwave-convective oven determined by sub-second in-situ synchrotron X-ray microtomography

A new concept has been developed for characterizing the real-time evolution of the three-dimensional pore and lamella microstructure of bread during baking using synchrotron X-ray microtomography (SR\ub5CT). A commercial, combined microwave-convective oven was modified and installed at the TOMCAT synchrotron tomography beamline at the Swiss Light Source (SLS), to capture the 3D dough-to-bread structural development in-situ at the micrometer scale with an acquisition time of 400 ms. This allowed characterization and quantitative comparison of three baking technologies: (1) convective heating, (2) microwave heating, and (3) a combination of convective and microwave heating. A workflow for automatic batchwise image processing and analysis of 3D bread structures (1530 analyzed volumes in total) was established for porosity, individual pore volume, elongation, coordination number and local wall thickness, which allowed for evaluation of the impact of baking technology on the bread structure evolution. The results showed that the porosity, mean pore volume and mean coordination number increase with time and that the mean local cell wall thickness decreases with time. Small and more isolated pores are connecting with larger and already more connected pores as function of time. Clear dependencies are established during the whole baking process between the mean pore volume and porosity, and between the mean local wall thickness and the mean coordination number. This technique opens new opportunities for understanding the mechanisms governing the structural changes during baking and discern the parameters controlling the final bread quality

In Vivo Time- Resolved Microtomography Reveals the Mechanics of the Blowfly Flight Motor

Dipteran flies are amongst the smallest and most agile of flying animals. Their wings are driven indirectly by large power muscles, which cause cyclical deformations of the thorax that are amplified through the intricate wing hinge. Asymmetric flight manoeuvres are controlled by 13 pairs of steering muscles acting directly on the wing articulations. Collectively the steering muscles account for <3% of total flight muscle mass, raising the question of how they can modulate the vastly greater output of the power muscles during manoeuvres. Here we present the results of a synchrotron-based study performing micrometre-resolution, time-resolved microtomography on the 145 Hz wingbeat of blowflies. These data represent the first four-dimensional visualizations of an organism's internal movements on sub-millisecond and micrometre scales. This technique allows us to visualize and measure the three-dimensional movements of five of the largest steering muscles, and to place these in the context of the deforming thoracic mechanism that the muscles actuate. Our visualizations show that the steering muscles operate through a diverse range of nonlinear mechanisms, revealing several unexpected features that could not have been identified using any other technique. The tendons of some steering muscles buckle on every wingbeat to accommodate high amplitude movements of the wing hinge. Other steering muscles absorb kinetic energy from an oscillating control linkage, which rotates at low wingbeat amplitude but translates at high wingbeat amplitude. Kinetic energy is distributed differently in these two modes of oscillation, which may play a role in asymmetric power management during flight control. Structural flexibility is known to be important to the aerodynamic efficiency of insect wings, and to the function of their indirect power muscles. We show that it is integral also to the operation of the steering muscles, and so to the functional flexibility of the insect flight motor