Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography.

Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.

Compact and versatile neutron imaging detector with sub-4µm spatial resolution based on a single-crystal thin-film scintillator.

A large and increasing number of scientific domains pushes for high neutron imaging resolution achieved in reasonable times. Here we present the principle, design and performance of a detector based on infinity corrected optics combined with a crystalline Gd3Ga5O12 : Eu scintillator, which provides an isotropic sub-4 µm true resolution. The exposure times are only of a few minutes per image. This is made possible also by the uniquely intense cold neutron flux available at the imaging beamline NeXT-Grenoble. These comparatively rapid acquisitions are compatible with multiple high quality tomographic acquisitions, opening new venues for in-operando testing, as briefly exemplified here.

Heterogeneity of the osteocyte lacuno-canalicular network architecture and material characteristics across different tissue types in healing bone.

Various tissue types, including fibrous connective tissue, bone marrow, cartilage, woven and lamellar bone, coexist in healing bone. Similar to most bone tissue type, healing bone contains a lacuno-canalicular network (LCN) housing osteocytes. These cells are known to orchestrate bone remodeling in healthy bone by sensing mechanical strains and translating them into biochemical signals. The structure of the LCN is hypothesized to influence mineralization processes. Hence, the aim of the present study was to visualize and match spatial variations in the LCN topology with mineral characteristics, within and at the interfaces of the different tissue types that comprise healing bone. We applied a correlative multi-method approach to visualize the LCN architecture and quantify mineral particle size and orientation within healing femoral bone in a mouse osteotomy model (26 weeks old C57BL/6 mice). This approach revealed structural differences across several length scales during endochondral ossification within the following regions: calcified cartilage, bony callus, cortical bone and a transition zone between the cortical and callus region analyzed 21 days after the osteotomy. In this transition zone, we observed a continuous convergence of mineral characteristics and osteocyte lacunae shape as well as discontinuities in the lacunae volume and LCN connectivity. The bony callus exhibits a 34% higher lacunae number density and 40% larger lacunar volume compared to cortical bone. The presented correlations between LCN architecture and mineral characteristics improves our understanding of how bone develops during healing and may indicate a contribution of osteocytes to bone (re)modeling.

3D micro structural analysis of human cortical bone in paired femoral diaphysis, femoral neck and radial diaphysis.

Human bone is known to adapt to its mechanical environment in a living body. Both its architecture and microstructure may differ between weight-bearing and non-weight-bearing bones. The aim of the current study was to analyze in three dimensions, the morphology of the multi-scale porosities on human cortical bone at different locations. Eight paired femoral diaphyses, femoral necks, and radial diaphyses were imaged using Synchrotron Radiation µCT with a 0.7 µm isotropic voxel size. The spatial resolution facilitates the investigation of the multiscale porosities of cortical bone, from the osteonal canals system down to the osteocyte lacunar system. Our results showed significant differences in the microstructural properties, regarding both osteonal canals and osteocytes lacunae, between the different anatomical locations. The radius presents significantly lower osteonal canal volume fraction and smaller osteonal canals than the femoral diaphysis or neck. Osteocytes lacunae observed in the radius are significantly different in shape than in the femur, and lacunar density is higher in the femoral neck. These results show that the radius, a non-weight-bearing bone, is significantly different in terms of its microstructure from a weight-bearing bone such as the femur. This implies that the cortical bone properties evaluated on the femoral diaphysis, the main location studied within the literature, cannot be generalized to other anatomical locations.

Synchrotron X-ray computed laminography of the three-dimensional anatomy of tomato leaves.

Synchrotron radiation computed laminography (SR-CL) is presented as an imaging method for analyzing the three-dimensional (3D) anatomy of leaves. The SR-CL method was used to provide 3D images of 1-mm² samples of intact leaves at a pixel resolution of 750 nm. The method allowed visualization and quantitative analysis of palisade and spongy mesophyll cells, and showed local venation patterns, aspects of xylem vascular structure and stomata. The method failed to image subcellular organelles such as chloroplasts. We constructed 3D computer models of leaves that can provide a basis for calculating gas exchange, light penetration and water and solute transport. The leaf anatomy of two different tomato genotypes grown in saturating light conditions was compared by 3D analysis. Differences were found in calculated values of tissue porosity, cell number density, cell area to volume ratio and cell volume and cell shape distributions of palisade and spongy cell layers. In contrast, the exposed cell area to leaf area ratio in mesophyll, a descriptor that correlates to the maximum rate of photosynthesis in saturated light conditions, was no different between spongy and palisade cells or between genotypes. The use of 3D image processing avoids many of the limitations of anatomical analysis with two-dimensional sections.

Real-time image-content-based beamline control for smart 4D X-ray imaging.

Real-time processing of X-ray image data acquired at synchrotron radiation facilities allows for smart high-speed experiments. This includes workflows covering parameterized and image-based feedback-driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high-level control system that manages low-level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four-dimensional in situ, in vivo and operando tomography and laminography.

Three-dimensional microscale modelling of CO2 transport and light propagation in tomato leaves enlightens photosynthesis.

We present a combined three-dimensional (3-D) model of light propagation, CO2 diffusion and photosynthesis in tomato (Solanum lycopersicum L.) leaves. The model incorporates a geometrical representation of the actual leaf microstructure that we obtained with synchrotron radiation X-ray laminography, and was evaluated using measurements of gas exchange and leaf optical properties. The combination of the 3-D microstructure of leaf tissue and chloroplast movement induced by changes in light intensity affects the simulated CO2 transport within the leaf. The model predicts extensive reassimilation of CO2 produced by respiration and photorespiration. Simulations also suggest that carbonic anhydrase could enhance photosynthesis at low CO2 levels but had little impact on photosynthesis at high CO2 levels. The model confirms that scaling of photosynthetic capacity with absorbed light would improve efficiency of CO2 fixation in the leaf, especially at low light intensity.

Gauging low-dose X-ray phase-contrast imaging at a single and large propagation distance.

The interactions of a beam of hard and spatio-temporally coherent X-rays with a soft-matter sample primarily induce a transverse distribution of exit phase variations δϕ (retardations or advancements in pieces of the wave front exiting the object compared to the incoming wave front) whose free-space propagation over a distance z gives rise to intensity contrast gz. For single-distance image detection and |δϕ| ≪ 1 all-order-in-z phase-intensity contrast transfer is linear in δϕ. Here we show that ideal coherence implies a decay of the (shot-)noise-to-signal ratio in gz and of the associated phase noise as z(-1/2) and z(-1), respectively. Limits on X-ray dose thus favor large values of z. We discuss how a phase-scaling symmetry, exact in the limit δϕ → 0 and dynamically unbroken up to |δϕ| ∼ 1, suggests a filtering of gz in Fourier space, preserving non-iterative quasi-linear phase retrieval for phase variations up to order unity if induced by multi-scale objects inducing phase variations δϕ of a broad spatial frequency spectrum. Such an approach continues to be applicable under an assumed phase-attenuation duality. Using synchrotron radiation, ex and in vivo microtomography on frog embryos exemplifies improved resolution compared to a conventional single-distance phase-retrieval algorithm.

Direct three-dimensional imaging of polymer-water interfaces by nanoscale hard X-ray phase tomography.

We report three-dimensional (3D) direct imaging of complex surface-liquid interfaces by hard X-ray phase contrast tomography as a non-destructive approach for the morphological characterization of surfaces at the micro- and nanoscale in contact with water. Specifically, we apply this method to study the solid-air-water interface in hydrophobic macroporous polymethacrylate surfaces, and the solid-oil-water interface in slippery liquid-infused porous surfaces (SLIPS). Varying the isotropic spatial resolution allows the 3D quantitative characterization of individual polymer globules, globular clusters (porosity) as well as the infused lubricant layer on SLIPS. Surface defects were resolved at the globular level. We show the first application of X-ray nanotomography to hydrated surface characterizations and we anticipate that X-ray nanoscale imaging will open new ways for various surface/interface studies.

Void space inside the developing seed of Brassica napus and the modelling of its function.

The developing seed essentially relies on external oxygen to fuel aerobic respiration, but it is currently unknown how oxygen diffuses into and within the seed, which structural pathways are used and what finally limits gas exchange. By applying synchrotron X-ray computed tomography to developing oilseed rape seeds we uncovered void spaces, and analysed their three-dimensional assembly. Both the testa and the hypocotyl are well endowed with void space, but in the cotyledons, spaces were small and poorly inter-connected. In silico modelling revealed a three orders of magnitude range in oxygen diffusivity from tissue to tissue, and identified major barriers to gas exchange. The oxygen pool stored in the voids is consumed about once per minute. The function of the void space was related to the tissue-specific distribution of storage oils, storage protein and starch, as well as oxygen, water, sugars, amino acids and the level of respiratory activity, analysed using a combination of magnetic resonance imaging, specific oxygen sensors, laser micro-dissection, biochemical and histological methods. We conclude that the size and inter-connectivity of void spaces are major determinants of gas exchange potential, and locally affect the respiratory activity of a developing seed.

Hierarchical radioscopy using polychromatic and partially coherent hard synchrotron radiation.

Pushing synchrotron x-ray radiography to increasingly higher image-acquisition rates (currently up to 100,000 fps) while maintaining spatial resolutions in the micrometer range implies drastically reduced fields of view. As a consequence, either imaging a small subregion of the sample with high spatial resolution or only the complete specimen with moderate resolution is applicable. We introduce a concept to overcome this limitation by making use of a semi-transparent x-ray detector positioned close to the investigated sample. The hard x-rays that pass through the sample either create an image on the first detector or keep on propagating until they are captured by a second x-ray detector located further downstream. In this way, a process can be imaged simultaneously in a hierarchical manner within a single exposure and a projection of the complete object with moderate resolution as well as a subregion with high resolution are obtained. As a proof-of-concept experiment, image sequences of an evolving liquid-metal foam are shown, employing frame rates of 1000 images/s (1.2 µm pixel size) and 15,000 images/s (18.1 µm pixel size) for the first and second detector, respectively.

Hierarchically guided in situ nanolaminography for the visualisation of damage nucleation in alloy sheets.

Hierarchical guidance is developed for three-dimensional (3D) nanoscale X-ray imaging, enabling identification, refinement, and tracking of regions of interest (ROIs) within specimens considerably exceeding the field of view. This opens up new possibilities for in situ investigations. Experimentally, the approach takes advantage of rapid multiscale measurements based on magnified projection microscopy featuring continuous zoom capabilities. Immediate and continuous feedback on the subsequent experimental progress is enabled by suitable on-the-fly data processing. For this, by theoretical justification and experimental validation, so-called quasi-particle phase-retrieval is generalised to conical-beam conditions, being key for sufficiently fast computation without significant loss of imaging quality and resolution compared to common approaches for holographic microscopy. Exploiting 3D laminography, particularly suited for imaging of ROIs in laterally extended plate-like samples, the potential of hierarchical guidance is demonstrated by the in situ investigation of damage nucleation inside alloy sheets under engineering-relevant boundary conditions, providing novel insight into the nanoscale morphological development of void and particle clusters under mechanical load. Combined with digital volume correlation, we study deformation kinematics with unprecedented spatial resolution. Correlation of mesoscale (i.e. strain fields) and nanoscale (i.e. particle cracking) evolution opens new routes for the understanding of damage nucleation within sheet materials with application-relevant dimensions.

Coalescence analysis for evolving foams via optical flow computation on projection image sequences.

A novel image-processing procedure is proposed for the analysis of sequences of two-dimensional projection images. Sudden events like the merging of bubbles in an evolving foam can be detected and spatio-temporally located in a given projection image sequence. The procedure is based on optical flow computations extended by a forward-backward check for each time step. Compared with prior methods, efficient suppression of noise or false events is achieved owing to uniform foam motion, and the reliability of detection is thus increased. The applicability of the proposed procedure in combination with synchrotron radiography is illustrated by a series of characteristic studies of foams of different kind. First, the detection of single-bubble collapses in aqueous foams is considered. Second, a spatial distribution of coalescence events in metals foamed in casting molds is estimated. Finally, the structural stability of polymer foams containing admixed solid nanoparticles is examined.

Comparison of image quality in computed laminography and tomography.

In computed tomography (CT), projection images of the sample are acquired over an angular range between 180 to 360 degrees around a rotation axis. A special case of CT is that of limited-angle CT, where some of the rotation angles are inaccessible, leading to artefacts in the reconstrucion because of missing information. The case of flat samples is considered, where the projection angles that are close to the sample surface are either i) completely unavailable or ii) very noisy due to the limited transmission at these angles. Computed laminography (CL) is an imaging technique especially suited for flat samples. CL is a generalization of CT that uses a rotation axis tilted by less than 90 degrees with respect to the incident beam. Thus CL avoids using projections from angles closest to the sample surface. We make a quantitative comparison of the imaging artefacts between CL and limited-angle CT for the case of a parallel-beam geometry. Both experimental and simulated images are used to characterize the effect of the artefacts on the resolution and visible image features. The results indicate that CL has an advantage over CT in cases when the missing angular range is a significant portion of the total angular range. In the case when the quality of the projections is limited by noise, CT allows a better tradeoff between the noise level and the missing angular range.

Phase contrast laminography based on Talbot interferometry.

Synchrotron laminography is combined with Talbot grating interferometry to address weakly absorbing specimens. Integrating both methods into one set-up provides a powerful x-ray diagnostical technique for multiple contrast screening of macroscopically large flat specimen and a subsequent non-destructive three-dimensional (3-D) inspection of regions of interest. The technique simultaneously yields the reconstruction of the 3-D absorption, phase, and the so-called dark-field contrast maps. We report on the theoretical and instrumental implementation of of this novel technique. Its broad application potential is exemplarily demonstrated for the field of cultural heritage, namely study of the historical Dead Sea parchment.

The Hydration State of Bone Tissue Affects Contrast in Neutron Tomographic Images.

Neutron tomography has emerged as a promising imaging technique for specific applications in bone research. Neutrons have a strong interaction with hydrogen, which is abundant in biological tissues, and they can penetrate through dense materials such as metallic implants. However, in addition to long imaging times, two factors have led to challenges in running in situ mechanical characterization experiments on bone tissue using neutron tomography: 1) the high water content in specimens reduces the visibility of internal trabecular structures; 2) the mechanical properties of bone are dependent on the hydration state of the tissue, with drying being reported to cause increased stiffness and brittleness. This study investigates the possibility of improving image quality in terms of neutron transmission and contrast between material phases by drying and rehydrating in heavy water. Rat tibiae and trabecular bovine bone plugs were imaged with neutron tomography at different hydration states and mechanical testing of the bone plugs was carried out to assess effects of drying and rehydration on the mechanical properties of bone. From analysis of image histograms, it was found that drying reduced the contrast between bone and soft tissue, but the contrast was restored with rehydration. Contrast-to-noise ratios and line profiles revealed that the contrast between bone tissue and background was reduced with increasing rehydration duration but remained sufficient for identifying internal structures as long as no free liquid was present inside the specimen. The mechanical analysis indicated that the proposed fluid exchange protocol had no adverse effects on the mechanical properties.

The scale of a martian hydrothermal system explored using combined neutron and x-ray tomography.

Nakhlite meteorites are igneous rocks from Mars that were aqueously altered ~630 million years ago. Hydrothermal systems on Earth are known to provide microhabitats; knowledge of the extent and duration of these systems is crucial to establish whether they could sustain life elsewhere in the Solar System. Here, we explore the three-dimensional distribution of hydrous phases within the Miller Range 03346 nakhlite meteorite using nondestructive neutron and x-ray tomography to determine whether alteration is interconnected and pervasive. The results reveal discrete clusters of hydrous phases within and surrounding olivine grains, with limited interconnectivity between clusters. This implies that the fluid was localized and originated from the melting of local subsurface ice following an impact event. Consequently, the duration of the hydrous alteration was likely short, meaning that the martian crust sampled by the nakhlites could not have provided habitable environments that could harbor any life on Mars during the Amazonian.

High-resolution neutron imaging of salt precipitation and water transport in zero-gap CO2 electrolysis.

The electrochemical reduction of CO2 is a pivotal technology for the defossilization of the chemical industry. Although pilot-scale electrolyzers exist, water management and salt precipitation remain a major hurdle to long-term operation. In this work, we present high-resolution neutron imaging (6 µm) of a zero-gap CO2 electrolyzer to uncover water distribution and salt precipitation under application-relevant operating conditions (200 mA cm-2 at a cell voltage of 2.8 V with a Faraday efficiency for CO of 99%). Precipitated salts penetrating the cathode gas diffusion layer can be observed, which are believed to block the CO2 gas transport and are therefore the major cause for the commonly observed decay in Faraday efficiency. Neutron imaging further shows higher salt accumulation under the cathode channel of the flow field compared to the land.

Water management in anion-exchange membrane water electrolyzers under dry cathode operation.

Dry cathode operation is a desired operation mode in anion-exchange membrane water electrolyzers to minimize contamination of the generated hydrogen. However, water management under such operation conditions makes it challenging to maintain reliable performance and durability. Here, we utilize high-resolution in situ neutron imaging (∼6 µm effective resolution) to analyze the water content inside the membrane-electrode-assembly of an anion-exchange membrane water electrolyzer. The ion-exchange capacity (IEC) and thus hydrophilicity of the polymer binder in the cathode catalyst layer is varied to study the influence on water content in the anode (mid IEC, 1.8-2.2 meq. g-1 and high IEC, 2.3-2.6 meq. g-1). The neutron radiographies show that a higher ion-exchange capacity binder allows improved water retention, which reduces the drying-out of the cathode at high current densities. Electrochemical measurements confirm a generally better efficiency for a high IEC cell above 600 mA cm-2. At 1.5 A cm-2 the high IEC has a 100 mV lower overpotential (2.1 V vs. 2.2 V) and a lower high frequency resistance (210 mΩ cm-2 vs. 255 mΩ cm-2), which is believed to be linked to the improved cathode water retention and membrane humidification. As a consequence, the performance stability of the high IEC cell at 1 A cm-2 is also significantly better than that of the mid IEC cell (45 mV h-1 vs. 75 mV h-1).

Synchrotron radiation computed laminography for polymer composite failure studies.

Synchrotron radiation computed laminography is applied to the three-dimensional micro-imaging of damage in large polymer composite plates with high spatial resolution. The influence of different experimental conditions is studied with respect to measurement time optimization, dose minimization and reduction of artefacts in the reconstructed images. Failures like delaminations, transverse ply cracks and splits are observed under in situ loads. The propagation of up to 2 mm-long cracks is non-destructively followed in situ and investigated in detail. By phase retrieval using a single detector distance, the failures can be easily visualized in three dimensions.