Motion compensated micro-CT reconstruction for in-situ analysis of dynamic processes

Joint iterative reconstruction and 3D rigid alignment for X-ray tomography

X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to the nanometer scale. The resolution and quality of the 3D reconstruction is limited by the availability of alignment parameters that correct for the mechanical shifts of the sample or sample stage for the images that constitute a scan. In this paper we describe an algorithm for marker-free, fully automated and accurately aligned and reconstructed X-ray tomography data. Our approach solves the tomographic reconstruction jointly with projection data alignment based on a rigid-body deformation model. We demonstrate the robustness of our method on both synthetic phantom and experimental data and show that our method is highly efficient in recovering relatively large alignment errors without prior knowledge of a low resolution approximation of the 3D structure or a reasonable estimate of alignment parameters.

Projection-based dynamic tomography

Objective. This paper proposes a 4D dynamic tomography framework that allows a moving sample to be imaged in a tomograph as well as the associated space-time kinematics to be measured with nothing more than a single conventional x-ray scan.Approach. The method exploits the consistency of the projection/reconstruction operations through a multi-scale procedure. The procedure is composed of two main parts solved alternatively: a motion-compensated reconstruction algorithm and a projection-based measurement procedure that estimates the displacement field directly on each projection.Main results. The method is applied to two studies: a numerical simulation of breathing from chest computed tomography (4D-CT) and a clinical cone-beam CT of a breathing patient acquired for image guidance of radiotherapy. The reconstructed volume, initially blurred by the motion, is cleaned from motion artifacts.Significance. Applying the proposed approach results in an improved reconstruction quality showing sharper edges and finer details.

Time-resolved in situ synchrotron-microCT: 4D deformation of bone and bone analogues using digital volume correlation

Digital volume correlation (DVC) in combination with high-resolution micro-computed tomography (microCT) imaging and in situ mechanical testing is gaining popularity for quantifying 3D full-field strains in bone and biomaterials. However, traditional in situ time-lapsed (i.e., interrupted) mechanical testing cannot fully capture the dynamic strain mechanisms in viscoelastic biological materials. The aim of this study was to investigate the time-resolved deformation of bone structures and analogues via continuous in situ synchrotron-radiation microCT (SR-microCT) compression and DVC to gain a better insight into their structure-function relationships. Fast SR-microCT imaging enabled the deformation behaviour to be captured with high temporal and spatial resolution. Time-resolved DVC highlighted the relationship between local strains and damage initiation and progression in the different biostructures undergoing plastic deformation, bending and/or buckling of their main microstructural elements. The results showed that SR-microCT continuous mechanical testing complemented and enhanced the information obtained from time-lapsed testing, which may underestimate the 3D strain magnitudes as a result of the stress relaxation occurring in between steps before image acquisition in porous biomaterials. Altogether, the findings of this study highlight the importance of time-resolved in situ experiments to fully characterise the time-dependent mechanical behaviour of biological tissues and biomaterials and to further explore their micromechanics under physiologically relevant conditions. STATEMENT OF SIGNIFICANCE: Time-resolved synchrotron X-ray tomography in combination with in situ mechanical testing provided the first four-dimensional analysis of the mechanical deformation of bone and bone analogues. To unravel the interplay of damage initiation and progression with local deformation, digital volume correlation was used to map the local strain field while microstructural changes were tracked with high temporal and spatial resolution. The results highlighted the importance of fast imaging and time-resolved in situ experiments to capture the real deformation of complex porous materials to fully characterize the local strain-damage relationship. The findings are notably improving the understanding of time-dependent mechanical behaviour of bone tissue, with the potential to be extend to highly viscoelastic biomaterials and soft tissues.

High-temperature deformation followed in situ by X-ray microtomography: a methodology to track features under large strain

Metallic materials processing such as rolling, extrusion or forging often involves high-temperature deformation. Usually under such conditions the samples are characterized post mortem, under pseudo in situ conditions with interrupted tests, or in situ with a limited strain rate. A full in situ 3D characterization, directly during high-temperature deformation with a prescribed strain-rate scheme, requires a dedicated sample environment and a dedicated image-analysis workflow. A specific sample environment has been developed to enable highly controlled (temperature and strain rate) high-temperature deformation mechanical testing to be conducted while performing in situ tomography on a synchrotron beamline. A dedicated digital volume correlation algorithm is used to estimate the strain field and track pores while the material endures large deformations. The algorithm is particularly suitable for materials with few internal features when the deformation steps between two images are large. An example of an application is provided: a high-temperature compression test on a porous aluminium alloy with individual pore tracking with a specific strain-rate scheme representative of rolling conditions.

Time-lapsed imaging of nanocomposite scaffolds reveals increased bone formation in dynamic compression bioreactors

Progress in bone scaffold development relies on cost-intensive and hardly scalable animal studies. In contrast to in vivo, in vitro studies are often conducted in the absence of dynamic compression. Here, we present an in vitro dynamic compression bioreactor approach to monitor bone formation in scaffolds under cyclic loading. A biopolymer was processed into mechanically competent bone scaffolds that incorporate a high-volume content of ultrasonically treated hydroxyapatite or a mixture with barium titanate nanoparticles. After seeding with human bone marrow stromal cells, time-lapsed imaging of scaffolds in bioreactors revealed increased bone formation in hydroxyapatite scaffolds under cyclic loading. This stimulatory effect was even more pronounced in scaffolds containing a mixture of barium titanate and hydroxyapatite and corroborated by immunohistological staining. Therefore, by combining mechanical loading and time-lapsed imaging, this in vitro bioreactor strategy may potentially accelerate development of engineered bone scaffolds and reduce the use of animals for experimentation.

Schädli et al. present a bioreactor system that combines mechanical loading with longitudinal microCT imaging to assess bone mineralization in a poly(lactic-co-glycolic acid) (PLGA) scaffold reinforced with nanoparticles. This approach allows rapid and rigorous evaluation of engineered bone scaffolds performance in vitro and might reduce the use of animals for experimentation.

Improving image quality in fast, time-resolved micro-CT by weighted back projection

Time-resolved micro-CT is an increasingly powerful technique for studying dynamic processes in materials and structures. However, it is still difficult to study very fast processes with this technique, since fast scanning is typically associated with high image noise levels. We present weighted back projection, a technique applicable in iterative reconstruction methods using two types of prior knowledge: (1) a virtual starting volume resembling the sample, for example obtained from a scan before the dynamic process was initiated, and (2) knowledge on which regions in the sample are more likely to undergo the dynamic process. Therefore, processes on which this technique is applicable are preferably occurring within a static grid. Weighted back projection has the ability to handle small errors in the prior knowledge, while similar 4D micro-CT techniques require the prior knowledge to be exactly correct. It incorporates the prior knowledge within the reconstruction by using a weight volume, representing for each voxel its probability of undergoing the dynamic process. Qualitative analysis on a sparse subset of projection data from a real micro-CT experiment indicates that this method requires significantly fewer projection angles to converge to a correct volume. This can lead to an improved temporal resolution.

Review of Microfluidic Devices and Imaging Techniques for Fluid Flow Study in Porous Geomaterials

Understanding transport phenomena and governing mechanisms of different physical and chemical processes in porous media has been a critical research area for decades. Correlating fluid flow behaviour at the micro-scale with macro-scale parameters, such as relative permeability and capillary pressure, is key to understanding the processes governing subsurface systems, and this in turn allows us to improve the accuracy of modelling and simulations of transport phenomena at a large scale. Over the last two decades, there have been significant developments in our understanding of pore-scale processes and modelling of complex underground systems. Microfluidic devices (micromodels) and imaging techniques, as facilitators to link experimental observations to simulation, have greatly contributed to these achievements. Although several reviews exist covering separately advances in one of these two areas, we present here a detailed review integrating recent advances and applications in both micromodels and imaging techniques. This includes a comprehensive analysis of critical aspects of fabrication techniques of micromodels, and the most recent advances such as embedding fibre optic sensors in micromodels for research applications. To complete the analysis of visualization techniques, we have thoroughly reviewed the most applicable imaging techniques in the area of geoscience and geo-energy. Moreover, the integration of microfluidic devices and imaging techniques was highlighted as appropriate. In this review, we focus particularly on four prominent yet very wide application areas, namely “fluid flow in porous media”, “flow in heterogeneous rocks and fractures”, “reactive transport, solute and colloid transport”, and finally “porous media characterization”. In summary, this review provides an in-depth analysis of micromodels and imaging techniques that can help to guide future research in the in-situ visualization of fluid flow in porous media.

In-Situ X-ray Imaging Of Sublimating Spin-Frozen Solutions

Spin-freeze-drying is a promising technique to enable long-term storage of pharmaceutical unit doses of aqueous drug solutions. To investigate the sublimation of the ice during the primary phase of freeze-drying, X-ray imaging can yield crucial temporally resolved information on the local dynamics. In this paper, we describe a methodology to investigate the sublimation front during single unit-dose freeze-drying using 4D in-situ X-ray imaging. Three spin-frozen samples of different solutions were imaged using this methodology and the process characteristics were analysed and reduced to two-dimensional feature maps.

Ab initio nonrigid X-ray nanotomography

Reaching the full potential of X-ray nanotomography, in particular for biological samples, is limited by many factors, of which one of the most serious is radiation damage. Although sample deformation caused by radiation damage can be partly mitigated by cryogenic protection, it is still present in these conditions and, as we exemplify here using a specimen extracted from scales of the Cyphochilus beetle, it will pose a limit to the achievable imaging resolution. We demonstrate a generalized tomographic model, which optimally follows the sample morphological changes and attempts to recover the original sample structure close to the ideal, damage-free reconstruction. Whereas our demonstration was performed using ptychographic X-ray tomography, the method can be adopted for any tomographic imaging modality. Our application demonstrates improved reconstruction quality of radiation-sensitive samples, which will be of increasing relevance with the higher brightness of 4th generation synchrotron sources.

Radiation induced sample deformation can be a limiting factor for X-ray imaging resolution at the nanoscale. The authors report a tomographic model that estimates and accounts for morphological changes during data acquisition and enables reconstruction of a high-resolution image ab initio.

In-Situ High Resolution Dynamic X-ray Microtomographic Imaging of Olive Oil Removal in Kitchen Sponges by Squeezing and Rinsing

Recent advances in high resolution X-ray tomography (μCT) technology have enabled in-situ dynamic μCT imaging (4D-μCT) of time-dependent processes inside 3D structures, non-destructively and non-invasively. This paper illustrates the application of 4D-μCT for visualizing the removal of fatty liquids from kitchen sponges made of polyurethane after rinsing (absorption), squeezing (desorption) and cleaning (adding detergents). For the first time, time-dependent imaging of this type of system was established with sufficiently large contrast gradient between water (with/without detergent) and olive oil (model fat) by the application of suitable fat-sensitive X-ray contrast agents. Thus, contrasted olive oil filled sponges were rinsed and squeezed in a unique laboratory loading device with a fluid flow channel designed to fit inside a rotating gantry-based X-ray μCT system. Results suggest the use of brominated vegetable oil as a preferred contrast agent over magnetite powder for enhancing the attenuation coefficient of olive oil in a multi fluid filled kitchen sponge. The contrast agent (brominated vegetable oil) and olive oil were mixed and subsequently added on to the sponge. There was no disintegration seen in the mixture of contrast agent and olive oil during the cleaning process by detergents. The application of contrast agents also helped in accurately tracking the movement and volume changes of soils in compressed open cell structures. With the in house-built cleaning device, it was quantified that almost 99% of cleaning was possible for contrasted olive oil (brominated vegetable oil with olive oil) dispersed in the sponge. This novel approach allowed for realistic mimicking of the cleaning process and provided closer evaluation of the effectiveness of cleaning by detergents to minimize bacterial growth.

Dynamic Tomographic Reconstruction of Deforming Volumes

The motion of a sample while being scanned in a tomograph prevents its proper volume reconstruction. In the present study, a procedure is proposed that aims at estimating both the kinematics of the sample and its standard 3D imaging from a standard acquisition protocol (no more projection than for a rigid specimen). The proposed procedure is a staggered two-step algorithm where the volume is first reconstructed using a “Dynamic Reconstruction” technique, a variant of Algebraic Reconstruction Technique (ART) compensating for a “frozen” determination of the motion, followed by a Projection-based Digital Volume Correlation (P-DVC) algorithm that estimates the space/time displacement field, with a “frozen” microstructure and shape of the sample. Additionally, this procedure is combined with a multi-scale approach that is essential for a proper separation between motion and microstructure. A proof-of-concept of the validity and performance of this approach is proposed based on two virtual examples. The studied cases involve a small number of projections, large strains, up to 25%, and noise.