Lab-based micro-CT Research Articles

Three-dimensional visualization of plant tissues and organs by X-ray micro-computed tomography.

Studies visualizing plant tissues and organs in three-dimension (3D) using micro-computed tomography (CT) published since approximately 2015 are reviewed. In this period, the number of publications in the field of plant sciences dealing with micro-CT has increased along with the development of high-performance lab-based micro-CT systems as well as the continuous development of cutting-edge technologies at synchrotron radiation facilities. The widespread use of commercially available lab-based micro-CT systems enabling phase-contrast imaging technique, which is suitable for the visualization of biological specimens composed of light elements, appears to have facilitated these studies. Unique features of the plant body, which are particularly utilized for the imaging of plant organs and tissues by micro-CT, are having functional air spaces and specialized cell walls, such as lignified ones. In this review, we briefly describe the basis of micro-CT technology first and then get down into details of its application in 3D visualization in plant sciences, which are categorized as follows: imaging of various organs, caryopses, seeds, other organs (reproductive organs, leaves, stems and petioles), various tissues (leaf venations, xylems, air-filled tissues, cell boundaries, cell walls), embolisms and root systems, hoping that wide users of microscopes and other imaging technologies will be interested also in micro-CT and obtain some hints for a deeper understanding of the structure of plant tissues and organs in 3D. Majority of the current morphological studies using micro-CT still appear to be at a qualitative level. Development of methodology for accurate 3D segmentation is needed for the transition of the studies from a qualitative level to a quantitative level in the future.

OCT Meets micro-CT: A Subject-Specific Correlative Multimodal Imaging Workflow for Early Chick Heart Development Modeling.

Structural and Doppler velocity data collected from optical coherence tomography have already provided crucial insights into cardiac morphogenesis. X-ray microtomography and other ex vivo methods have elucidated structural details of developing hearts. However, by itself, no single imaging modality can provide comprehensive information allowing to fully decipher the inner workings of an entire developing organ. Hence, we introduce a specimen-specific correlative multimodal imaging workflow combining OCT and micro-CT imaging which is applicable for modeling of early chick heart development-a valuable model organism in cardiovascular development research. The image acquisition and processing employ common reagents, lab-based micro-CT imaging, and software that is free for academic use. Our goal is to provide a step-by-step guide on how to implement this workflow and to demonstrate why those two modalities together have the potential to provide new insight into normal cardiac development and heart malformations leading to congenital heart disease.

Substantiating microCT for diagnosing bioerosion in archaeological bone using a new Virtual Histological Index (VHI)

Recent technological advances have broadened the application of palaeoradiology for non-destructive investigation of ancient remains. X-ray microtomography (microCT) in particular is increasingly used as an alternative to histological bone sections for interpreting pathological alterations, trauma, microstructure, and, more recently, bioerosion with direct or ancillary use of histological indices. However, no systematic attempt has been made to confirm the reliability of microCT for histotaphonomic analysis of archaeological bone. The objective of this study is therefore to compare thin sections of human femora rated with the Oxford Histological Index to microCT sections using the newly developed Virtual Histological Index in order to provide an accessible methodology for the evaluation of bioerosion in archaeological bone. We provide detailed descriptions of virtual sections and assess the efficacy of the method on cranial and postcranial elements, cremated long bones, and faunal samples. The traditional histological and virtual methods showed a strong correlation, providing the first systematic data substantiating lab-based microCT as a suitable alternative tool for reconstructing post-mortem history in the archaeological record, and for the reliable, non-destructive screening of samples for further analyses.

MiTiSegmenter: Software for high throughput segmentation and meshing of microCT data in microtiter plate arrays

Lab-based microCT is a powerful means of visualising the internal structure of physical specimens deployed across the physical sciences, engineering and the arts. As its popularity has grown, demand for bulk digitisation of multiple samples within a single scan has increased. High throughput workflows can increase sample sizes and reduce scan time, yet downstream segmentation and meshing remain a bottleneck. We present MiTiSegmenter as a new tool for the bulk archiving of valuable zooarchaeological and palaeontological remains. We foresee MiTiSegmenter as particularly useful when incorporated into workflows that ultimately require the destructive testing of specimens, including sampling for ancient DNA and proteomics. The software may also play an important role in national museums' ongoing mass digitisation efforts, facilitating the high-speed archiving of specimen 3D morphology across extensive collections with very minimal user intervention or prior training. •We present MiTiSegmenter, a software package for semi-automated image processing and segmentation of array-based batch microCT data.•Implemented in Python, MiTiSegmenter expedites cropping, meshing and exporting samples within stacked microtiter plates, facilitating the rapid digitisation of hundreds-thousands of samples per scan.•We illustrate MiTiSegmenter's capabilities when applied to bulk archiving of valuable zooarchaeological and palaeontological remains

Nanoscale state-of-charge heterogeneities within polycrystalline nickel-rich layered oxide cathode materials

Nickel-rich cathodes (LiNi x Mn y Co 1-x-y O 2 , x > 0.6) permit higher energy in lithium-ion rechargeable batteries but suffer from accelerated degradation at potentials above 4.1 V versus Li/Li + . Here, we present a proof-of-concept in situ pouch cell and methodology for correlative 2D synchrotron transmission X-ray microscopy with 3D lab-based micro-CT. XANES analysis of the TXM data enables tracking of Ni edge energy within and between the polycrystalline NMC811 particles embedded in the operating electrode through its initial delithiation. By using edge energy as a proxy, state-of-charge heterogeneities can be tracked at the nanoscale, revealing the role of cracked particles as potential nucleation points for failure and highlighting the challenges in achieving uniform (de-)lithiation. We propose, in future work, to leverage the pouch cell design presented here for longitudinal TXM-XANES studies of nickel-rich cathodes across multiple cycles and operating variables and investigate the effect of dopants and microstructural optimization in mitigating degradation. In situ pouch cell design that is adaptable to various characterization methods Combined lab-based micro-CT and synchrotron XANES imaging approach Insights into spatio-temporal dependence of degradation in NMC811 There is significant interest in the energy storage community for in situ studies because of the codependence of spatial and temporal effects on the performance of an electrochemical cell. Tan et al. report a tab pouch cell design that maintains fidelity to commercially relevant cells while still allowing 3D measurements at the nanoscale.

Visualization of different anatomical parts of the enucleated human eye using X-ray micro-CT imaging

Micro-CT visualization allows reconstruction of eye structures with the resolution of light microscopy and estimation of tissue densities. Moreover, this method excludes damaging procedures and allows further histological staining due to the similar steps in the beginning. We have shown the feasibility of the lab-based micro-CT machine usage for visualization of clinically important compartments of human eye such as trabecular outflow pathway, retina, iris and ciliary body after pre-treatment with iodine in ethanol. We also identified the challenges of applying this contrasting technique to lens, cornea, and retina and proposed alternative staining methods for these tissues. Thereby this work provides a starting point for other studies for imaging of human eyes in normal and pathological conditions using lab-based micro-CT systems.

High-speed Dynamic Lab-based Micro-CT for Optically Opaque Flows

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<p class="HeadingRunIn"><strong>Comparison of 2D SEM imaging with 3D micro-tomographic imaging for phylogenetic inference in brittle stars (Echinodermata: Ophiuroidea)</strong></p>

Recent efforts to reconstruct the phylogeny of brittle stars (ophiuroids) have shown the need for more objective and reproducible data collection methods than the traditional visual examination and verbal description of morphological characters. Complex skeletal structures may be better understood in three dimensions than in two dimensions obtained from techniques like scanning electron microscopy (SEM). We test this hypothesis using three types of three-dimensional tomographic imaging methods—lab-based micro-CT, X-ray microscopy and synchrotron-based tomography—to examine the morphology of ophiuroid arms, and compare them with two-dimensional data obtained from SEM. We describe the advantages and disadvantages of each instrument and set of parameters in terms of the ease and efficiency of data collection for morphometric analyses. We present new morphological observations obtained by digital sectioning of three-dimensional images that could not be achieved with SEM. Overall, our findings suggest that three-dimensional imaging has a high potential to address the gaps in knowledge of the internal ophiuroid skeleton, which will be pivotal to providing morphological characters that will aid in phylogenetic reconstructions.

Investigating the microstructure of plant leaves in 3D with lab-based X-ray computed tomography

BackgroundLeaf cellular architecture plays an important role in setting limits for carbon assimilation and, thus, photosynthetic performance. However, the low density, fine structure, and sensitivity to desiccation of plant tissue has presented challenges to its quantification. Classical methods of tissue fixation and embedding prior to 2D microscopy of sections is both laborious and susceptible to artefacts that can skew the values obtained. Here we report an image analysis pipeline that provides quantitative descriptors of plant leaf intercellular airspace using lab-based X-ray computed tomography (microCT). We demonstrate successful visualisation and quantification of differences in leaf intercellular airspace in 3D for a range of species (including both dicots and monocots) and provide a comparison with a standard 2D analysis of leaf sections.ResultsWe used the microCT image pipeline to obtain estimates of leaf porosity and mesophyll exposed surface area (Smes) for three dicot species (Arabidopsis, tomato and pea) and three monocot grasses (barley, oat and rice). The imaging pipeline consisted of (1) a masking operation to remove the background airspace surrounding the leaf, (2) segmentation by an automated threshold in ImageJ and then (3) quantification of the extracted pores using the ImageJ ‘Analyze Particles’ tool. Arabidopsis had the highest porosity and lowest Smes for the dicot species whereas barley had the highest porosity and the highest Smes for the grass species. Comparison of porosity and Smes estimates from 3D microCT analysis and 2D analysis of sections indicates that both methods provide a comparable estimate of porosity but the 2D method may underestimate Smes by almost 50%. A deeper study of porosity revealed similarities and differences in the asymmetric distribution of airspace between the species analysed.ConclusionsOur results demonstrate the utility of high resolution imaging of leaf intercellular airspace networks by lab-based microCT and provide quantitative data on descriptors of leaf cellular architecture. They indicate there is a range of porosity and Smes values in different species and that there is not a simple relationship between these parameters, suggesting the importance of cell size, shape and packing in the determination of cellular parameters proposed to influence leaf photosynthetic performance.

Linear iterative near-field phase retrieval (LIPR) for dual-energy x-ray imaging and material discrimination.

Near-field x-ray refraction (phase) contrast is unavoidable in many lab-based micro-CT imaging systems. Quantitative analysis of x-ray refraction (a.k.a. phase retrieval) is in general an under-constrained problem. Regularizing assumptions may not hold true for interesting samples; popular single-material methods are inappropriate for heterogeneous samples, leading to undesired blurring and/or over-sharpening. In this paper, we constrain and solve the phase-retrieval problem for heterogeneous objects, using the Alvarez-Macovski model for x-ray attenuation. Under this assumption we neglect Rayleigh scattering and pair production, considering only Compton scattering and the photoelectric effect. We formulate and test the resulting method to extract the material properties of density and atomic number from single-distance, dual-energy imaging of both strongly and weakly attenuating multi-material objects with polychromatic x-ray spectra. Simulation and experimental data are used to compare our proposed method with the Paganin single-material phase-retrieval algorithm, and an innovative interpretation of the data-constrained modeling phase-retrieval technique.

Multimodal imaging of the human knee down to the cellular level

Computed tomography reaches the best spatial resolution for the three-dimensional visualization of human tissues among the available nondestructive clinical imaging techniques. Nowadays, sub-millimeter voxel sizes are regularly obtained. Regarding investigations on true micrometer level, lab-based micro-CT (μCT) has become gold standard. The aim of the present study is firstly the hierarchical investigation of a human knee post mortem using hard X-ray μCT and secondly a multimodal imaging using absorption and phase contrast modes in order to investigate hard (bone) and soft (cartilage) tissues on the cellular level. After the visualization of the entire knee using a clinical CT, a hierarchical imaging study was performed using the lab-system nanotom® m. First, the entire knee was measured with a pixel length of 65 μm. The highest resolution with a pixel length of 3 μm could be achieved after extracting cylindrically shaped plugs from the femoral bones. For the visualization of the cartilage, grating-based phase contrast μCT (I13-2, Diamond Light Source) was performed. With an effective voxel size of 2.3 μm it was possible to visualize individual chondrocytes within the cartilage.