Biology subjects

Lee, P. D.

Publications and source records attributed to Lee, P. D..

29 records · Page 2Linked to original sources

bioRxiv2024

Synchrotron Tomography-Based Finite Element Analysis of Vertebral Endplate Loading Reveals Functional Roles for Architectural Features

Lower back pain is linked to vertebral biomechanics, with vertebral endplates (VEPs) playing a key role. Finite element modelling (FEM) is a powerful tool for studying VEP biomechanics but relies on accurate material property inputs, which remain difficult to obtain. Synchrotron computed tomography (sCT) allows for detailed visualisation of the microstructure of intact VEPs under near-physiological loads and, when coupled with digital volume correlation (DVC), can be used to quantify three-dimensional (3D) strain fields, providing experimental reference data for FEM validation. We developed an inversion pipeline to spatially couple DVC data with an image-based FE model, and thus to estimate the elastic properties of rat VEPs. On the first rat lumbar FEM, the pipeline estimated a VEP elastic modulus of 129 MPa and a Poissons ratio of 0.24. Welchs ANOVA revealed statistically significant differences between FEM and DVC strain distributions (p < 0.001) but with small effect sizes ({superscript 2} = 0.1%-0.6%), indicating high practical similarity. Its efficacy was further validated using Bland-Altman analysis, demonstrating over 95% spatial agreement between the FEM-predicted strains and the DVC measurements across multiple loading steps. The pipelines consistency was further evaluated across multiple rat lumbar FE models (n = 3), yielding an estimated VEP elastic modulus = 145 {+/-} 18 MPa and a Poissons ratio = 0.28 {+/-} 0.04. Statistically significant regional variations of strain distribution in VEPs were also identified (p < 0.05 to p < 0.001, {superscript 2} up to 41.8%). This study highlighted the efficacy of the developed pipeline in estimating the isotropic elastic modulus and Poissons ratio of VEP FEMs in a physiologically relevant, complex load transfer system. Our pipeline may be used in estimating properties of VEP in larger animals and humans.

bioengineering↗

bioRxiv2024

Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys

Efficient algorithms are needed to segment vasculature in new three-dimensional (3D) medical imaging datasets at scale for a wide range of research and clinical applications. Manual segmentation of vessels in images is time-consuming and expensive. Computational approaches are more scalable but have limitations in accuracy. We organized a global machine learning competition, engaging 1,401 participants, to help develop new deep learning methods for 3D blood vessel segmentation. This paper presents a detailed analysis of the top-performing solutions using manually curated 3D Hierarchical Phase-Contrast Tomography datasets of the human kidney, focusing on the segmentation accuracy and morphological analysis, thereby establishing a benchmark for future studies in blood vessel segmentation within phase-contrast tomography imaging.

bioinformatics↗

bioRxiv2024

Multimodal imaging reveals multiscale mechanical interplay in vertebral endplate microarchitecture during intervertebral disc loading

The function of all musculoskeletal joints depends on hierarchical structures spanning the molecular to whole joint scales. Investigating biomechanics across length scales requires correlative multiscale experimental methods. This study applies multimodal in situ synchrotron imaging techniques to spinal joints - focussing on the vertebral endplates - to explore relationships between structure and mechanical strain across spatial scales. Strain mapping using digital volume correlation combined with microarchitectural analysis reveals that high tensile and shear strains play a role in the cartilage to bone transition. Correlative imaging and diffraction show that bone contains narrower mineral nano-crystallites under greater compressive prestrain compared to calcified cartilage. We hypothesise that this multiscale structural adaptation supports the mechanical function of the intervertebral disc. Future applications of the techniques presented here have potential to help unravel biomechanical underpinnings of pathologies affecting mineralised tissue structure. The multiscale structure-function relationships uncovered here may inspire the design of biomaterials and orthopaedic implants.

bioengineering↗

bioRxiv2024

Micro to macro scale anatomical analysis of the human hippocampal arteries with synchrotron Hierarchical Phase-Contrast Tomography

PurposeTo date, no non-invasive imaging modality has been employed to profile the structural intricacies of the hippocampal arterial microvasculature in humans. We hypothesised that synchrotron-based imaging of the human hippocampus would enable precise characterisation of the arterial microvasculature. MethodsTwo preserved human brains from, a 69-year-old female and a 63-year-old male body donors were imaged using hierarchical phase-contrast tomography (HiP-CT) with synchrotron radiation at multiple voxel resolutions from 25.08 m down to 2.45 m. Subsequent manual and semi-automatic artery segmentation were performed followed by morphometric analyses. These data were compared to published data from alternative methodologies. ResultsHiP-CT made it possible to segment in context the arterial architecture of the human hippocampus. Our analysis identified anterior, medial and posterior hippocampal arteries arising from the P2 segment of the posterior cerebral artery on the image slices. We mapped arterial branches with external diameters greater than 50 m in the hippocampal region. We visualised vascular asymmetry and quantified arterial structures with diameters as small as 7 m. ConclusionsThrough the application of HiP-CT, we have provided the first imaging visualisation and quantification of the arterial system of the human hippocampus at high resolution in the context of whole brain imaging. Our results bridge the gap between anatomical and histological scales.

neuroscience↗

bioRxiv2024

Cryogenic non-invasive 3D X-ray phase-contrast imaging of unfixed, intact mouse joints reveals shifting chondrocyte hypertrophy across the endochondral interface

Objectivesi) develop and use a new cryogenically-enhanced phase contrast method to visualise hyaline articular cartilage (HAC); ii) to measure HAC, articular calcified cartilage (ACC) and total articular cartilage thicknesses in male STR/Ort (osteoarthritis, OA) and CBA (healthy) mouse tibial epiphyses, reflecting divergent OA predisposition, at three age timepoints chosen to reflect pre-OA, OA onset and late-progression; iii) to compare HAC, trans-zonal and ACC 3D chondrocyte anatomy in tibial epiphyses. MethodsSTR/Ort and CBA mouse knees (n=4 per age and strain group) were synchrotron-CT scanned at high-resolution while fresh frozen, without staining, fixation, dissection or dehydration of the joint capsule. Both cartilage thickness and cellular characteristics (chondrocyte n=420) were manually measured and statistically compared (SPSS). ResultsCryo-enhanced phase contrast allowed cartilage to be seen in full thickness with cellular detail. HAC was thicker in STR/Ort than age-matched CBA mice in 16/24 knee joint compartments and timepoints (all p<0.04). In contrast, HAC was thicker only in the posterior lateral femur of CBA mice at 10weeks (p<0.001, Table 1). ACC and total cartilage were also thicker in STR/Orts. Trans-zonal chondrocytes were smaller than ACC and HAC chondrocytes (p-values<0.001, volumes 878, 1,567m3 and 1,348m3 respectively). O_TBL View this table: org.highwire.dtl.DTLVardef@191d5a9org.highwire.dtl.DTLVardef@162523borg.highwire.dtl.DTLVardef@4b7caorg.highwire.dtl.DTLVardef@1be6005org.highwire.dtl.DTLVardef@192143d_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTABLE 1:C_FLOATNO O_TABLECAPTIONCondylar compartments in which HAC thickness was measured, and the presence or absence of a significant difference between STR/Ort and CBA mouse strains. * indicates a significant difference between strains (p<0.05). Note that the posterior lateral femur at 10 weeks of age is the only region in which STR/Ort mice have significantly thinner HAC than CBA mice. C_TABLECAPTION C_TBL ConclusionsCryogenically-enhanced phase-contrast imaging allowed cellular detail to be seen in 3D as never before in HAC in this (or any other) model. Our findings challenge current understanding by associating STR/Ort OA vulnerability with regions of thick, rather than thinning-with-age, cartilage. Our data affirm an association between excessively hypertrophic chondrocytes and OA is present in STR/Ort mice.

physiology↗

bioRxiv2023

Multidimensional Analysis of the Adult Human Heart in Health and Disease using Hierarchical Phase-Contrast Tomography (HiP-CT)

Cardiovascular diseases (CVDs) are a leading cause of death worldwide. Current clinical imaging modalities provide resolution adequate for diagnosis but are unable to provide detail of structural changes in the heart, across length-scales, necessary for understanding underlying pathophysiology of disease. Hierarchical Phase-Contrast Tomography (HiP-CT), using new (4th) generation synchrotron sources, potentially overcomes this limitation, allowing micron resolution imaging of intact adult organs with unprecedented detail. In this proof of principle study (n=2), we show the utility of HiP-CT to image whole adult human hearts ex-vivo: one control without known cardiac disease and one with multiple known cardiopulmonary pathologies. The resulting multiscale imaging was able to demonstrate exemplars of anatomy in each cardiac segment along with novel findings in the cardiac conduction system, from gross (20 um/voxel) to cellular scale (2.2 um/voxel), non-destructively, thereby bridging the gap between macroscopic and microscopic investigations. We propose that the technique represents a significant step in virtual autopsy methods for studying structural heart disease, facilitating research into abnormalities across scales and age-groups. It opens up possibilities for understanding and treating disease; and provides a cardiac blueprint with potential for in-silico simulation, device design, virtual surgical training, and bioengineered heart in the future.

pathology↗

bioRxiv2023

Micro to macro scale analysis of the intact human renal arterial tree with Synchrotron Tomography

The architecture of the kidney vasculature is essential for its function. Although structural profiling of the intact rodent kidney vasculature has been performed, it is challenging to map vascular architecture of larger human organs. We hypothesised that hierarchical phase-contrast tomography (HiP-CT) would enable quantitative analysis of the entire human kidney vasculature. Combining label-free HiP-CT imaging of an intact kidney from a 63-year-old male with topology network analysis, we quantitated vasculature architecture in the human kidney down to the scale of arterioles. Although human and rat kidney vascular topologies are comparable, vascular radius decreases at a significantly faster rate in humans as vessels branch from artery towards the cortex. At branching points of large vessels, radii are theoretically optimised to minimise flow resistance, an observation not found for smaller arterioles. Structural differences in the vasculature were found in different spatial zones of the kidney reflecting their unique functional roles. Overall, this represents the first time the entire arterial vasculature of a human kidney has been mapped providing essential inputs for computational models of kidney vascular flow and synthetic vascular architectures, with implications for understanding how the structure of individual blood vessels collectively scales to facilitate organ function.

bioengineering↗

bioRxiv2023

A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging

Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image quality and integrity of the samples. By combining in-line phase-contrast cineradiography with operando gas chromatography, we were able to track the onset and evolution of high-energy X-ray-induced gas bubbles in ethanol-embedded soft tissue samples for tens of minutes (2 to 3 times the typical scan times). We demonstrate quantitatively that vacuum degassing of the sample during preparation can significantly delay bubble formation, offering up to a twofold improvement in dose tolerance, depending on the tissue type. However, once nucleated, bubble growth is faster in degassed than undegassed samples, indicating their distinct metastable states at bubble onset. Gas chromatography analysis shows increased solvent vaporization concurrent with bubble formation, yet the quantities of dissolved gases remain unchanged. Coupling features extracted from the radiographs with computational analysis of bubble characteristics, we uncover dose-controlled kinetics and nucleation site-specific growth. These hallmark signatures provide quantitative constraints on the driving mechanisms of bubble formation and growth. Overall, the observations highlight bubble formation as a critical, yet often overlooked hurdle in upscaling X-ray imaging for biological tissues and soft materials and we offer an empirical foundation for their understanding and imaging protocol optimization. More importantly, our approaches establish a top-down scheme to decipher the complex, multiscale radiation-matter interactions in these applications. Significance statementBetter probing the X-ray radiation dose limit of bubble formation in biological tissue and developing mitigation methods is essential for improving imaging techniques involving X-ray, such as synchrotron X-ray tomography or crystallography. Here, we combined operando gas chromatography with in-line X-ray phase-contrast radiography on human lung and brain tissue to investigate bubble formation under high-energy X-ray irradiation. We demonstrate that vacuum degassing delays bubble nucleation up to a factor two, depending on the tissue type. Gas chromatography analysis showed increased solvent vaporization during bubble formation; however, the quantities of dissolved gases remained unchanged. Moreover, depending on the nucleation site, bubble growth can be geometrically constrained by sample microstructure, which influence its dynamics.

biochemistry↗

bioRxiv2022

Preparation of large biological samples for high-resolution, hierarchical, multi-modal imaging

Imaging the different scales of biological tissue is essential for understanding healthy organ behavior and pathophysiological changes. X-ray micro-tomography using both laboratory ({micro}CT) and synchrotron sources (sCT) is a promising tool to image the 3D morphology at the macro- and micro-scale of large samples, including intact human organs. Preparation of large samples for high resolution imaging techniques remains a challenge due to limitations with current methods, such as sample shrinkage, insufficient contrast, movement of the sample and bubble formation during mounting or scanning. Here, we describe a protocol to prepare, stabilize, and image large soft-tissue samples with X-ray microtomography. We demonstrate the protocol using intact human organs and Hierarchical Phase-Contrast Tomography (HiP-CT) imaging at the European Synchrotron Radiation Facility, but the protocol is equally applicable to a range of biological samples, including complete organisms, for both laboratory and synchrotron source tomography. Our protocol enhances the contrast of the sample, while preventing sample motion during the scan, even in case of different sample orientations. Bubbles trapped during mounting and those formed during scanning (in case of synchrotron X-ray imaging) are mitigated by multiple degassing steps. The sample preparation is also compatible with magnetic resonance imaging (MRI), CT, and histological observation. We describe a protocol for sample preparation and mounting which requires 25 to 34 days for a large organ such as an intact human brain or heart. This preparation time varies depending on the composition, size, and fragility of the tissue. Use of the protocol enables scanning of intact organs with a diameter of 150 mm with a local pixel size of one micron using HiP-CT.

physiology↗

bioRxiv2021

A multiscale X-ray phase-contrast tomography dataset of whole human left lung

Technological advancements in X-ray imaging using bright and coherent synchrotron sources now allows to decouple sample size and resolution, while maintaining high sensitivity to the microstructure of soft, partially dehydrated tissues. The recently developed imaging technique, hierarchical phase-contrast tomography, is a comprehensive approach to address the challenge of organ-scale (up to tens of centimeters) soft tissue imaging with resolution and sensitivity down to the cellular level. Using this technique, we imaged ex vivo an entire human left lung at an isotropic voxel size of 25.08 m along with local zooms down to 6.05 - 6.5 m and 2.45 - 2.5 m in voxel size. The high tissue contrast offered by the fourth-generation synchrotron source at the European Synchrotron Radiation Facility reveals complex multiscale anatomical constitution of the human lung from the macroscopic (centimeter) down to the microscopic (micrometer) scale. The dataset provides complete organ-scale 3D information of the secondary pulmonary lobules and delineates the microstructure of lung nodules with unprecedented detail.

physiology↗

bioRxiv2021

Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography

Human organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique utilising the European Synchrotron Radiation Facilitys Extremely Brilliant Source: the worlds first high-energy 4th generation X-ray source. HiP-CT enabled three-dimensional and non-destructive imaging at near-micron resolution in soft tissues at one hundred thousand times the voxel size whilst maintaining the organs structure. We applied HiP-CT to image five intact human parenchymal organs: brain, lung, heart, kidney and spleen. These were hierarchically assessed with HiP-CT, providing a structural overview of the whole organ alongside detail of the organs individual functional units and cells. The potential applications of HiP-CT were demonstrated through quantification and morphometry of glomeruli in an intact human kidney, and identification of regional changes to the architecture of the air-tissue interface and alveolar morphology in the lung of a deceased COVID-19 patient. Overall, we show that HiP-CT is a powerful tool which can provide a comprehensive picture of structural information for whole intact human organs, encompassing precise details on functional units and their constituent cells to better understand human health and disease.

physiology↗