Biology subjects

Brunet, J.

Publications and source records attributed to Brunet, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Revealing multiscale architecture of the intact human spine using hierarchical phase contrast tomography

Background: Computed tomography (CT) and magnetic resonance imaging (MRI) provide detailed clinical assessment of the human spine; however, their millimeter-scale spatial resolution limits direct visualization of tissue microarchitecture and interfaces. Hierarchical phase-contrast tomography (HiP-CT) enables ex vivo non-destructive, micron-resolution imaging of intact human organs without exogenous contrast agents, extending anatomical assessment to spatial scales inaccessible to conventional clinical imaging. Purpose: To evaluate the capability of HiP-CT to visualize macro- to microanatomy of an intact adult human spine ex vivo. Methods: An intact spine (C1-L5) from a 62-year-old male donor without known skeletal disease was formalin-fixed and imaged by HiP-CT at the European Synchrotron. Whole-spine imaging was performed at 16.26 m isotropic voxels, with selected regions of interest imaged using 2.2 m voxels. Ex vivo MRI using clinical sequences was performed for anatomical comparison. Three-dimensional segmentation and quantitative analyses included intervertebral disc (IVD) grading, annulus fibrosus fiber tracing, and vertebral trabecular micro-morphometry. Results: HiP-CT enabled high spatial-resolution, multiscale imaging of the intact human spine, simultaneously visualizing vertebral bone and endplate, IVDs, spinal cord and meninges, nerve roots and ganglia, vasculature, ligaments, and musculature. Three-dimensional segmentation and virtual sectioning mapped neurovascular anatomy and vertebral vascular supply, without exogenous contrast enhancement, while preserving their relationships with surrounding tissues. Whole-spine images enabled quantitative analysis of annulus fibrosus fiber organization and vertebral trabecular microarchitecture, permitting the detection of focal posterolateral fiber disruption at the L4-L5 IVD and regional differences in trabecular architecture between cervical and lumbar vertebral bodies. Local tomography resolved annulus fibrosus lamellae, vertebral endplate Haversian systems, and facet joint hyaline cartilage at micron resolution. Conclusions: HiP-CT enables non-destructive, multiscale three-dimensional imaging of the intact human spine while preserving tissue relationships across spatial scales and hard-soft tissue boundaries. HiP-CT could provide an ex vivo microanatomical reference for future correlation with clinical imaging investigations of spinal disease and in the development and validation of imaging biomarkers.

bioengineering↗

bioRxiv2026

Articular calcified cartilage microarchitecture has a predictive role in abnormal osteochondral strain distributions in murine age-related osteoarthritis

Even though osteoarthritis is considered a disease of the whole joint, integrated analysis of articular calcified cartilage (ACC) behaviour with adjacent tissues remains a persistent limitation. Herein, we performed synchrotron X-ray computed tomography in intact loaded joints and coupled anatomical analysis with digital volume correlation to examine whether microarchitectural ACC features serve as predictive mechano-biomarkers of osteoarthritis. We reveal that male osteoarthritis-prone STR/Ort mice have thicker yet more porous ACC that contains larger but less spherical chondrocyte lacunae than their healthy parental-control CBA mice. This was linked to asymmetrical distribution of tensile and compressive strains generated under physiological loads in the ACC and underlying subchondral bone in tibial epiphyses of STR/Ort mice. Together these data suggest that murine ACC microarchitecture has a mechano-predictive role in age-related osteoarthritis.

physiology↗

bioRxiv2026

Multiscale mapping of venous remodelling in idiopathic pulmonary fibrosis

The integrity of the pulmonary vasculature is a key determinant of lung health, yet challenges in visualisation and quantification have hindered interrogation of its pathophysiological role in chronic lung disease. Here, we align recent advances in microscale image acquisition with novel computer vision-based vessel segmentation models to demonstrate expansion of the bronchial and pulmonary veins across varying severities of tissue remodelling in idiopathic pulmonary fibrosis (IPF). Relating these imaging findings to molecular data in control, mild, and severe fibrosis, we show that bronchial venous endothelial cells expand beyond their physiological peribronchial niche even in mild disease, acquiring persistent angiogenic, inflammatory, and matrix-remodelling programmes that define a specialised fibrovascular-immune interface. Finally, we relate these microscale and molecular observations to clinical CT imaging, demonstrating that intrapulmonary vein enlargement independently associates with worsened survival across three IPF cohorts. Collectively, our multimodal, multiscale approach connects previously unresolved three-dimensional venous architecture to its molecular endothelial correlate, establishing venous enlargement as a prognostically significant and clinically relevant feature of IPF. Our analytical approach also demonstrates how biological discoveries made in intact ex vivo human organs can translate into measurable phenotypes in living patients, providing a template for other organs and diseases.

pathology↗

bioRxiv2026

BigHeart: Mapping connectivity in the adult human heart at the micron scale

The human heart depends on coordinated muscular, electrical, vascular, lymphatic, and neural systems, but their three-dimensional relationships remain unresolved at microscopic resolution across an intact adult organ. Using hierarchical phase-contrast tomography, we generated a continuous three-dimensional structural reference of a whole adult human heart at 8.01 micrometer isotropic voxel size, without sectioning or staining. Organ-wide imaging revealed hierarchical myocardial architecture, and quantitative orientation analysis identified regional differences in myocardial cell aggregate organization. The atrioventricular conduction axis was traced into a distinct subendocardial Purkinje network interfacing with working myocardium. Integrated segmentation showed that coronary vessels, lymphatic collectors, and autonomic nerves occupy shared epicardial corridors. This publicly accessible dataset integrates cardiac systems within a common spatial framework for anatomy, computational modeling, and future molecular atlases.

physiology↗

bioRxiv2026

Multimodal Hypersampling of the adult human heart resolves tissue-specific cell states and disease-associated variants

Cardiovascular diseases often arise in anatomically specialised regions of the heart that remain poorly represented in existing single-cell and spatial atlas references. Here we profiled 28 regions of the adult human heart from 36 donors, combining paired single-nucleus RNA and chromatin accessibility assays with spatial transcriptomics. The resulting atlas integrates 1,059,175 expression profiles and 452,614 chromatin accessibility profiles, and defines spatial niches across the heart. In cardiac valves, we identify a valve fibroblast-macrophage niche that is polarised to the non-fibrosa surface and expands with age. Aortic stenosis genetic risk was enriched in inflammatory regulatory programmes of the Valve Fibroblast Immune cell state. In pulmonary veins, we define PITX2+ Myocardial Sleeve Cells, a region-restricted cardiomyocyte population in which a fine-mapped 4q25 atrial fibrillation variant intersects a cell type-specific open chromatin region. In coronary arteries, we resolve a RUNX1-marked synthetic smooth muscle layer in the subintima that provides a molecular identity for diffuse intimal thickening, a constitutive feature of the healthy vessel wall and a substrate for atherosclerosis, and show by perturbation in human smooth muscle cells that RUNX1 promotes cell-cycle entry while restraining inflammatory cytokine gene expression. Finally, allele-specific accessibility together with deep learning models fine-tuned to predict regulatory activity from DNA sequence identify cell type-specific regulatory effects at GWAS loci for atrial fibrillation, coronary artery disease and calcific aortic valve stenosis, including a variant whose Valve Fibroblast-specific effect on the polyamine transporter ATP13A3 is opposite in direction to the effect seen in bulk-tissue eQTL references that lack valve cells. Together with these cardiac sequence models and CardioSleuth, an AI-powered exploration engine for cardiac regulatory effects, this atlas links cardiac anatomy, gene regulation and disease genetics at single-cell resolution. By placing genetic risk in its precise cellular and anatomical context, it provides a foundation for mechanistic disease understanding, cell-state-specific therapeutic target nomination, and improved interpretation of inherited cardiovascular risk to inform future therapy and management.

Cell Biology↗

bioRxiv2026

Revisiting the Structure of the Ventricular Myocardium in Tetralogy of Fallot Using Hierarchical Phase Contrast Tomography and Structure Tensor Analysis

BACKGROUNDIn tetralogy of Fallot (ToF), changes in right ventricular function (as assessed by strain or TAPSE) reflect altered myocardial structure. Direct three-dimensional anatomical evidence supporting these changes remains limited. The objective of this study was to non-destructively characterize myocardial architecture in pediatric ToF hearts using Hierarchical Phase-Contrast Tomography (HiP-CT) and structure tensor analysis. METHODSTwenty ToF and control pediatric hearts were imaged at the European Synchrotron, ESRF. Myocyte orientation was assessed through structure tensor analysis and distributed high-performance computing. A region-specific framework was developed for analysis of the right ventricle. The predominant direction of myocardial aggregates (their helical angle) was compared across ventricular regions. RESULTSSignificant differences in orientation were found in all ToF segments vs controls (left ventricle, right ventricular inlet, right ventricular outflow tract, septum; p < 0.001). Myocytes in the ToF right ventricular inlet were more circumferential overall, with regional heterogeneity. Contrary to traditional models, no discrete middle layer was found in the ToF right ventricle; instead, a shift towards more circumferentially orientated myocytes and disrupted septal and outflow components was observed. Right ventricular contribution to the septum was greater in ToF (47.3% vs 34.0%; p = 0.0026), with extension of ventricular insertion points disrupting septal architecture. There were more longitudinally oriented myocytes in the ToF right ventricular outflow tract, consistent with hypertrophied septoparietal trabeculations. Left ventricular structure in ToF demonstrated a greater proportion of circumferentially oriented myocytes compared to controls. CONCLUSIONSWe reveal profound alterations in ToF myocardial organization which broadly align with clinical observations and provide the first open-access HiP-CT congenital heart disease data as a basis for future computational modelling. Clinical PerspectiveWhole-heart HiP-CT demonstrates a loss of normal LV-RV distinction in the ToF myocardium, alongside extensive septal disarray. These findings provide a structural substrate for RV dysfunction, ventricular-ventricular interaction, and arrhythmogenesis in ToF, challenging traditional layer-based models of ventricular myocardium. Understanding myocardial organization as a continuous, developmentally patterned three-dimensional structure is essential for accurate interpretation of ventricular mechanics and disease progression. Although HiP-CT imaging is not applicable in vivo, the structural phenotypes identified in this study generate testable hypotheses for clinical imaging. Future work should focus on correlating ex-vivo measures with in-vivo imaging markers derived from cardiac magnetic resonance, including strain, TAPSE, and assessment of ventricular interactions. Investigating myocardial phenotype across the life-course, from fetal life to adulthood, paired with multi-omics mapped to these three-dimensional datasets, may help elucidate mechanisms underlying myocardial remodeling in ToF and support the development of novel therapeutic approaches.

physiology↗

bioRxiv2026

Bridging the microstructural gap in human connectomics using hierarchical phase-contrast tomography as a reference for diffusion MRI in the human brain

Diffusion MRI (dMRI) allows us to image the human connectome non-invasively, yet it provides indirect estimates of axonal orientations based on the diffusion of water molecules in millimeter-scale voxels, hence struggling to resolve complex micrometer-scale fiber geometries. Invasive methods for imaging axonal orientations ex vivo, e.g. histology, are destructive and limited to small volumes, creating a critical need for a non-destructive modality for imaging microscopic fiber orientations in 3D. Here, we use Hierarchical Phase-Contrast Tomography (HiP-CT) to characterize white matter architecture at the microscale. Applying structure-tensor analysis to HiP-CT data, we compute fiber Orientation Distribution Functions and perform tractography analogous to dMRI. Across multiple brain regions, HiP-CT derived fiber architecture shows strong correspondence with that derived from dMRI while revealing substantially greater microstructural complexity. Despite its label-free nature, we demonstrate that vascular structures minimally confound HiP-CT orientation estimates. These results establish HiP-CT as a reference microscopic modality that can complement dMRI in multi-scale studies of white-matter organization.

neuroscience↗

bioRxiv2026

Hierarchical X-ray microscopy and mesoscopic diffusion MRI in the same brain reveal the human connectome across scales

We present a multimodal pipeline for 3D imaging of cerebral white-matter archi-tecture across scales, from whole-brain axonal projections down to individual myelinated axons. After diffusion MRI, an adult ex vivo human hemisphere undergoes label-free imaging with Hierarchical Phase-Contrast Tomography (HiP-CT) from 20 {micro}m/voxel in the whole hemisphere to 2 {micro}m/voxel in areas of interest, with intrinsic cross-scale alignment. A 4 cm tissue block extracted from the hemisphere is reimaged with HiP-CT at 0.857 {micro}m/voxel, enabling direct visualisation of single myelinated axons. After osmium staining, micro-CT at 0.364 {micro}m/voxel and electron microscopy at 4 nm/voxel are acquired in biop-sies from the tissue block to validate the presence of myelinated axons in the label-free HiP-CT contrast. Spanning three orders of magnitude in resolution, these co-registered multimodal datasets bridge microscopic wiring and macro-scopic brain organisation, providing a foundation for anatomically grounded whole-brain connectomics.

neuroscience↗

bioRxiv2026

Neuroanatomy of the clitoris

The clitoris is one of the least studied organs of the human body. The detailed anatomy of the clitoris is challenging to address through a gross dissection, as most of its parts are embedded internally, surrounded by pubic bone and several pelvic organs. While clinical imaging methods such as magnetic resonance imaging can capture the gross 3D morphology, they lack the spatial resolution required to resolve the detailed structures. In this study, we generated micron-scale computed tomography images of the female pelvises, leveraging a synchrotron radiation X-ray source. This unique data revealed the complex trajectory of the dorsal nerve of the clitoris, the main sensory nerve of the clitoris. Notably, the nerve trunks within the clitoral glans were revealed, with the maximum diameter ranging from 0.2 to 0.7 mm. They showed a tree-like branching pattern projecting towards the surface of the glans. We also revealed that some branches of the dorsal nerve of the clitoris ramify to innervate the clitoral hood and mons pubis. Finally, the posterior labial nerve, a branch of the perineal nerves, was shown to innervate the surroundings of the clitoris and the labial structures. These findings have an immediate impact on operations performed around the vulva area, such as gender-affirmation surgery and reconstruction surgery after genital mutilation.

neuroscience↗

bioRxiv2026

The Extremely Brilliant Brain: An Isotropic Microscale Human Brain Dataset

We present an isotropic 7.72 {micro}m/voxel post-mortem human brain dataset acquired using Hierarchical Phase-Contrast Tomography (HiP-CT) at the ESRF Extremely Brilliant Source, beamline BM18. This fills a critical gap between whole-brain MRI at 100 {micro}m resolution and serial-section histological reconstructions at 20 {micro}m or finer. HiP-CT contrast, derived from X-ray phase shifts, enables rich 3D visualisation of complex neuroanatomy including white-matter bundles, microvasculature, and sub-nuclei. We provide open-source workflows for online data exploration, subvolume download, segmentation, and reintegration of analyses into the full dataset. We demonstrate the potential of this resource by tracing vasculature over long distances, segmenting nuclei, and extracting whitematter orientations with 3D structure-tensor analysis. High-resolution human brain datasets are transformative for quantitative neuroanatomy, circuit mapping, and validation of clinical imaging; this openly available resource is a critical step for global access to next-generation multiscale brain imaging.

neuroscience↗

bioRxiv2026

Hierarchical Phase-Contrast Tomography Imaging: Applicability in biomedical research

ObjectivesHierarchical Phase-Contrast Tomography (HiP-CT) enables non-destructive, multi-scale imaging of whole human organs. We describe how HiP-CT is utilized for biomedical research within the Human Organ Atlas Hub through three case studies: mapping the enteric nervous system (ENS) of the human colon, analysing myocardial and AV conduction architecture in Tetralogy of Fallot (TOF), and characterizing ductal organization in breast carcinoma. The challenges we faced with this novel biomedical data are discussed. MethodsWhole-organ and region-of-interest scans of three types of human organs were acquired at the European Synchrotron Radiation Facility (ESRF) with isotropic voxel sizes ranging from 20 {micro}m to 0.8 {micro}m. For the colon, voxel binning and RootPainter were employed to tackle data size to segment the ENS. For the heart, voxel-wise myocyte orientation mapping was calculated in terabyte-scale datasets with a high-performance computational framework (Cardiotensor). Breast carcinoma samples were correlated with histopathology for structure validation. ResultsHiP-CT revealed the large-scale organization of the ENS in the colon, enabling visualisation of the 3D structures of the ENS across the colon In TOF hearts, analysis uncovered abnormal myocardial structure and heterogeneous conduction system morphology. In breast carcinoma, HiP-CT resolved the full hierarchy of ductal structures and vascular relationships within tumour and peritumoral regions. ConclusionsHiP-CT provides unprecedented, hierarchical insight into intact human organ structure, bridging the gap between histology and radiology. Advances in knowledgeHiP-CT establishes a new ex vivo radiological modality capable of linking microscale pathology to whole-organ context, advancing translational research in neurogastroenterology, cardiology, and oncology

biophysics↗

bioRxiv2026

Evolution of Hierarchical Phase-Contrast Tomography on the European Synchrotron beamlines BM05 and BM18: a whole adult human brain imaging case study

Hierarchical Phase-Contrast Tomography (HiP-CT) was recently developed to enable the ex-vivo imaging of human organs at multiple scales from whole organ down to cellular level. Using whole adult human brain imaging as a case study, this manuscript shows the evolution of this technique from its initial development at the BM05 beamline to its transition and current status at BM18. Thanks to the higher coherence, larger beam size, higher energies and larger propagation distances available at BM18 and due to the European Synchrotrons Extremely Brilliant Source upgrade (ESRF-EBS), this transition resulted in significantly improved data quality, resolution, sensitivity and speed. More recently, the implementation of a new generation of larger sCMOS cameras, helical scanning (including dedicated reconstruction algorithm developments), binning at the chip and projections levels, and the design of high-efficiency optics allowed to progressively improve the trade-off between dose and image quality, while simultaneously reducing scanning times. All these acquisition schemes present the current status of full organ imaging using HiP-CT and represent the constant efforts for the improvement of the technique towards the investigation of human organs in health, disease and aging. SynopsisThis manuscript shows the evolution of Hierarchical Phase-Contrast Tomography (HiP-CT) from its origins at the BM05 beamline to its transition to BM18 (ESRF-EBS). The novel hardware and scanning approach developments resulted in significantly improved data quality, resolution, sensitivity and speed. The case of whole adult brain imaging is presented to demonstrate the current possibilities of full organ imaging with local micron resolution using HiP-CT.

neuroscience↗

bioRxiv2025

Resolving near-micron scale features within a whole sheep head using Hierarchical Phase-Contrast Tomography

BackgroundHierarchical Phase-Contrast Tomography (HiP-CT) was developed to image ex vivo intact human soft-tissue organs with local near-micron scale resolution. PurposeWe demonstrate the application of HiP-CT in combination with the recently developed Eikonal Phase Retrieval (EPR) for resolving anatomical features in large hard and soft tissue structures on a sheep head, and show the applicability for zooming to resolve anatomical features with near-micron scale resolution. Materials and MethodsWe imaged an entire skinned sheep head prepared in 70 % ethanol with HiP-CT at an isotropic voxel size of 16.5 {micro}m using the recently developed Eikonal Phase Retrieval (EPR) to reduce artefacts from bones. Local tomography zooms were taken in regions of interest: the eye (4.23 {micro}m voxels) and the coronal suture (2.20 {micro}m voxels). To compare to clinical imaging, we acquired T2-weighted MRI and CT of the sheep head and evaluated the contrast-to-noise ratio for differentiation of white and grey matter in the brain for all modalities. Further evaluations on HiP-CT images include structure tensor analysis for structural orientation in the brain as well as fibre tracking in the coronal suture. ResultsHiP-CT combined with EPR achieved high contrast for both hard and soft tissue. Comparison to MRI showed similar soft-tissue contrast, but much higher spatial resolution. Structure tensor analysis in the brain revealed the orientation of the major white matter bundles. In the eye, near-micron scale features such as retinal layers and the bundles in the optic nerve were visualized. Fiber tracking allowed analysis of the orientation of collagen fiber bundles in the coronal suture. ConclusionThis work highlights the potential of HiP-CT to image a complete sheep head, ex vivo, and hierarchically zoom without sectioning to resolve few-microns features locally, enabling comprehensive three-dimensional visualization of intricate cranial structures and their spatial interrelations. Summary statementTechnical developments in HiP-CT enable ex vivo X-ray imaging of an intact sheep head with local resolution to near-micron scale, demonstrating future viability on a human head. Key resultsO_LIA whole sheep head was imaged with synchrotron-based hierarchical phase-contrast tomography coupled with Eikonal Phase-retrieval with 16.5 {micro}m isotropic voxels. C_LIO_LIThe high contrast for both hard and soft tissue enabled differentiation of brain white and grey matter, the optic nerve and bone features within the skull. C_LIO_LILocal tomography zoom scans in an eye (4.23 {micro}m voxels) and coronal suture (2.20 {micro}m voxels) allowed visualization and analysis of near-micron sized features. C_LI

bioengineering↗

bioRxiv2025

In situ profiling of nanoscale displacements uncovers mechano-architectural predictors of osteoarthritis emergence

Mechanical and anatomical interplay between the distinct tissues of the knee joint is essential for maintaining functional integrity during healthy ageing and contributes to the mechanisms that drive osteoarthritis (OA). In this study, we investigate how age- and disease-associated alterations in joint anatomy influence load transmission and tissue-level strain distribution. Using full-field synchrotron X-ray computed tomography coupled with digital volume correlation, we hierarchically characterised in situ nanoscale strains generated in response to mechanical loading across the tibial epiphysis. Our findings show that greater compressive strains accumulate in the articular condyle of male OA-prone (STR/Ort) epiphyses. Finite element modelling further demonstrated that these strain concentrations are associated with reduced load-bearing capacity, which arise from architectural differences localised to the subchondral bone plate. By coupling high-resolution imaging with computational modelling, our work provides new insights into how structural-function changes to joint anatomy contribute to the initiation and progression of mechanically driven OA. Our approach offers a means to identify early imaging biomarkers prior to OA diagnosis and has potential for monitoring interventions aimed at preserving joint mechanics while promoting healthy joint ageing.

bioengineering↗

bioRxiv2025

The Heterogeneous Nature of Atrioventricular Conduction Tissues in Tetralogy of Fallot demonstrated by Hierarchical Phase-contrast Tomography - redefining the anatomic substrate

ObjectivesPostoperative arrhythmias are frequent after Tetralogy of Fallot (ToF) repair, yet anatomic substrate and preventive strategies remain poorly defined. Using hierarchical phase-contrast tomography (HiP-CT) the atrioventricular conduction system in pediatric ToF specimens was investigated non-destructively and in 3D. MethodsEighteen whole-heart specimens (11 ToF, 7 controls) were imaged at the European Synchrotron, ESRF. Segmentation and 3D renderings demonstrated gross morphology. Morphology, size, depth and course of the non-branching bundle and right bundle branch (RBB) were quantified using custom computational pipelines. Segmentations were visualized in VheaRts, a Unity3D-based XR platform. ResultsThe ToF conduction system was more draped than in controls, bilaterally spanning the septum, resembling early embryonic architecture. The RBB was variable in origin, course and morphologic structure with significantly smaller indexed cross-sectional area in native ToF versus controls (0.05 {+/-} 0.20 vs 0.50 {+/-} 0.20 mm{superscript 2}, p = 0.005). One anomalous fasciculo-ventricular connection and six dead-end tracts were found. Regions at surgical risk included the posterior-inferior margin of the ventricular septal defect (VSD) and the septal crest along its nadir. The superior margin of the VSD at its intersection with the aortic root was free of conduction tissue. The HiP-CT to VR pipeline enabled interactive 3D visualization of conduction pathways relative to key structures. ConclusionsThis first pediatric cardiac HiP-CT series reveals a broader anomalous conduction complex in ToF, including variable RBB origin and hypoplasia, providing insight into preoperative vulnerability, arrhythmia, and surgical risk. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/692356v1_fig7.gif" ALT="Figure 7"> View larger version (50K): org.highwire.dtl.DTLVardef@1b39e89org.highwire.dtl.DTLVardef@16d49c2org.highwire.dtl.DTLVardef@5884borg.highwire.dtl.DTLVardef@136fc24_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 7:C_FLOATNO Graphical Abstract C_FIG

developmental biology↗

bioRxiv2025

Multimodal X-ray imaging reveals hierarchical fibre mechanics

Fibrous materials--ranging from connective tissues to engineered composites--are vital to many biological and man-made systems, optimised to withstand complex in-operando or in-vivo loading. The spines intervertebral discs (IVD) load-bearing capacity depends on a hierarchical extracellular matrix, where plywood-like lamellae of collagen fibres in the annulus fibrosus contain nanometre-scale fibrils built from staggered triple-helical monomers. How intact IVDs couple fibril-scale mechanics to fibre-scale organisation under load remains unresolved. Here we introduce TomoSAXS, a full-field 3D small-angle X-ray scattering tomography that maps fibril-to-fibre mechanics across an intact tissue. We show that intrafibrillar molecular pre-strain (D-period stagger) is lamellar textured and tightly correlated with microscale fibre strain. Pre-strain is inversely related to fibril strain and its variability, consistent with load-sharing through molecular unwinding. Radial strain bridges and high-curvature zones at the annulus fibrosus-nucleus pulposus interfaces emerge as critical regulators of local mechanics. These findings reveal concerted fibril-fibre interactions that sustain mechanical equilibrium in the IVD, preserving elasticity and shape. More broadly, TomoSAXS establishes a platform to visualise nano- to micro-scale matrix mechanics across biological and synthetic fibrous materials, with applications in ageing and disease, therapeutic evaluation, and the design of bio-based and bioinspired materials.

bioengineering↗

bioRxiv2025

The Human Organ Atlas

We present the Human Organ Atlas (HOA), an open data repository making accessible multiscale 3D imaging of human organs. The repository also provides software tools and training resources enabling worldwide access, sharing, and analysis of these datasets, facilitating further research and the continued expansion of the HOA. The images are generated using a synchrotron imaging technique - Hierarchical Phase-Contrast Tomography (HiP-CT) that uses the ESRFs Extremely Brilliant Source, spanning whole organ imaging at around 20 m/voxel with local volumes of interest within the intact organs imaged down to [~] 1 m/voxel. This offers a comprehensive exploration of human anatomy, providing unparalleled insights into intricate structures and spatial relationships. The Human Organ Atlas offers researchers, clinicians, and educators a valuable resource for anatomical study, image analysis, medical education, and large-scale data mining.

bioinformatics↗

bioRxiv2025

Multiscale Segmentation using Hierarchical Phase-contrast Tomography and Deep Learning

Biomedical systems span multiple spatial scales, encompassing tiny functional units to entire organs. Interpreting these systems through image segmentation requires the effective propagation and integration of information across different scales. However, most existing segmentation methods are optimised for single-scale imaging modalities, limiting their ability to capture and analyse small functional units throughout complete human organs. To facilitate multiscale biomedical image segmentation, we utilised Hierarchical Phase-Contrast Tomography (HiP-CT), an advanced imaging modality that can generate 3D multiscale datasets from high-resolution volumes of interest (VOIs) at ca. 1 {micro}m/voxel to whole-organ scans at ca. 20 {micro}m/voxel. Building on these hierarchical multiscale datasets, we developed a deep learning-based segmentation pipeline that is initially trained on manually annotated high-resolution HiP-CT data and then extended to lower-resolution whole-organ scans using pseudo-labels generated from high-resolution predictions and multiscale image registration. As a case study, we focused on glomeruli in human kidneys, benchmarking four 3D deep learning models for biomedical image segmentation on a manually annotated high-resolution dataset extracted from VOIs, at 2.58 to ca. 5 {micro}m/voxel, of four human kidneys. Among them, nnUNet demonstrated the best performance, achieving an average test Dice score of 0.906, and was subsequently used as the baseline model for multiscale segmentation in the pipeline. Applying this pipeline to two low-resolution full-organ data at ca. 25 {micro}m/voxel, the model identified 1,019,890 and 231,179 glomeruli in a 62-year-old donor without kidney diseases and a 94-year-old hypertensive donor, enabling comprehensive morphological analyses, including cortical spatial statistics and glomerular distributions, which aligned well with previous anatomical studies. Our results highlight the effectiveness of the proposed pipeline for segmenting small functional units in multiscale bioimaging datasets and suggest its broader applicability to other organ systems.

bioinformatics↗