Multiscale pink-beam microCT imaging at the ESRF-ID17 biomedical beamline

Insights into the Osteosarcoma Microenvironment: Multiscale Analysis of Structural and Mineral Heterogeneity

Osteosarcoma (OS) is a malignant and heterogeneous disease that typically originates in the long bones of children and adolescents. It is characterized by the presence of immature cells having an aggressive phenotype and rapid uncontrolled proliferation. OS progression induces significant molecular and cellular changes locally within the bone, resulting in the development of an abnormal tumor microenvironment (TME). The OS TME plays a crucial role in tumor progression and development, however, the precise effects of OS on bone structure and mineralization still remain poorly understood. In this study, we examined the OS TME by analyzing samples from osteoblastic, parosteal, and periosteal osteosarcomas. Employing advanced synchrotron-based X-ray techniques, we performed a multiscale analysis to evaluate the structural and mineral complexity of tumor-affected bone. Our results revealed marked morphological differences among the osteosarcoma subtypes, while confirming that biomineralization remains active through the production of hydroxyapatite (HA). X-ray diffraction identified two distinct hydroxyapatite crystalline phases across all samples, suggesting a critical behavior of minerals in bone. Additionally, we observed that the bone mineral structure in periosteal and parosteal osteosarcomas exhibited crystal deformations along the c-axis, whereas the osteoblastic osteosarcoma displayed a mineral profile comparable to control bone. Micro-X-ray absorption near-edge spectroscopy revealed the occurrence of a dysregulated biomineralization in the parosteal and periosteal subtypes, marked by the presence of calcium compounds different from HA, in contrast to the mature mineral state found in the osteoblastic variant. These findings highlight the complexity of osteosarcoma repercussion on bone tissue, offering new insights into the interactions within the OS TME. STATEMENT OF SIGNIFICANCE: This study investigates the tumor microenvironment (TME) of osteosarcoma (OS), a rare and aggressive bone cancer mainly affecting children and adolescents. Using advanced synchrotron-based X-ray techniques, we analyzed structural and mineral alterations in bone from three OS subtypes: osteoblastic, parosteal, and periosteal. The results reveal distinct subtype-specific differences in bone mineralization and crystallinity, highlighting the heterogeneity of OS and the pivotal role of its microenvironment in driving disease progression. This research contributes to our understanding of OS pathophysiology and provides foundation for future studies aimed at developing targeted therapies and improving diagnostic approaches.

High-speed computed tomography to visualise the 3D microstructural dynamics of oil uptake in deep-fried foods

Oil serves as both the high-temperature heating medium during deep-frying unit operations and a contributor to the organoleptic properties of deep-fried foods. Its absorption is linked to structural deformations during deep-frying that create pathways for oil to enter the food microstructure. This study proposes a 4D imaging system (three spatial dimensions and time) using fast synchrotron radiation tomography for in-situ visualisation during deep-frying and post-frying cooling to understand the mechanisms behind oil absorption. Using wheat flour dough as a model food system, we investigate the impact of frying oil temperature on structural deformation and pore formation in the crust and core, pore structure integrity, and oil uptake and distribution. The results show that higher temperatures lead to the formation of a distinguished crust with surface openings, facilitating greater oil absorption in small crust pores through capillary action. Comparing 3D microstructures attained at different frying oil temperatures, final oil content reaches 14.4% at 180 °C, 12.2% at 150 °C, and 1.3% at 120 °C, with temperature-dependent structural changes in pore connectivity and network integrity significantly impacting the rate of oil uptake and its distribution.

3D virtual histology of rodent and primate cochleae with multi-scale phase-contrast X-ray tomography

Multi-scale X-ray phase contrast tomography (XPCT) enables three-dimensional (3D), non-destructive imaging of intact small animal cochlea and apical cochlear turns. Here we report on post-mortem imaging of excised non-human primate and rodent cochleae at different [Formula: see text]-CT and nano-CT synchrotron instruments. We explore different sample embeddings, stainings and imaging regimes. Under optimized conditions of sample preparation, instrumentation, imaging protocol, and phase retrieval, high image quality and detail level can be achieved in 3D reconstructions. The showcased instrumentation and imaging protocols along with the reconstucted volumes can serve as benchmarks and reference for multi-scale microanatomy and 3D histology. The provided benchmarks and imaging protocols of this work cover a wide range of scales and are intended as augmented imaging tools for auditory research.

Investigating gut alterations in Alzheimer's disease: In-depth analysis with micro- and nano-3D X-ray phase contrast tomography

Alzheimer's disease (AD), a debilitating neurodegenerative disorder, remains one of the foremost public health challenges affecting more than 30 million people worldwide with the etiology still largely enigmatic. The intricate gut-brain axis, serving as a vital communication network between the gut and the brain, appears to wield influence in the progression of AD. Our study showcases the remarkable precision of x-ray phase-contrast tomography (XPCT) in conducting an advanced three-dimensional examination of gut cellular composition and structure. The exploitation of micro- and nano-XPCT on various AD mouse models unveiled relevant alterations in villi and crypts, cellular transformations in Paneth and goblet cells, along with the detection of telocytes, neurons, erythrocytes, and mucus secretion by goblet cells within the gut cavity. The observed gut structural variations may elucidate the transition from dysbiosis to neurodegeneration and cognitive decline. Leveraging XPCT could prove pivotal in early detection and prognosis of the disease.

Three-dimensional structure of entire hydrated murine hearts at histological resolution

Imaging the entire cardiomyocyte network in entire small animal hearts at single cell resolution is a formidable challenge. Optical microscopy provides sufficient contrast and resolution in 2d, however fails to deliver non-destructive 3d reconstructions with isotropic resolution. It requires several invasive preparation steps, which introduce structural artefacts, namely dehydration, physical slicing and staining, or for the case of light sheet microscopy also clearing of the tissue. Our goal is to provide 3d reconstructions of the cardiomyocyte network in entire hydrated murine hearts, and to develop a methodology for quantitative analysis of heart pathologies based on X-ray phase contrast computed tomography (XPCT). We have used XPCT at two beamlines of the extremely brilliant source (EBS) at the European Synchrotron Radiation Facility (ESRF) to scan wild-type murine hearts at high resolution, as well as a series of murine hearts of different pathological models, at reduced resolution and higher throughput. All hearts were obtained from the small animal facility of the university medical center in Göttingen. The hearts were fixed in formalin, stored and measured non-destructively in phosphate buffer solution. The high resolution dataset allows to discern individual cardiomyocytes in the tissue. All datasets have been analyzed using semi-automated image segmentation of the ventricles, rotation into a common coordinate system, classification into different anatomical compartments, and finally the structure tensor approach. A 3d streamline representation of the cardiomyocyte orientation vector field is provided. The different cardiovascular disease models are analysed based on metrics derived from the 3d structure tensor. An entire hydrated murine heart has been covered at an isotropic voxel size of 1.6 μ m (distributed over several volumes). A binned and fused dataset of this heart is available at 3.2 μ m, and has been analyzed by the structure tensor approach to yield the ventricular cardiomyocyte network or mesh, i.e. the aggregation of the cardiomyocyte chains in particular in the ventricular wall. Semi-automatic determination of structural metrics is already achieved and the corresponding tools and resulting data are made publically available. XPCT using extremely brilliant undulator radiation is close to achieve single cell reconstruction in an entire small animal organ.

BEATS: BEAmline for synchrotron X-ray microTomography at SESAME

The ID10 beamline of the SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East) synchrotron light source in Jordan was inaugurated in June 2023 and is now open to scientific users. The beamline, which was designed and installed within the European Horizon 2020 project BEAmline for Tomography at SESAME (BEATS), provides full-field X-ray radiography and microtomography imaging with monochromatic or polychromatic X-rays up to photon energies of 100 keV. The photon source generated by a 2.9 T wavelength shifter with variable gap, and a double-multilayer monochromator system allow versatile application for experiments requiring either an X-ray beam with high intensity and flux, and/or a partially spatial coherent beam for phase-contrast applications. Sample manipulation and X-ray detection systems are designed to allow scanning samples with different size, weight and material, providing image voxel sizes from 13 µm down to 0.33 µm. A state-of-the-art computing infrastructure for data collection, three-dimensional (3D) image reconstruction and data analysis allows the visualization and exploration of results online within a few seconds from the completion of a scan. Insights from 3D X-ray imaging are key to the investigation of specimens from archaeology and cultural heritage, biology and health sciences, materials science and engineering, earth, environmental sciences and more. Microtomography scans and preliminary results obtained at the beamline demonstrate that the new beamline ID10-BEATS expands significantly the range of scientific applications that can be targeted at SESAME.

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 imaging with gas chromatography in real time, 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 (two to three 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 gasses remain unchanged. By 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.

The Study of the Caudal Vertebrae of Thick-Toed Geckos after a Prolonged Space Flight by X-ray Phase-Contrast Micro-CT

The proximal caudal vertebrae and notochord in thick-toed geckos (TG) (Chondrodactylus turneri, Gray, 1864) were investigated after a 30-day space flight onboard the biosatellite Bion-M1. This region has not been explored in previous studies. Our research focused on finding sites most affected by demineralization caused by microgravity (G0). We used X-ray phase-contrast tomography to study TG samples without invasive prior preparation to clarify our previous findings on the resistance of TG's bones to demineralization in G0. The results of the present study confirmed that geckos are capable of preserving bone mass after flight, as neither cortical nor trabecular bone volume fraction showed statistically significant changes after flight. On the other hand, we observed a clear decrease in the mineralization of the notochordal septum and a substantial rise in intercentrum volume following the flight. To monitor TG's mineral metabolism in G0, we propose to measure the volume of mineralized tissue in the notochordal septum. This technique holds promise as a sensitive approach to track the demineralization process in G0, given that the volume of calcification within the septum is limited, making it easy to detect even slight changes in mineral content.

Evaluation of high intensity synchrotron radiation x-ray imaging using Si crystals with lapped surface at 33.3 keV

In x-ray imaging methods, such as synchrotron radiation microangiography, the x-ray intensity has become more important in recent years for real-time dynamic observations to evaluate temporal changes in samples. Many synchrotron radiation facilities use x-rays monochromated by diffraction from perfect Si crystals to improve the spatial resolution of x-ray images and obtain detailed information about a sample. In this paper, monochromatic synchrotron x-ray images were acquired using Si crystals lapped with abrasives to enhance the x-ray intensity using white synchrotron radiation x-rays for observing dynamic changes in samples. The x-ray intensity, spatial resolution, and contrast noise ratio (CNR) in the acquired x-ray images were quantitatively evaluated using a state-of-the-art high-spatial-resolution detector. The x-ray intensity was substantially increased by a factor of ∼8 when a lapped Si crystal was used. When the lapped Si crystal was used, the spatial resolution of x-ray images in the diffraction-plane direction was ∼70% lower than when an etched Si crystal was used at a spatial resolution of 10 lp/mm. By contrast, the CNR in x-ray images, which is important for observing the interior of a sample, increased threefold when a contrast agent containing iodine at a concentration of 38 wt. % was used. It was confirmed that the combination of white synchrotron radiation x-rays and a lapped crystal produces an intense monochromatic x-ray, providing an important evaluation for the use of optics for each research purpose.

Multiscale X-ray phase-contrast tomography: From breast CT to micro-CT for virtual histology

Phase-contrast imaging techniques address the issue of poor soft-tissue contrast encountered in traditional X-ray imaging. This can be accomplished with the propagation-based phase-contrast technique by employing a coherent photon beam, which is available at synchrotron facilities, as well as long sample-to-detector distances. This study demonstrates the optimization of propagation-based phase-contrast computed tomography (CT) techniques for multiscale X-ray imaging of the breast at the Elettra synchrotron facility (Trieste, Italy). Two whole breast mastectomy samples were acquired with propagation-based breast-CT using a monochromatic synchrotron beam at a pixel size of 60 µm. Paraffin-embedded blocks sampled from the same tissues were scanned with propagation-based micro-CT imaging using a polychromatic synchrotron beam at a pixel size of 4 µm. Images of both methodologies and of the same sample were spatially registered. The resulting images showed the transition from whole breast imaging with propagation-based breast-CT methodology to virtual histology with propagation-based micro-CT imaging of the same sample. Additionally, conventional histological images were matched to virtual histology images. Phase-contrast images offer a high resolution with low noise, which allows for a highly precise match between virtual and conventional histology. Furthermore, those techniques allow a clear discernment of breast structures, lesions, and microcalcifications, being a promising clinically-compatible tool for breast imaging in a multiscale approach, to either assist in the detection of cancer in full volume breast samples or to complement structure identification in paraffin-embedded breast tissue samples.

Preparation of large biological samples for high-resolution, hierarchical, synchrotron phase-contrast tomography with multimodal imaging compatibility

Imaging across different scales is essential for understanding healthy organ morphology and pathophysiological changes. The macro- and microscale three-dimensional morphology of large samples, including intact human organs, is possible with X-ray microtomography (using laboratory or synchrotron sources). Preparation of large samples for high-resolution imaging, however, is challenging due to limitations such as sample shrinkage, insufficient contrast, movement of the sample and bubble formation during mounting or scanning. Here, we describe the preparation, stabilization, dehydration and mounting of large soft-tissue samples for X-ray microtomography. We detail the protocol applied to whole human organs and hierarchical phase-contrast tomography at the European Synchrotron Radiation Facility, yet it is applicable to a range of biological samples, including complete organisms. The protocol enhances the contrast when using X-ray imaging, while preventing sample motion during the scan, even with different sample orientations. Bubbles trapped during mounting and those formed during scanning (in the case of synchrotron X-ray imaging) are mitigated by multiple degassing steps. The sample preparation is also compatible with magnetic resonance imaging, computed tomography and histological observation. The sample preparation and mounting require 24-36 d for a large organ such as a whole human brain or heart. The 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 voxel size of 1 μm. The protocol requires users with expertise in handling human or animal organs, laboratory operation and X-ray imaging.

Characterization of a CdTe single-photon-counting detector for biomedical imaging applications

PURPOSE

The Eiger 2X CdTe 1 M-W (Dectris ltd, Baden, Switzerland) single photon counting detector was characterized for imaging applications at the biomedical beamline ID17 of the European Synchrotron Radiation Facility.

METHODS

Linearity, Modulation Transfer Function, Noise Power Spectrum and Detective Quantum Efficiency were measured as a function of photon energy and flux in the range 26-80 keV.

RESULTS

The linearity was confirmed in the flux range specified by Dectris and a detection efficiency higher than 60 % was measured for energies up to 80 keV. The spatial resolution was inferred from the Modulation Transfer Function and was found to be compatible with the pixel size of the detector (75 μm), except at energies just above the K-edge of Cd and Te where it reached 150 μm. The study of the Noise Power Spectrum showed a time-dependency in the response of the sensor, which is mitigated at low photon fluxes (<2⨯10⁸ ph mm^-2 s^-1).

CONCLUSIONS

This work was the first characterization of the Eiger 2X CdTe 1 M-W for imaging applications with monochromatic synchrotron radiation. The spatial resolution and the quantum efficiency are compatible with low-dose imaging applications.

Reduced volume of diabetic pancreatic islets in rodents detected by synchrotron X-ray phase-contrast microtomography and deep learning network

The pancreatic islet is a highly structured micro-organ that produces insulin in response to rising blood glucose. Here we develop a label-free and automatic imaging approach to visualize the islets in situ in diabetic rodents by the synchrotron radiation X-ray phase-contrast microtomography (SRμCT) at the ID17 station of the European Synchrotron Radiation Facility. The large-size images (3.2 mm × 15.97 mm) were acquired in the pancreas in STZ-treated mice and diabetic GK rats. Each pancreas was dissected by 3000 reconstructed images. The image datasets were further analysed by a self-developed deep learning method, AA-Net. All islets in the pancreas were segmented and visualized by the three-dimension (3D) reconstruction. After quantifying the volumes of the islets, we found that the number of larger islets (=>1500 μm³) was reduced by 2-fold (wt 1004 ± 94 vs GK 419 ± 122, P < 0.001) in chronically developed diabetic GK rat, while in STZ-treated diabetic mouse the large islets were decreased by half (189 ± 33 vs 90 ± 29, P < 0.001) compared to the untreated mice. Our study provides a label-free tool for detecting and quantifying pancreatic islets in situ. It implies the possibility of monitoring the state of pancreatic islets in vivo diabetes without labelling.

Double-multilayer monochromators for high-energy and large-field X-ray imaging applications with intense pink beams at SPring-8 BL20B2

In this study, double-multilayer monochromators that generate intense, high-energy, pink X-ray beams are designed, installed and evaluated at the SPring-8 medium-length (215 m) bending-magnet beamline BL20B2 for imaging applications. Two pairs of W/B₄C multilayer mirrors are designed to utilize photon energies of 110 keV and 40 keV with bandwidths of 0.8% and 4.8%, respectively, which are more than 100 times larger when compared with the Si double-crystal monochromator (DCM) with a bandwidth of less than 0.01%. At an experimental hutch located 210 m away from the source, a large and uniform beam of size 14 mm (V) × 300 mm (H) [21 mm (V) × 300 mm (H)] was generated with a high flux density of 1.6 × 10⁹ photons s^-1 mm^-2 (6.9 × 10¹⁰ photons s^-1 mm^-2) at 110 keV (40 keV), which marked a 300 (190) times increase in the photon flux when compared with a DCM with Si 511 (111) diffraction. The intense pink beams facilitate advanced X-ray imaging for large-sized objects such as fossils, rocks, organs and electronic devices with high speed and high spatial resolution.

Lung tissue biomechanics imaged with synchrotron phase contrast microtomography in live rats

The magnitude and distribution of strain imposed on the peripheral airspaces by mechanical ventilation at the microscopic level and the consequent deformations are unknown despite their importance for understanding the mechanisms occurring at the onset of ventilator-induced lung injury. Here a 4-Dimensional (3D + time) image acquisition and processing technique is developed to assess pulmonary acinar biomechanics at microscopic resolution. Synchrotron radiation phase contrast CT with an isotropic voxel size of 6 µm3 is applied in live anesthetized rats under controlled mechanical ventilation. Video animations of regional acinar and vascular strain are acquired in vivo. Maps of strain distribution due to positive-pressure breaths and cardiovascular activity in lung acini and blood vessels are derived based on CT images. Regional strain within the lung peripheral airspaces takes average values of 0.09 ± 0.02. Fitting the expression S = kVn, to the changes in peripheral airspace area (S) and volume (V) during a positive pressure breath yields an exponent n = 0.82 ± 0.03, suggesting predominant alveolar expansion rather than ductal expansion or alveolar recruitment. We conclude that this methodology can be used to assess acinar conformational changes during positive pressure breaths in intact peripheral lung airspaces.

X-ray Phase Contrast 3D virtual histology: evaluation of lung alterations after micro-beam irradiation

PURPOSE

This study provides the first experimental application of multiscale three-dimensional (3D) X-ray Phase Contrast Imaging Computed Tomography (XPCI-CT) virtual histology for the inspection and quantitative assessment of the late stage effects of radio-induced lesions on lungs in a small animal model.

METHODS AND MATERIALS

Healthy male Fischer rats were irradiated with X-ray standard broad beams and Microbeam Radiation Therapy (MRT), a high dose rate (14 kGy/s), FLASH spatially-fractionated X-ray therapy to avoid the beamlets smearing due to cardiosynchronous movements of the organs during the irradiation. After organ dissection, ex-vivo XPCI-CT was applied to all the samples and the results were quantitatively analysed and correlated to histologic data.

RESULTS

XPCI-CT enables the 3D visualization of lung tissues with unprecedented contrast and sensitivity allowing alveoli, vessels and bronchi hierarchical visualization. XPCI-CT discriminates in 3D radio-induced lesions such as fibrotic scars, Ca/Fe deposits and, in addition, allows a full-organ accurate quantification of the fibrotic tissue within the irradiated organs. The radiation-induced fibrotic tissue content is less than 10% of the analyzed volume for all the MRT treated organs while it reaches the 34% in the case of irradiations with 50 Gy using a broad beam.

CONCLUSIONS

XPCI-CT is an effective imaging technique able to provide detailed 3D information for the assessment of lung pathology and treatment efficacy in a small animal model.

A Multi-Scale and Multi-Technique Approach for the Characterization of the Effects of Spatially Fractionated X-ray Radiation Therapies in a Preclinical Model

The purpose of this study is to use a multi-technique approach to detect the effects of spatially fractionated X-ray Microbeam (MRT) and Minibeam Radiation Therapy (MB) and to compare them to seamless Broad Beam (BB) irradiation. Healthy- and Glioblastoma (GBM)-bearing male Fischer rats were irradiated in-vivo on the right brain hemisphere with MRT, MB and BB delivering three different doses for each irradiation geometry. Brains were analyzed post mortem by multi-scale X-ray Phase Contrast Imaging-Computed Tomography (XPCI-CT), histology, immunohistochemistry, X-ray Fluorescence (XRF), Small- and Wide-Angle X-ray Scattering (SAXS/WAXS). XPCI-CT discriminates with high sensitivity the effects of MRT, MB and BB irradiations on both healthy and GBM-bearing brains producing a first-time 3D visualization and morphological analysis of the radio-induced lesions, MRT and MB induced tissue ablations, the presence of hyperdense deposits within specific areas of the brain and tumor evolution or regression with respect to the evaluation made few days post-irradiation with an in-vivo magnetic resonance imaging session. Histology, immunohistochemistry, SAXS/WAXS and XRF allowed identification and classification of these deposits as hydroxyapatite crystals with the coexistence of Ca, P and Fe mineralization, and the multi-technique approach enabled the realization, for the first time, of the map of the differential radiosensitivity of the different brain areas treated with MRT and MB. 3D XPCI-CT datasets enabled also the quantification of tumor volumes and Ca/Fe deposits and their full-organ visualization. The multi-scale and multi-technique approach enabled a detailed visualization and classification in 3D of the radio-induced effects on brain tissues bringing new essential information towards the clinical implementation of the MRT and MB radiation therapy techniques.

The white beam station at imaging beamline BL-4, Indus-2

The high flux density of synchrotron white beam offers several advantages in X-ray imaging such as higher resolution and signal-to-noise ratio in 3D/4D micro-tomography, higher frame rate in real-time imaging of transient phenomena, and higher penetration in thick and dense materials especially at higher energies. However, these advantages come with additional challenges to beamline optics, camera and sample due to increased heat load and radiation damage, and to personal safety due to higher radiation dose and ozone gas hazards. In this work, a white beam imaging facility at imaging beamline BL-4, Indus-2, has been developed, while taking care of various instrumental and personal safety challenges. The facility has been tested to achieve 1.5 µm spatial resolution, increased penetration depth up to 900 µm in steel, and high temporal resolutions of ∼10 ms (region of interest 2048 × 2048 pixels) and 70 µs (256 × 2048 pixels). The facility is being used successfully for X-ray imaging, non-destructive testing and dosimetry experiments.

Multiscale X-ray phase contrast imaging of human cartilage for investigating osteoarthritis formation

Background

The evolution of cartilage degeneration is still not fully understood, partly due to its thinness, low radio-opacity and therefore lack of adequately resolving imaging techniques. X-ray phase-contrast imaging (X-PCI) offers increased sensitivity with respect to standard radiography and CT allowing an enhanced visibility of adjoining, low density structures with an almost histological image resolution. This study examined the feasibility of X-PCI for high-resolution (sub-) micrometer analysis of different stages in tissue degeneration of human cartilage samples and compare it to histology and transmission electron microscopy.

Methods

Ten 10%-formalin preserved healthy and moderately degenerated osteochondral samples, post-mortem extracted from human knee joints, were examined using four different X-PCI tomographic set-ups using synchrotron radiation the European Synchrotron Radiation Facility (France) and the Swiss Light Source (Switzerland). Volumetric datasets were acquired with voxel sizes between 0.7 × 0.7 × 0.7 and 0.1 × 0.1 × 0.1 µm³. Data were reconstructed by a filtered back-projection algorithm, post-processed by ImageJ, the WEKA machine learning pixel classification tool and VGStudio max. For correlation, osteochondral samples were processed for histology and transmission electron microscopy.

Results

X-PCI provides a three-dimensional visualization of healthy and moderately degenerated cartilage samples down to a (sub-)cellular level with good correlation to histologic and transmission electron microscopy images. X-PCI is able to resolve the three layers and the architectural organization of cartilage including changes in chondrocyte cell morphology, chondrocyte subgroup distribution and (re-)organization as well as its subtle matrix structures.

Conclusions

X-PCI captures comprehensive cartilage tissue transformation in its environment and might serve as a tissue-preserving, staining-free and volumetric virtual histology tool for examining and chronicling cartilage behavior in basic research/laboratory experiments of cartilage disease evolution.

Convolutional neuronal networks combined with X-ray phase-contrast imaging for a fast and observer-independent discrimination of cartilage and liver diseases stages

We applied transfer learning using Convolutional Neuronal Networks to high resolution X-ray phase contrast computed tomography datasets and tested the potential of the systems to accurately classify Computed Tomography images of different stages of two diseases, i.e. osteoarthritis and liver fibrosis. The purpose is to identify a time-effective and observer-independent methodology to identify pathological conditions. Propagation-based X-ray phase contrast imaging WAS used with polychromatic X-rays to obtain a 3D visualization of 4 human cartilage plugs and 6 rat liver samples with a voxel size of 0.7 × 0.7 × 0.7 µm³ and 2.2 × 2.2 × 2.2 µm³, respectively. Images with a size of 224 × 224 pixels are used to train three pre-trained convolutional neuronal networks for data classification, which are the VGG16, the Inception V3, and the Xception networks. We evaluated the performance of the three systems in terms of classification accuracy and studied the effect of the variation of the number of inputs, training images and of iterations. The VGG16 network provides the highest classification accuracy when the training and the validation-test of the network are performed using data from the same samples for both the cartilage (99.8%) and the liver (95.5%) datasets. The Inception V3 and Xception networks achieve an accuracy of 84.7% (43.1%) and of 72.6% (53.7%), respectively, for the cartilage (liver) images. By using data from different samples for the training and validation-test processes, the Xception network provided the highest test accuracy for the cartilage dataset (75.7%), while for the liver dataset the VGG16 network gave the best results (75.4%). By using convolutional neuronal networks we show that it is possible to classify large datasets of biomedical images in less than 25 min on a 8 CPU processor machine providing a precise, robust, fast and observer-independent method for the discrimination/classification of different stages of osteoarthritis and liver diseases.