Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae

Tissue phenotyping is foundational to understanding and assessing the cellular aspects of disease in organismal context and an important adjunct to molecular studies in the dissection of gene function, chemical effects, and disease. As a first step toward computational tissue phenotyping, we explore the potential of cellular phenotyping from 3-Dimensional (3D), 0.74 µm isotropic voxel resolution, whole zebrafish larval images derived from X-ray histotomography, a form of micro-CT customized for histopathology. As proof of principle towards computational tissue phenotyping of cells, we created a semi-automated mechanism for the segmentation of blood cells in the vascular spaces of zebrafish larvae, followed by modeling and extraction of quantitative geometric parameters. Manually segmented cells were used to train a random forest classifier for blood cells, enabling the use of a generalized cellular segmentation algorithm for the accurate segmentation of blood cells. These models were used to create an automated data segmentation and analysis pipeline to guide the steps in a 3D workflow including blood cell region prediction, cell boundary extraction, and statistical characterization of 3D geometric and cytological features. We were able to distinguish blood cells at two stages in development (4- and 5-days-post-fertilization) and wild-type vs. polA2 huli hutu ( hht ) mutants. The application of geometric modeling across cell types to and across organisms and sample types may comprise a valuable foundation for computational phenotyping that is more open, informative, rapid, objective, and reproducible.

Ultrasound fusion imaging for improving diagnostic and therapeutic strategies of focal liver lesions: A preliminary study

PURPOSE

To assess the effect of ultrasound (US) fusion imaging on the clinical diagnostic and therapeutic strategies of focal liver lesions, which are difficult to detect or diagnose by conventional US.

METHODS

From November 2019 to June 2022, 71 patients with invisible or undiagnosed focal liver lesions who underwent fusion imaging combining US with CT or MR were included in this retrospective study. The reasons for US fusion imaging were as follows: (1) lesions that were undetectable or inconspicuous on B-mode US; (2) post-ablation lesions that could not be assessed accurately by B-mode US; (3) to evaluate whether the lesions detected by B-mode US that were consistent with those presented on MRI/CT images.

RESULTS

Of the 71 cases, 43 cases were single lesions, and 28 cases were multiple lesions. Among the 46 cases which were invisible on conventional US, the display rate of lesions using US-CT/MRI fusion imaging was 30.8%, and that combined with CEUS was 76.9%. US-guided biopsy was performed in 30 patients after the detection and localization determined by fusion imaging, with a positive rate of 73.3%. Six patients with recurrence after ablation therapy were all detected and located accurately after fusion imaging, and 4 of them successfully underwent ablation therapy again.

CONCLUSION

Fusion imaging contributes to the understanding of the anatomical relationship between lesion location and blood vessels. Additionally, fusion imaging can improve the diagnostic confidence, be helpful to guide interventional operations, and hence be conducive to clinical therapeutic strategies.

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.

Revealing the three-dimensional murine brain microstructure by contrast-enhanced computed tomography

To improve our understanding of the brain microstructure, high-resolution 3D imaging is used to complement classical 2D histological assessment techniques. X-ray computed tomography allows high-resolution 3D imaging, but requires methods for enhancing contrast of soft tissues. Applying contrast-enhancing staining agents (CESAs) ameliorates the X-ray attenuating properties of soft tissue constituents and is referred to as contrast-enhanced computed tomography (CECT). Despite the large number of chemical compounds that have successfully been applied as CESAs for imaging brain, they are often toxic for the researcher, destructive for the tissue and without proper characterization of affinity mechanisms. We evaluated two sets of chemically related CESAs (organic, iodinated: Hexabrix and CA4+ and inorganic polyoxometalates: 1:2 hafnium-substituted Wells-Dawson phosphotungstate and Preyssler anion), for CECT imaging of healthy murine hemispheres. We then selected the CESA (Hexabrix) that provided the highest contrast between gray and white matter and applied it to a cuprizone-induced demyelination model. Differences in the penetration rate, effect on tissue integrity and affinity for tissue constituents have been observed for the evaluated CESAs. Cuprizone-induced demyelination could be visualized and quantified after Hexabrix staining. Four new non-toxic and non-destructive CESAs to the field of brain CECT imaging were introduced. The added value of CECT was shown by successfully applying it to a cuprizone-induced demyelination model. This research will prove to be crucial for further development of CESAs for ex vivo brain CECT and 3D histopathology.

Lesion extension and neuronal loss following spinal cord injury using X-ray phase-contrast tomography in mice

Following a spinal cord injury (SCI) the degree of functional (motor, autonomous or sensory) correlates with the severity of nervous tissue disruption. An imaging technique able to capture non-invasively and simultaneously the complex mechanisms of neuronal loss, vascular damages and perilesional tissue reorganization is currently lacking in experimental SCI studies. Synchrotron X-ray phase-contrast Tomography (SXPCT) has emerged as a non-destructive 3D neuroimaging technique with high contrast and spatial resolution. In this framework, we developed a multimodal approach combining SXPCT, histology and correlative methods to study neuro-vascular architecture in normal and C4-contused mouse spinal cords (C57BL/6J mice, age 2-3 months). The evolution of SCI lesion was imaged at the cell resolution level during the acute (30 minutes) and subacute (7 days) phases. Spared motor neurons were segmented and quantified in different volumes localized at and away from the epicenter. SXPCT was able to capture neuronal loss and blood-brain barrier breakdown following SCI. 3D quantification based on SXPCT acquisitions showed no additional motor neuron loss between 30 minutes and 7 days post-SCI. In addition, the analysis of hemorrhagic (at 30 minutes) and lesion (at 7 days) volumes revealed a high similarity in size, suggesting no extension of tissue degeneration between early and later time points. Moreover, glial scar borders were unevenly distributed, with rostral edges being the most extended. In conclusion, SXPCT capability to image at high-resolution cellular changes in 3D enables understanding the relationship between hemorrhagic events and nervous structure damages in SCI.

A wide-field micro-computed tomography detector: micron resolution at half-centimetre scale

Ideal three-dimensional imaging of complex samples made up of micron-scale structures extending over mm to cm, such as biological tissues, requires both wide field of view and high resolution. For existing optics and detectors used for micro-CT (computed tomography) imaging, sub-micron pixel resolution can only be achieved for fields of view of <2 mm. This article presents a unique detector system with a 6 mm field-of-view image circle and 0.5 µm pixel size that can be used in micro-CT units utilizing both synchrotron and commercial X-ray sources. A resolution-test pattern with linear microstructures and whole adult Daphnia magna were imaged at beamline 8.3.2 of the Berkeley Advanced Light Source. Volumes of 10000 × 10000 × 7096 isotropic 0.5 µm voxels were reconstructed over a 5.0 mm × 3.5 mm field of view. Measurements in the projection domain confirmed a 0.90 µm measured spatial resolution that is largely Nyquist-limited. This unprecedented combination of field of view and resolution dramatically reduces the need for sectional scans and computational stitching for large samples, ultimately offering the means to elucidate changes in tissue and cellular morphology in the context of larger, whole, intact model organisms and specimens. This system is also anticipated to benefit micro-CT imaging in materials science, microelectronics, agricultural science and biomedical engineering.

3D visualization and morphometric analysis of spinal motion segments and vascular networks: A synchrotron radiation-based micro-CT study in mice

The structure of spinal motion segments and spinal vasculature is complicated. Visualizing the three-dimensional (3D) structure of the spine may provide guidance for spine surgery. However, conventional imaging techniques fail to simultaneously obtain 3D images of soft and hard tissues, and achieving such coimaging states of the spine and its vascular networks remains a challenge. Synchrotron radiation micro-CT (SRμCT) provides a relatively effective and novel method of acquiring detailed 3D information. In this study, specimens of the thoracic spine were obtained from six mice. SRμCT was employed to acquire 3D images of the structure, and histologic staining was performed for comparisons with the SRμCT images. The whole spinal motion segments and the spinal vascular network were simultaneously explored at high resolution. The mean thickness of the cartilaginous end plates (CEPs) and the volume of the intervertebral discs (IVDs) were calculated. The surface of the CEPs and the facet joint cartilage (FJC) were presented as heat maps, which allowed for direct visualization of the thickness distribution. Regional division revealed heterogeneity among the ventral, central, and dorsal parts of the CEPs and between the superior and inferior parts of the facet processes. Moreover, the connections and spatial morphology of the spinal vascular network were visualized. Our study indicates that SRμCT imaging is an ideal method for high-resolution visualization and 3D morphometric analysis of the whole spinal motion segments and spinal vascular network.

3D ring artifacts removal algorithm combined low-rank tensor decomposition with spatial-sequential total variation regularization and its application in phase-contrast microtomography

PURPOSE

High-resolution synchrotron radiation X-ray phase contrast microtomography (PC-μCT) images often suffer from severe ring artifacts, which are mainly caused by undesirable responses of detector elements. In the medical imaging field, the existence of ring artifacts can lead to degraded visual quality and can directly affect diagnosis accuracy. Thus, removing or at least effectively reducing ring artifacts is indispensable.

METHOD

The existing ring artifacts removal algorithms mainly focus on two-dimensional (matrix-based) priors, and these algorithms fail to consider correlations hidden in sequential computed tomography (CT) images. This paper proposed a novel three-dimensional (tensor-based) ring artifacts removal algorithm for synchrotron radiation X-ray PC-μCT images. In the sinogram domain, ring artifacts manifest as vertical stripe artifacts. From an image decomposition perspective, a degraded sinogram can be decomposed into a stripe artifacts component and an underlying clean sinogram component. The proposed algorithm is designed to detect and remove stripe artifacts from a degraded sinogram by fully identifying the characteristics of the two components. Specifically, for the stripe artifacts component, tensor Tucker decomposition is used to describe its low-rank character. For the underlying clean sinogram component, spatial-sequential total variation regularization is adopted to enhance the piecewise smoothness. Moreover, the Frobenius norm term is further used to model Gaussian noise. An efficient augmented Lagrange multiplier method is designed to solve the proposed optimization model.

RESULTS

The proposed method is evaluated utilizing both simulations and real data containing different ring artifacts patterns. In the simulations, the human chest CT images are used for evaluating the proposed method. We compare the peak signal-to-noise ratio (PSNR), structural similarity (SSIM), and mean absolute error (MAE) results of our algorithm with the Naghia's method, the RRRTV method, the wavelet-FFT method, and the SDRSD-GIF method. The proposed method was also evaluated on real data from rat liver samples and rat tooth samples. Our proposed method outperforms the competing methods in terms of both qualitative and quantitative evaluation results. Additionally, the 3D visualization results were presented to make the ring artifacts removal effect more intuitive.

CONCLUSION

The experimental results on simulations and real data clearly demonstrated that the proposed algorithm can significantly improve the quality of PC-μCT images compared with the existing popular algorithms, and it has great potential to promote the application of high-resolution imaging for visualizing biological tissues.

Three-dimensional virtual histology of the cerebral cortex based on phase-contrast X-ray tomography

In this work, we optimize the setups and experimental parameters of X-ray phase-contrast computed-tomography for the three-dimensional imaging of the cyto- and myeloarchitecture of cerebral cortex, including both human and murine tissue. We present examples for different optical configurations using state-of-the art synchrotron instruments for holographic tomography, as well as compact laboratory setups for phase-contrast tomography in the direct contrast (edge-enhancement) regime. Apart from unstained and paraffin-embedded tissue, we tested hydrated tissue, as well as heavy metal stained and resin-embedded tissue using two different protocols. Further, we show that the image quality achieved allows to assess the neuropathology of multiple sclerosis in a biopsy sample collected during surgery.

Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography

Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)'s Extremely Brilliant Source (EBS). The spatial coherence of the ESRF-EBS combined with our beamline equipment, sample preparation and scanning developments enabled us to perform non-destructive, three-dimensional (3D) scans with hierarchically increasing resolution at any location in whole human organs. We applied HiP-CT to image five intact human organ types: brain, lung, heart, kidney and spleen. HiP-CT provided a structural overview of each whole organ followed by multiple higher-resolution volumes of interest, capturing organotypic functional units and certain individual specialized cells within intact human organs. We demonstrate the potential applications of HiP-CT through quantification and morphometry of glomeruli in an intact human kidney and identification of regional changes in the tissue architecture in a lung from a deceased donor with coronavirus disease 2019 (COVID-19).

Dynamic Multicontrast X-Ray Imaging Method Applied to Additive Manufacturing

We present a dynamic implementation of the beam-tracking x-ray imaging method providing absorption, phase, and ultrasmall angle scattering signals with microscopic resolution and high frame rate. We demonstrate the method's ability to capture dynamic processes with 22-ms time resolution by investigating the melting of metals in laser additive manufacturing, which has so far been limited to single-modality synchrotron radiography. The simultaneous availability of three contrast channels enables earlier segmentation of droplets, tracking of powder dynamic, and estimation of unfused powder amounts, demonstrating that the method can provide additional information on melting processes.

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.

Simultaneous 3D Visualization of the Microvascular and Neural Network in Mouse Spinal Cord Using Synchrotron Radiation Micro-Computed Tomography

Effective methods for visualizing neurovascular morphology are essential for understanding the normal spinal cord and the morphological alterations associated with diseases. However, ideal techniques for simultaneously imaging neurovascular structure in a broad region of a specimen are still lacking. In this study, we combined Golgi staining with angiography and synchrotron radiation micro-computed tomography (SRμCT) to visualize the 3D neurovascular network in the mouse spinal cord. Using our method, the 3D neurons, nerve fibers, and vasculature in a broad region could be visualized in the same image at cellular resolution without destructive sectioning. Besides, we found that the 3D morphology of neurons, nerve fiber tracts, and vasculature visualized by SRμCT were highly consistent with that visualized using the histological method. Moreover, the 3D neurovascular structure could be quantitatively evaluated by the combined methodology. The method shown here will be useful in fundamental neuroscience studies.

Insight into Bile Duct Reaction to Obstruction from a Three-dimensional Perspective Using ex Vivo Phase-Contrast CT

Background Biliary obstruction leads to an increase in biliary pressure within the biliary system, which induces the morphologic adaptation of the biliary tree. Purpose To observe and to quantify the morphologic characteristics of the adaptation in a bile duct ligation rat model and verify it in patients with biliary atresia in a three-dimensional (3D) manner using x-ray phase-contrast CT. Materials and Methods A bile duct ligation model was induced in 40 male Sprague-Dawley rats, which were divided into five groups: the control group (no ligation) and groups 2, 4, 6, and 8 weeks after bile duct ligation (eight animals in each group). Liver tissue samples (approximately 1.8 cm in length and 1.3 cm in height) were imaged by using phase-contrast CT and compared with histologic analysis. With a combination of phase-contrast CT and 3D visualization technology, the entire biliary system and the intrahepatic vascular system were quantitatively analyzed according to downstream, midstream, and upstream domains based on bile duct volume, surface area, and other parameters. Additionally, liver explant tissues from 28 patients with biliary atresia were studied to determine the impact of biliary tract reconstruction. Results To offset the increased biliary pressure within the biliary system, the ductular reaction in the downstream, midstream, and upstream domains manifested as dilatation, spiderweb-like looping, and interconnected honeycomb-like patterns, respectively. The most severe ductular reaction occurred in the upstream domain, and the relative surface area (mean, 0.02 μm^-1 ± 0.01, 0.04 μm^-1 ± 0.01, 0.07 μm^-1 ± 0.02, and 0.10 μm^-1 ± 0.02 for the 2-8-week groups, respectively; P < .01 among the groups) and volume fraction of ductules (mean, 16.54% ± 4.62, 19.69% ± 6.41, 26.92% ± 5.82, and 38.34% ± 10.36 for the 2-8-week groups, respectively; P < .01 among the groups except between the 2- and 4-week groups [P = .062]) significantly increased over time. In patients with biliary atresia, it was observed that both fibrosis and proliferative ductules regressed after successful biliary tract reconstruction following Kasai portoenterostomy. Furthermore, ductular reaction was accompanied by a progressive increase in the arterial supply but a loss of portal blood supply. Conclusion X-ray phase-contrast CT with three-dimensional rendering of the biliary system in a bile duct ligation rat model provides key insights into ductular reaction or biliary self-adaptation triggered by increased biliary pressure. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Vannier and Wang in this issue.