Phase-contrast x-ray tomography of neuronal tissue at laboratory sources with submicron resolution

Integrating X-ray phase-contrast imaging and histology for comparative evaluation of breast tissue malignancies in virtual histology analysis

Detecting breast tissue alterations is essential for cancer diagnosis. However, inherent bidimensionality limits histological procedures' effectiveness in identifying these changes. Our study applies a 3D virtual histology method based on X-ray phase-contrast microtomography (PhC μ CT), performed at a synchrotron facility, to investigate breast tissue samples including different types of lesions, namely intraductal papilloma, micropapillary intracystic carcinoma, and invasive lobular carcinoma. One-to-one comparisons of X-ray and histological images explore the clinical potential of 3D X-ray virtual histology. Results show that PhC μ CT technique provides high spatial resolution and soft tissue sensitivity, while being non-destructive, not requiring a dedicated sample processing and being compatible with conventional histology. PhC μ CT can enhance the visualization of morphological characteristics such as stromal tissue, fibrovascular core, terminal duct lobular unit, stromal/epithelium interface, basement membrane, and adipocytes. Despite not reaching the (sub) cellular level, the three-dimensionality of PhC μ CT images allows to depict in-depth alterations of the breast tissues, potentially revealing pathologically relevant details missed by a single histological section. Compared to serial sectioning, PhC μ CT allows the virtual investigation of the sample volume along any orientation, possibly guiding the pathologist in the choice of the most suitable cutting plane. Overall, PhC μ CT virtual histology holds great promise as a tool adding to conventional histology for improving efficiency, accessibility, and diagnostic accuracy of pathological evaluation.

High Throughput Tomography (HiTT) on EMBL beamline P14 on PETRA III

Here, high-throughput tomography (HiTT), a fast and versatile phase-contrast imaging platform for life-science samples on the EMBL beamline P14 at DESY in Hamburg, Germany, is presented. A high-photon-flux undulator beamline is used to perform tomographic phase-contrast acquisition in about two minutes which is linked to an automated data processing pipeline that delivers a 3D reconstructed data set less than a minute and a half after the completion of the X-ray scan. Combining this workflow with a sophisticated robotic sample changer enables the streamlined collection and reconstruction of X-ray imaging data from potentially hundreds of samples during a beam-time shift. HiTT permits optimal data collection for many different samples and makes possible the imaging of large sample cohorts thus allowing population studies to be attempted. The successful application of HiTT on various soft tissue samples in both liquid (hydrated and also dehydrated) and paraffin-embedded preparations is demonstrated. Furthermore, the feasibility of HiTT to be used as a targeting tool for volume electron microscopy, as well as using HiTT to study plant morphology, is demonstrated. It is also shown how the high-throughput nature of the work has allowed large numbers of `identical' samples to be imaged to enable statistically relevant sample volumes to be studied.

Neodymium acetate as a contrast agent for X-ray phase-contrast tomography

Purpose

X-ray phase-contrast tomography (XPCT) is a non-destructive, three-dimensional imaging modality that provides higher contrast in soft tissue than absorption-based CT and allows one to cover the cytoarchitecture from the centi- and millimeter scale down to the nanoscale. To further increase contrast and resolution of XPCT, for example, in view of addressing connectivity issues in the central nervous system (CNS), metal staining is indispensable. However, currently used protocols, for example, based on osmium and/or uranium are less suited for XPCT, due to an excessive β / δ -ratio. In this work, we explore the suitability of different staining agents for XPCT. Particularly, neodymium(III)-acetate (NdAc), which has recently been proposed as a non-toxic, non-radioactive easy to use alternative contrast agent for uranyl acetate (UAc) in electron microscopy, is investigated. Due to its vertical proximity to UAc in the periodic table, similar chemical but better suited optical properties for phase contrast can be expected.

Approach

Differently stained whole eye samples of wild type mouse and tissues of the CNS are embedded into EPON epoxy resin and scanned using synchrotron as well as with laboratory radiation. Phase retrieval is performed on the projection images, followed by tomographic reconstruction, which enables a quantitative analysis based on the reconstructed electron densities. Segmentation techniques and rendering software is used to visualize structures of interest in the sample.

Results

We show that staining neuronal samples with NdAc enhances contrast, in particular for laboratory scans, allowing high-resolution imaging of biological soft tissue in-house. For the example of murine retina, specifically rods and cones as well as the sclera and the Ganglion cell layer seem to be targeted by the stain. A comparison of electron density by the evaluation of histograms allowed to determine quantitative measures to describe the difference between the examined stains.

Conclusion

The results suggest NdAc to be an effective stain for XPCT, with a preferential binding to anionic groups, such as phosphate and carboxyl groups at cell surfaces, targeting certain layers of the retina with a stronger selectivity compared to other staining agents. Due to the advantageous X-ray optical properties, the stain seems particularly well-suited for phase contrast, with a comparably small number density and an overall superior image quality at laboratory sources.

Optimization of phase contrast imaging with a nano-focus x-ray tube

Propagation-based phase contrast imaging with a laboratory x-ray source is a valuable tool for studying samples that show only low absorption contrast, either because of low density, elemental composition, or small feature size. If a propagation distance between sample and detector is introduced and the illumination is sufficiently coherent, the phase shift in the sample will cause additional contrast around interfaces, known as edge enhancement fringes. The strength of this effect depends not only on sample parameters and energy but also on the experimental geometry, which can be optimized accordingly. Recently, x-ray lab sources using transmission targets have become available, which provide very small source sizes in the few hundred nanometer range. This allows the use of a high-magnification geometry with a very short source-sample distance, while still achieving sufficient spatial coherence at the sample position. Moreover, the high geometrical magnification makes it possible to use detectors with a larger pixel size without reducing the image resolution. Here, we explore the influence of magnification on the edge enhancement fringes in such a geometry. We find experimentally and theoretically that the fringes become maximal at a magnification that is independent of the total source-detector distance. This optimal magnification only depends on the source size, the steepness of the sample feature, and the detector resolution. A stronger influence of the sample feature on the optimal magnification compared to low-magnification geometries is observed.

DiI-CT-A bimodal neural tracer for X-ray and fluorescence imaging

Here, we present an X-ray-visible neural tracer, referred to as DiI-CT, which is based on the well-established lipophilic indocarbocyanine dye DiI, to which we conjugated two iodine atoms. The tracer is visible with microfocus computed tomography (microCT) imaging and shares the excellent fluorescent tracing properties of DiI. We document the discovery potential of DiI-CT by analyzing the vibrissa follicle-sinus complex, a structure where visual access is poor and 3D tissue structure matters and reveal innervation patterns of the intact follicle in unprecedented detail. In the brain, DiI-CT tracing holds promise for verification evaluation of indirect connectivity measures, such as diffusion tensor imaging. We conclude that the bimodal dye DiI-CT opens new avenues for neuroanatomy.

A versatile laboratory setup for high resolution X-ray phase contrast tomography and scintillator characterization

BACKGROUND

X-ray micro-tomography (μCT) is a powerful non-destructive 3D imaging method applied in many scientific fields. In combination with propagation-based phase-contrast, the method is suitable for samples with low absorption contrast. Phase contrast tomography has become available in the lab with the ongoing development of micro-focused tube sources, but it requires sensitive and high-resolution X-ray detectors. The development of novel scintillation detectors, particularly for microscopy, requires more flexibility than available in commercial tomography systems.

OBJECTIVE

We aim to develop a compact, flexible, and versatile μCT laboratory setup that combines absorption and phase contrast imaging as well as the option to use it for scintillator characterization. Here, we present details on the design and implementation of the setup.

METHODS

We used the setup for μCT in absorption and propagation-based phase-contrast mode, as well as to study a perovskite scintillator.

RESULTS

We show the 2D and 3D performance in absorption and phase contrast mode, as well as how the setup can be used for testing new scintillator materials in a realistic imaging environment. A spatial resolution of around 1.3μm is measured in 2D and 3D.

CONCLUSIONS

The setup meets the needs for common absorption μCT applications and offers increased contrast in phase contrast mode. The availability of a versatile laboratory μCT setup allows not only for easy access to tomographic measurements, but also enables a prompt monitoring and feedback beneficial for advances in scintillator fabrication.

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.

A quality optimization approach to image Achilles tendon microstructure by phase-contrast enhanced synchrotron micro-tomography

Achilles tendons are mechanosensitive, and their complex hierarchical structure is in part the result of the mechanical stimulation conveyed by the muscles. To fully understand how their microstructure responds to mechanical loading a non-invasive approach for 3D high resolution imaging suitable for soft tissue is required. Here we propose a protocol that can capture the complex 3D organization of the Achilles tendon microstructure, using phase-contrast enhanced synchrotron micro-tomography (SR-PhC-μCT). We investigate the effects that sample preparation and imaging conditions have on the resulting image quality, by considering four types of sample preparations and two imaging setups (sub-micrometric and micrometric final pixel sizes). The image quality is assessed using four quantitative parameters. The results show that for studying tendon collagen fibers, conventional invasive sample preparations such as fixation and embedding are not necessary or advantageous. Instead, fresh frozen samples result in high-quality images that capture the complex 3D organization of tendon fibers in conditions as close as possible to natural. The comprehensive nature of this innovative study by SR-PhC-μCT breaks ground for future studies of soft complex biological tissue in 3D with high resolution in close to natural conditions, which could be further used for in situ characterization of how soft tissue responds to mechanical stimuli on a microscopic level.

X-Ray Ptychography with a Laboratory Source

X-ray ptychography has revolutionized nanoscale phase contrast imaging at large-scale synchrotron sources in recent years. We present here the first successful demonstration of the technique in a small-scale laboratory setting. An experiment was conducted with a liquid metal-jet x-ray source and a single photon-counting detector with a high spectral resolution. The experiment used a spot size of 5  μm to produce a ptychographic phase image of a Siemens star test pattern with a submicron spatial resolution. The result and methodology presented show how high-resolution phase contrast imaging can now be performed at small-scale laboratory sources worldwide.

3d phase-contrast nanotomography of unstained human skin biopsies may identify morphological differences in the dermis and epidermis between subjects

BACKGROUND

Enteric neuropathy is described in most patients with gastrointestinal dysmotility and may be found together with reduced intraepidermal nerve fiber density (IENFD). The aim of this pilot study was to assess whether three-dimensional (3d) imaging of skin biopsies could be used to examine various tissue components in patients with gastrointestinal dysmotility.

MATERIAL AND METHODS

Four dysmotility patients of different etiology and two healthy volunteers were included. From each subject, two 3-mm punch skin biopsies were stained with antibodies against protein gene product 9.5 or evaluated as a whole with two X-ray phase-contrast computed tomography (CT) setups, a laboratory µCT setup and a dedicated synchrotron radiation nanoCT end-station.

RESULTS

Two patients had reduced IENFD, and two normal IENFD, compared with controls. µCT and X-ray phase-contrast holographic nanotomography scanned whole tissue specimens, with optional high-resolution scans revealing delicate structures, without differentiation of various fibers and cells. Irregular architecture of dermal fibers was observed in the patient with Ehlers-Danlos syndrome and the patient with idiopathic dysmotility showed an abundance of mesenchymal ground substance.

CONCLUSIONS

3d phase-contrast tomographic imaging may be useful to illustrate traits of connective tissue dysfunction in various organs and to demonstrate whether disorganized dermal fibers could explain organ dysfunction.

X-ray tomography with multiple ultranarrow cone beams

Hollow glass microcapillaries or x-ray waveguides very efficiently confine x-rays to submicron or nanospots, which can be used for point projection imaging. However, x-ray beams exiting from such devices have ultranarrow cones that are limited by the critical angle for the total external reflection to a few milliradians. Narrow cone beams result in small fields of view, and the application of multiple-reflection optics to cone beam tomography is challenging. In this work, we describe a new nonconventional tomographic geometry realized with multiple confocal ultranarrow cone beams. The geometry enables an increase in the effective radiation cone to over 10^° without resolution reduction. The proposed tomographic scans can be performed without truncations of the field of view or limitations of the angular range and do not require sample translations, which are inherent to other multibeam x-ray techniques. Volumetric imaging is possible with a simultaneous iterative reconstruction technique or with a fast approximate noniterative two-step approach. A proof-of-principle experiment was performed in the multipoint projection geometry with polycapillary optics and a multi-pinhole mask inserted upstream of the optics. The geometry is suited for phase-contrast tomography with polychromatic laboratory and synchrotron sources.