Correlative cryo-soft X-ray tomography and cryo-structured illumination microscopy reveal changes to lysosomes in amyloid-β-treated neurons

Protein misfolding is common to neurodegenerative diseases (NDs) including Alzheimer's disease (AD), which is partly characterized by the self-assembly and accumulation of amyloid-beta in the brain. Lysosomes are a critical component of the proteostasis network required to degrade and recycle material from outside and within the cell and impaired proteostatic mechanisms have been implicated in NDs. We have previously established that toxic amyloid-beta oligomers are endocytosed, accumulate in lysosomes, and disrupt the endo-lysosomal system in neurons. Here, we use pioneering correlative cryo-structured illumination microscopy and cryo-soft X-ray tomography imaging techniques to reconstruct 3D cellular architecture in the native state revealing reduced X-ray density in lysosomes and increased carbon dense vesicles in oligomer treated neurons compared with untreated cells. This work provides unprecedented visual information on the changes to neuronal lysosomes inflicted by amyloid beta oligomers using advanced methods in structural cell biology.

Automated quantification of vacuole fusion and lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning

During starvation in the yeast Saccharomyces cerevisiae vacuolar vesicles fuse and lipid droplets (LDs) can become internalized into the vacuole in an autophagic process named lipophagy. There is a lack of tools to quantitatively assess starvation-induced vacuole fusion and lipophagy in intact cells with high resolution and throughput. Here, we combine soft X-ray tomography (SXT) with fluorescence microscopy and use a deep-learning computational approach to visualize and quantify these processes in yeast. We focus on yeast homologs of mammalian NPC1 (NPC intracellular cholesterol transporter 1; Ncr1 in yeast) and NPC2 proteins, whose dysfunction leads to Niemann Pick type C (NPC) disease in humans. We developed a convolutional neural network (CNN) model which classifies fully fused versus partially fused vacuoles based on fluorescence images of stained cells. This CNN, named Deep Yeast Fusion Network (DYFNet), revealed that cells lacking Ncr1 (ncr1∆ cells) or Npc2 (npc2∆ cells) have a reduced capacity for vacuole fusion. Using a second CNN model, we implemented a pipeline named LipoSeg to perform automated instance segmentation of LDs and vacuoles from high-resolution reconstructions of X-ray tomograms. From that, we obtained 3D renderings of LDs inside and outside of the vacuole in a fully automated manner and additionally measured droplet volume, number, and distribution. We find that ncr1∆ and npc2∆ cells could ingest LDs into vacuoles normally but showed compromised degradation of LDs and accumulation of lipid vesicles inside vacuoles. Our new method is versatile and allows for analysis of vacuole fusion, droplet size and lipophagy in intact cells.Abbreviations: BODIPY493/503: 4,4-difluoro-1,3,5,7,8-pentamethyl-4-bora-3a,4a-diaza-s-Indacene; BPS: bathophenanthrolinedisulfonic acid disodium salt hydrate; CNN: convolutional neural network; DHE; dehydroergosterol; npc2∆, yeast deficient in Npc2; DSC, Dice similarity coefficient; EM, electron microscopy; EVs, extracellular vesicles; FIB-SEM, focused ion beam milling-scanning electron microscopy; FM 4-64, N-(3-triethylammoniumpropyl)-4-(6-[4-{diethylamino} phenyl] hexatrienyl)-pyridinium dibromide; LDs, lipid droplets; Ncr1, yeast homolog of human NPC1 protein; ncr1∆, yeast deficient in Ncr1; NPC, Niemann Pick type C; NPC2, Niemann Pick type C homolog; OD600, optical density at 600 nm; ReLU, rectifier linear unit; PPV, positive predictive value; NPV, negative predictive value; MCC, Matthews correlation coefficient; SXT, soft X-ray tomography; UV, ultraviolet; YPD, yeast extract peptone dextrose.

Laboratory based correlative cryo-soft X-ray tomography and cryo-fluorescence microscopy

Cryo-soft X-ray tomography is the unique technology that can image whole intact cells in 3D under normal and pathological conditions without labelling or fixation, at high throughput and spatial resolution. The sample preparation is relatively straightforward; requiring just fast freezing of the specimen before transfer to the microscope for imaging. It is also possible to image chemically fixed samples where necessary. The technique can be correlated with cryo fluorescence microscopy to localize fluorescent proteins to organelles within the whole cell volume. Cryo-correlated light and soft X-ray tomography is particularly useful for the study of gross morphological changes brought about by disease or drugs. For example, viral fluorescent tags can be co-localized to sites of viral replication in the soft X-ray volume. In general this approach is extremely useful in the study of complex 3D organelle structure, nanoparticle uptake or in the detection of rare events in the context of whole cell structure. The main challenge of soft X-ray tomography is that the soft X-ray illumination required for imaging has heretofore only been available at a small number of synchrotron labs worldwide. Recently, a compact device with a footprint small enough to fit in a standard laboratory setting has been deployed ("the SXT-100") and is routinely imaging cryo prepared samples addressing a variety of disease and drug research applications. The SXT-100 facilitates greater access to this powerful technique and greatly increases the scope and throughput of potential research projects. Furthermore, the availability of cryo-soft X-ray tomography in the laboratory will accelerate the development of novel correlative and multimodal workflows by integration with light and electron microscope based approaches. It also allows for co-location of this powerful imaging modality at BSL3 labs or other facilities where safety or intellectual property considerations are paramount. Here we describe the compact SXT-100 microscope along with its novel integrated cryo-fluorescence imaging capability.

Three-Dimensional Remodeling of SARS-CoV2-Infected Cells Revealed by Cryogenic Soft X-ray Tomography

Plus-strand RNA viruses are proficient at remodeling host cell membranes for optimal viral genome replication and the production of infectious progeny. These ultrastructural alterations result in the formation of viral membranous organelles and may be observed by different imaging techniques, providing nanometric resolution. Guided by confocal and electron microscopy, this study describes the generation of wide-field volumes using cryogenic soft-X-ray tomography (cryo-SXT) on SARS-CoV-2-infected human lung adenocarcinoma cells. Confocal microscopy showed accumulation of double-stranded RNA (dsRNA) and nucleocapsid (N) protein in compact perinuclear structures, preferentially found around centrosomes at late stages of the infection. Transmission electron microscopy (TEM) showed accumulation of membranous structures in the vicinity of the infected cell nucleus, forming a viral replication organelle containing characteristic double-membrane vesicles and virus-like particles within larger vesicular structures. Cryo-SXT revealed viral replication organelles very similar to those observed by TEM but indicated that the vesicular organelle observed in TEM sections is indeed a vesiculo-tubular network that is enlarged and elongated at late stages of the infection. Overall, our data provide additional insight into the molecular architecture of the SARS-CoV-2 replication organelle.

Dehydration as alternative sample preparation for soft X-ray tomography

Soft X-ray tomography (SXT) is an imaging technique to visualise whole cells without fixation, staining, and sectioning. For SXT imaging, cells are cryopreserved and imaged at cryogenic conditions. Such 'near-to-native' state imaging is in high demand and initiated the development of the laboratory table-top SXT microscope. As many laboratories do not have access to cryogenic equipment, we asked ourselves whether SXT imaging is feasible on dry specimens. This paper shows how the dehydration of cells can be used as an alternative sample preparation to obtain ultrastructure information. We compare different dehydration processes on mouse embryonic fibroblasts in terms of ultrastructural preservation and shrinkage. Based on this analysis, we chose critical point (CPD) dried cells for SXT imaging. In comparison to cryopreserved and air-dried cells, CPD dehydrated cells show high structural integrity although with about 3-7 times higher X-ray absorption for cellular organelles. As the difference in X-ray absorption values between organelles is preserved, 3D anatomy of CPD-dried cells can be segmented and analysed, demonstrating the applicability of CPD-dried sample preparation for SXT imaging. LAY DESCRIPTION: Soft X-ray tomography (SXT) is an imaging technique that allows to see the internal structures of cells without the need for special treatments like fixation or staining. Typically, SXT imaging involves freezing and imaging cells at very low temperatures. However, since many labs lack the necessary equipment, we explored whether SXT imaging could be done on dry samples instead. We compared different dehydration methods and found that critical point drying (CPD) was the most promising for SXT imaging. CPD-dried cells showed high structural integrity, although they absorbed more X-rays than hydrated cells, demonstrating that CPD-dried sample preparation is a viable alternative for SXT imaging.

Radiation Dose Reduction in Contrast-Enhanced Abdominal CT: Comparison of Photon-Counting Detector CT with 2nd Generation Dual-Source Dual-Energy CT in an oncologic cohort

RATIONAL AND OBJECTIVES

Comparison of radiation dose and image quality in routine abdominal and pelvic contrast-enhanced computed tomography (CECT) between a photon-counting detector CT (PCD-CT) and a dual energy dual source CT (DSCT).

MATERIALS AND METHODS

70 oncologic patients (mean age 66 ± 12 years, 29 females) were prospectively enrolled between November 2021 and February 2022. Abdominal CECT were clinically indicated and performed first on a 2nd-generation DSCT and at follow-up on a 1st-generation dual-source PCD-CT. The same contrast media (Imeron 350, Bracco imaging) and pump protocol was used for both scans. For both scanners, polychromatic images were reconstructed with 3mm slice thickness and comparable kernel (I30f[DSCT] and Br40f[PCD-CT]); for PCD-CT data from all counted events above the lowest energy threshold at 20 keV ("T3D") were used. Results were compared in terms of radiation dose metrics of CT dose index (CTDIvol), dose length product (DLP) and size-specific dose estimation (SSDE), objective and subjective measurements of image quality were scored by two emergency radiologists including lesion conspicuity.

RESULTS

Median time interval between the scans was 4 months (IQR: 3-6). CNRvessel and SNRvessel of T3D reconstructions from PCD-CT were significantly higher than those of DSCT (all, p < 0.05). Qualitative image noise analysis from PCD-CT and DSCT yielded a mean of 4 each. Lesion conspicuity was rated significantly higher in PCD-CT (Q3 strength) compared to DSCT images. CTDI, DLP and SSDE mean values for PCD-CT and DSCT were 7.98 ± 2.56 mGy vs. 14.11 ± 2.92 mGy, 393.13 ± 153.55 mGy*cm vs. 693.61 ± 185.76 mGy*cm and 9.98 ± 2.41 vs. 14.63 ± 1.63, respectively, translating to a dose reduction of around 32% (SSDE).

CONCLUSION

PCD-CT enables oncologic abdominal CT with a significantly reduced dose while keeping image quality similar to 2nd-generation DSCT.

Soft X-ray tomograms provide a structural basis for whole-cell modeling

Developing in silico models that accurately reflect a whole, functional cell is an ongoing challenge in biology. Current efforts bring together mathematical models, probabilistic models, visual representations, and data to create a multi-scale description of cellular processes. A realistic whole-cell model requires imaging data since it provides spatial constraints and other critical cellular characteristics that are still impossible to obtain by calculation alone. This review introduces Soft X-ray Tomography (SXT) as a powerful imaging technique to visualize and quantify the mesoscopic (~25 nm spatial scale) organelle landscape in whole cells. SXT generates three-dimensional reconstructions of cellular ultrastructure and provides a measured structural framework for whole-cell modeling. Combining SXT with data from disparate technologies at varying spatial resolutions provides further biochemical details and constraints for modeling cellular mechanisms. We conclude, based on the results discussed here, that SXT provides a foundational dataset for a broad spectrum of whole-cell modeling experiments.

Correlative Cryo-imaging Using Soft X-Ray Tomography for the Study of Virus Biology in Cells and Tissues

Viruses are obligate intracellular pathogens that depend on their host cell machinery and metabolism for their replicative life cycle. Virus entry, replication, and assembly are dynamic processes that lead to the reorganisation of host cell components. Therefore, a complete understanding of the viral processes requires their study in the cellular context where advanced imaging has been proven valuable in providing the necessary information. Among the available imaging techniques, soft X-ray tomography (SXT) at cryogenic temperatures can provide three-dimensional mapping to 25 nm resolution and is ideally suited to visualise the internal organisation of virus-infected cells. In this chapter, the principles and practices of synchrotron-based cryo-soft X-ray tomography (cryo-SXT) in virus research are presented. The potential of the cryo-SXT in correlative microscopy platforms is also demonstrated through working examples of reovirus and hepatitis research at Beamline B24 (Diamond Light Source Synchrotron, UK) and BL09-Mistral beamline (ALBA Synchrotron, Spain), respectively.

Soft X-ray Tomography Reveals HSV-1-Induced Remodeling of Human B Cells

Upon infection, viruses hijack the cell machinery and remodel host cell structures to utilize them for viral proliferation. Since viruses are about a thousand times smaller than their host cells, imaging virus-host interactions at high spatial resolution is like looking for a needle in a haystack. Scouting gross cellular changes with fluorescent microscopy is only possible for well-established viruses, where fluorescent tagging is developed. Soft X-ray tomography (SXT) offers 3D imaging of entire cells without the need for chemical fixation or labeling. Here, we use full-rotation SXT to visualize entire human B cells infected by the herpes simplex virus 1 (HSV-1). We have mapped the temporospatial remodeling of cells during the infection and observed changes in cellular structures, such as the presence of cytoplasmic stress granules and multivesicular structures, formation of nuclear virus-induced dense bodies, and aggregates of capsids. Our results demonstrate the power of SXT imaging for scouting virus-induced changes in infected cells and understanding the orchestration of virus-host remodeling quantitatively.

A guide into the world of high-resolution 3D imaging: the case of soft X-ray tomography for the life sciences

In the world of bioimaging, every choice made determines the quality and content of the data collected. The choice of imaging techniques for a study could showcase or dampen expected outcomes. Synchrotron radiation is indispensable for biomedical research, driven by the need to see into biological materials and capture intricate biochemical and biophysical details at controlled environments. The same need drives correlative approaches that enable the capture of heterologous but complementary information when studying any one single target subject. Recently, the applicability of one such synchrotron technique in bioimaging, soft X-ray tomography (SXT), facilitates exploratory and basic research and is actively progressing towards filling medical and industrial needs for the rapid screening of biomaterials, reagents and processes of immediate medical significance. Soft X-ray tomography at cryogenic temperatures (cryoSXT) fills the imaging resolution gap between fluorescence microscopy (in the hundreds of nanometers but relatively accessible) and electron microscopy (few nanometers but requires extensive effort and can be difficult to access). CryoSXT currently is accessible, fully documented, can deliver 3D imaging to 25 nm resolution in a high throughput fashion, does not require laborious sample preparation procedures and can be correlated with other imaging techniques. Here, we present the current state of SXT and outline its place within the bioimaging world alongside a guided matrix that aids decision making with regards to the applicability of any given imaging technique to a particular project. Case studies where cryoSXT has facilitated a better understanding of biological processes are highlighted and future directions are discussed.

A protocol for full-rotation soft X-ray tomography of single cells

The protocol describes step-by-step sample preparation, data acquisition, and segmentation of cellular organelles with soft X-ray tomography. It is designed for microscopes built to perform full-rotation data acquisition on specimens in cylindrical sample holders, such as the XM-2 microscope at the Advanced Light Source, LBNL; however, it might be generalized for similar sample holder designs for both synchrotron and table-top microscopes. For complete details on the use and execution of this profile, please refer to Loconte et al. (2021).

Soft X-ray tomography to map and quantify organelle interactions at the mesoscale

Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due to the range of scales encountered in cell biology and the throughput limitations of traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used to rapidly map ultrastructural reorganization and inter-organelle interactions in intact cells. SXT takes advantage of the naturally occurring, differential X-ray absorption of the carbon-rich compounds in each organelle. Specifically, we use SXT to map the spatiotemporal evolution of insulin vesicles and their co-localization and interaction with mitochondria in pancreatic β cells during insulin secretion and in response to different stimuli. We quantify changes in the morphology, biochemical composition, and relative position of mitochondria and insulin vesicles. These findings highlight the importance of a comprehensive and unbiased mapping at the mesoscale to characterize cell reorganization that would be difficult to detect with other existing methodologies.

Evaluation of the Role of Bacterial Amyloid on Nucleoid Structure Using Cryo-Soft X-Ray Tomography

Bacterial chromosomal DNA is packed within a non-membranous structure, the nucleoid, thanks to nucleoid associated proteins (NAPs). The role of bacterial amyloid has recently emerged among these NAPs, particularly with the nucleoid-associated protein Hfq that plays a direct role in DNA compaction. In this chapter, we present a 3D imaging technique, cryo-soft X-ray tomography (cryo-SXT) to obtain a detailed 3D visualization of subcellular bacterial structures, especially the nucleoid. Cryo-SXT imaging of native unlabeled cells enables observation of the nucleoid in 3D with a high resolution, allowing to evidence in vivo the role of amyloids on DNA compaction. The precise experimental methods to obtain 3D tomograms will be presented.

Using soft X-ray tomography for rapid whole-cell quantitative imaging of SARS-CoV-2-infected cells

High-resolution and rapid imaging of host cell ultrastructure can generate insights toward viral disease mechanism, for example for a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Here, we employ full-rotation soft X-ray tomography (SXT) to examine organelle remodeling induced by SARS-CoV-2 at the whole-cell level with high spatial resolution and throughput. Most of the current SXT systems suffer from a restricted field of view due to use of flat sample supports and artifacts due to missing data. In this approach using cylindrical sample holders, a full-rotation tomogram of human lung epithelial cells is performed in less than 10 min. We demonstrate the potential of SXT imaging by visualizing aggregates of SARS-CoV-2 virions and virus-induced intracellular alterations. This rapid whole-cell imaging approach allows us to visualize the spatiotemporal changes of cellular organelles upon viral infection in a quantitative manner.

Imaging of Virus-Infected Cells with Soft X-ray Tomography

Viruses are obligate parasites that depend on a host cell for replication and survival. Consequently, to fully understand the viral processes involved in infection and replication, it is fundamental to study them in the cellular context. Often, viral infections induce significant changes in the subcellular organization of the host cell due to the formation of viral factories, alteration of cell cytoskeleton and/or budding of newly formed particles. Accurate 3D mapping of organelle reorganization in infected cells can thus provide valuable information for both basic virus research and antiviral drug development. Among the available techniques for 3D cell imaging, cryo-soft X-ray tomography stands out for its large depth of view (allowing for 10 µm thick biological samples to be imaged without further thinning), its resolution (about 50 nm for tomographies, sufficient to detect viral particles), the minimal requirements for sample manipulation (can be used on frozen, unfixed and unstained whole cells) and the potential to be combined with other techniques (i.e., correlative fluorescence microscopy). In this review we describe the fundamentals of cryo-soft X-ray tomography, its sample requirements, its advantages and its limitations. To highlight the potential of this technique, examples of virus research performed at BL09-MISTRAL beamline in ALBA synchrotron are also presented.

Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images

Correlation of 3D images acquired on different microscopes can be a daunting prospect even for experienced users. This protocol describes steps for registration of images from soft X-ray absorption contrast imaging and super-resolution fluorescence imaging of hydrated biological materials at cryogenic temperatures. Although it is developed for data generated at synchrotron beamlines that offer the above combination of microscopies, it is applicable to all analogous imaging systems where the same area of a sample is examined using successive non-destructive imaging techniques. For complete details on the use and execution of this protocol, please refer to Kounatidis et al. (2020).

Assaying three-dimensional cellular architecture using X-ray tomographic and correlated imaging approaches

Much of our understanding of the spatial organization of and interactions between cellular organelles and macromolecular complexes has been the result of imaging studies utilizing either light- or electron-based microscopic analyses. These classical approaches, while insightful, are nonetheless limited either by restrictions in resolution or by the sheer complexity of generating multidimensional data. Recent advances in the use and application of X-rays to acquire micro- and nanotomographic data sets offer an alternative methodology to visualize cellular architecture at the nanoscale. These new approaches allow for the subcellular analyses of unstained vitrified cells and three-dimensional localization of specific protein targets and have served as an essential tool in bridging light and electron correlative microscopy experiments. Here, we review the theory, instrumentation details, acquisition principles, and applications of both soft X-ray tomography and X-ray microscopy and how the use of these techniques offers a succinct means of analyzing three-dimensional cellular architecture. We discuss some of the recent work that has taken advantage of these approaches and detail how they have become integral in correlative microscopy workflows.

Correlation of weight loss with residual gastric volume on computerized tomography in patients undergoing sleeve gastrectomy: A systematic review

Laparoscopic Sleeve gastrectomy (LSG) is the most commonly performed bariatric surgical procedure worldwide. There is wide variation however in post-operative weight loss on long term follow-up, and residual gastric volume (RGV) is believed to be an important variable. Multiple studies have correlated RGV as assessed by Computerized Tomography volumetry with excess weight loss (EWL%) following LSG, but definite consensus is lacking. This article systematically reviews the published studies in English literature to ascertain whether any correlation exists between the RGV and EWL% following LSG. Ten studies were included in this review, and significant differences were noted in the technique of RGV assessment, and timing of RGV and EWL% assessment. Five studies found a statistically significant correlation between the RGV and EWL%. One study found a correlation which did not reach statistical significance. Two additional studies reported that the resected volume rather than RGV correlated with the EWL%. Meta-analysis of studies reporting correlation between RGV and EWL% showed that up to 26.3% (95% CI: 5.1%-56.1%) of variability in EWL% can be explained by variations in RGV. A lower RGV is likely to result in a better post-operative weight loss following LSG. There is need for standardization of technique and timing of RGV assessment.

Genetic Variation at PPP1R3B Increases Hepatic CT Attenuation and Interacts With Prandial Status on Plasma Glucose

CONTEXT

A common genetic variant near PPP1R3B (rs4841132G > A) has been associated with increased hepatic computed tomography (CT) attenuation and with plasma levels of glucose and liver enzymes.

OBJECTIVE

To elucidate the association of rs4841132 with hepatic CT attenuation, and to test if synergistic effects modify the association of the variant with plasma glucose and liver enzymes.

DESIGN

Population-based cohort study.

SETTING AND PARTICIPANTS

The Copenhagen City Heart Study and the Copenhagen General Population Study combined, totaling 107 192 individuals from the Danish general population. Hepatic CT scans were available in 6445 individuals.

MAIN OUTCOME MEASURES

Hepatic CT attenuation and plasma levels of glucose and liver enzymes.

RESULTS

The rs4841132 A-allele (rs4841132-A) was associated with higher hepatic CT attenuation (P = 5 × 10-6). The probability of carrying rs4841132-A increased with higher hepatic CT attenuation in the range above 65 Hounsfield units, but remained constant at the range below (P = 4 × 10-8 for nonlinearity). Rs4841132-A was associated with up to 0.17 mmol/L higher plasma glucose in fasting individuals, but with up to 0.17 mmol/L lower glucose in postprandial individuals (P = 6 × 10-5 for interaction between rs4841132 and time since last meal on plasma glucose). Finally, rs4841132-A was associated with up to 2 U/L higher plasma alanine transaminase (P = 3 × 10-6). This association was not modified by adiposity, alcohol intake, or steatogenic genetic risk.

CONCLUSIONS

Rs4841132-A associates with higher hepatic CT attenuation in a distinctly nonlinear manner, and its association with plasma glucose depends on prandial status. The overall association pattern supports that rs4841132-A promotes hepatic glycogen synthesis postprandially.

From 2D STXM to 3D Imaging: Soft X-ray Laminography of Thin Specimens

X-ray tomography has become an indispensable tool for studying complex 3D interior structures with high spatial resolution. Three-dimensional imaging using soft X-rays offers powerful contrast mechanisms but has seen limited success with tomography due to the restrictions imposed by the much lower energy of the probe beam. The generalized geometry of laminography, characterized by a tilted axis of rotation, provides nm-scale 3D resolution for the investigation of extended (mm range) but thin (μm to nm) samples that are well suited to soft X-ray studies. This work reports on the implementation of soft X-ray laminography (SoXL) at the scanning transmission X-ray spectromicroscope of the PolLux beamline at the Swiss Light Source, Paul Scherrer Institut, which enables 3D imaging of extended specimens from 270 to 1500 eV. Soft X-ray imaging provides contrast mechanisms for both chemical sensitivity to molecular bonds and oxidation states and magnetic dichroism due to the much stronger attenuation of X-rays in this energy range. The presented examples of applications range from functionalized nanomaterials to biological photonic crystals and sophisticated nanoscaled magnetic domain patterns, thus illustrating the wide fields of research that can benefit from SoXL.

Switchable resolution in soft x-ray tomography of single cells

The diversity of living cells, in both size and internal complexity, calls for imaging methods with adaptable spatial resolution. Soft x-ray tomography (SXT) is a three-dimensional imaging technique ideally suited to visualizing and quantifying the internal organization of single cells of varying sizes in a near-native state. The achievable resolution of the soft x-ray microscope is largely determined by the objective lens, but switching between objectives is extremely time-consuming and typically undertaken only during microscope maintenance procedures. Since the resolution of the optic is inversely proportional to the depth of focus, an optic capable of imaging the thickest cells is routinely selected. This unnecessarily limits the achievable resolution in smaller cells and eliminates the ability to obtain high-resolution images of regions of interest in larger cells. Here, we describe developments to overcome this shortfall and allow selection of microscope optics best suited to the specimen characteristics and data requirements. We demonstrate that switchable objective capability advances the flexibility of SXT to enable imaging cells ranging in size from bacteria to yeast and mammalian cells without physically modifying the microscope, and we demonstrate the use of this technology to image the same specimen with both optics.

Soft X-ray tomography: virtual sculptures from cell cultures

Cellular complexity is represented best in high-spatial resolution, three-dimensional (3D) reconstructions. Soft X-ray tomography (SXT) generates detailed volumetric reconstructions of cells preserved in a near-to-native, frozen-hydrated state. SXT is broadly applicable and can image specimens ranging from bacteria to large mammalian cells. As a reference, we summarize light and electron microscopic methods. We then present an overview of SXT and discuss its role in cellular imaging. We detail the methods used to image biological specimens and present recent highlights that illustrate the capabilities of the technique. We conclude by discussing correlative imaging, specifically the combination of SXT and fluorescence microscopy performed on the same specimen. This correlated approach combines the structural morphology of a cell with its physiological characteristics to build a deeply informative composite view.

Imaging cell morphology and physiology using X-rays

Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.

[Oxygenation with extracorporeal membrane in obstructive shock secondary to lymphoproliferative disease]

The arteriovenous extracorporeal membrane is used in patients with hemodynamic and respiratory failure, unresponsive to conventional treatment. It provides transitory hemodynamic support, oxygenation and removal of CO2, allowing pulmonary rest. Moreover it offers the possibility of ultraprotective ventilation and avoids generation of VILI (Ventilation-Induced Lung Injury). It is not frequently used in patients with hemodynamic failure secondary to obstructive shock due to mediastinal compromise. We present the case of a patient with obstructive shock, mediastinal mass of lymphoproliferative origin that was treated with extracorporeal arteriovenous circulation membrane.

X-ray Fluorescence Nanotomography of Single Bacteria with a Sub-15 nm Beam

X-ray Fluorescence (XRF) microscopy is a growing approach for imaging the trace element concentration, distribution, and speciation in biological cells at the nanoscale. Moreover, three-dimensional nanotomography provides the added advantage of imaging subcellular structure and chemical identity in three dimensions without the need for staining or sectioning of cells. To date, technical challenges in X-ray optics, sample preparation, and detection sensitivity have limited the use of XRF nanotomography in this area. Here, XRF nanotomography was used to image the elemental distribution in individual E. coli bacterial cells using a sub-15 nm beam at the Hard X-ray Nanoprobe beamline (HXN, 3-ID) at NSLS-II. These measurements were simultaneously combined with ptychography to image structural components of the cells. The cells were embedded in small (3-20 µm) sodium chloride crystals, which provided a non-aqueous matrix to retain the three-dimensional structure of the E. coli while collecting data at room temperature. Results showed a generally uniform distribution of calcium in the cells, but an inhomogeneous zinc distribution, most notably with concentrated regions of zinc at the polar ends of the cells. This work demonstrates that simultaneous two-dimensional ptychography and XRF nanotomography can be performed with a sub-15 nm beam size on unfrozen biological cells to co-localize elemental distribution and nanostructure simultaneously.

Error analysis of speed of sound reconstruction in ultrasound limited angle transmission tomography

We have investigated limited angle transmission tomography to estimate speed of sound (SOS) distributions for breast cancer detection. That requires both accurate delineations of major tissues, in this case by segmentation of prior B-mode images, and calibration of the relative positions of the opposed transducers. Experimental sensitivity evaluation of the reconstructions with respect to segmentation and calibration errors is difficult with our current system. Therefore, parametric studies of SOS errors in our bent-ray reconstructions were simulated. They included mis-segmentation of an object of interest or a nearby object, and miscalibration of relative transducer positions in 3D. Close correspondence of reconstruction accuracy was verified in the simplest case, a cylindrical object in homogeneous background with induced segmentation and calibration inaccuracies. Simulated mis-segmentation in object size and lateral location produced maximum SOS errors of 6.3% within 10 mm diameter change and 9.1% within 5 mm shift, respectively. Modest errors in assumed transducer separation produced the maximum SOS error from miscalibrations (57.3% within 5 mm shift), still, correction of this type of error can easily be achieved in the clinic. This study should aid in designing adequate transducer mounts and calibration procedures, and in specification of B-mode image quality and segmentation algorithms for limited angle transmission tomography relying on ray tracing algorithms.

Soft X-Ray Imaging of Cellular Carbon and Nitrogen Distributions in Heterocystous Cyanobacteria

Soft x-ray microscopy (SXM) is a minimally invasive technique for single-cell high-resolution imaging as well as the visualization of intracellular distributions of light elements such as carbon, nitrogen, and oxygen. We used SXM to observe photosynthesis and nitrogen fixation in the filamentous cyanobacterium Anabaena sp. PCC 7120, which can form heterocysts during nitrogen starvation. Statistical and spectroscopic analyses from SXM images around the K-absorption edge of nitrogen revealed a significant difference in the carbon-to-nitrogen (C/N) ratio between vegetative cells and heterocysts. Application of this analysis to soft x-ray images of Anabaena sp. PCC 7120 revealed inhomogenous C/N ratios in the cells. Furthermore, soft x-ray tomography of Anabaena sp. PCC 7120 revealed differing cellular C/N ratios, indicating different carbon and nitrogen distributions between vegetative cells and heterocysts in three dimensions.

Peripheral Quantitative Computed Tomography (pQCT) Measures Contribute to the Understanding of Bone Fragility in Older Patients With Low-trauma Fracture

Dual-energy X-ray absorptiometry (DXA) as currently used has limitations in identifying patients with osteoporosis and predicting occurrence of fracture. We aimed to express peripheral quantitative computed tomography (pQCT) variables of patients with low-trauma fracture as T-scores by using T-score scales obtained from healthy young women, and to evaluate the potential clinical utility of pQCT for the assessment of bone fragility. Fracture patients were recruited from a fracture liaison service at the Royal Melbourne Hospital. Reference pQCT data were obtained from studies on women's health conducted by our group. A study visit was arranged with fracture patients, during which DXA and pQCT were applied to measure their bone strength. A total of 59 fracture patients were recruited, and reference data were obtained from 78 healthy young females. All DXA variables and most pQCT variables were significantly different between healthy young females and fracture patients (p < 0.05), except polar stress-strain index (p = 0.34) and cortical bone density (p = 0.19). Fracture patients were divided into osteoporosis and non-osteoporosis groups according to their DXA T-scores. Significant differences were observed in most pQCT variables (p < 0.05), except trabecular area and cortical density (p > 0.9 and p = 0.5, respectively). By applying pQCT T-scores, 11 (27%) of patients who were classified as having low or medium risk of osteoporosis on DXA T-scores alone were reclassified as high risk. Results of logistic regression suggested trabecular bone density as an independent predictor of osteoporosis status. More patients can be identified with osteoporosis by applying pQCT T-score variables in older people with low-trauma fracture. Peripheral QCT T-scores contribute to the understanding of bone fragility in this population.

Digital Tomography for Detection of Acute Occult Scaphoid Fractures

Diagnosis of occult scaphoid fractures remains a challenge. Traditional management consisting of 2 weeks of immobilization and repeat radiographs results in unnecessary immobilization of many patients without fracture. Magnetic resonance imaging (MRI) is sensitive but expensive. Digital tomography (DT) is an imaging technique that provides fine-cut visualization with minimal radiation exposure and may be used when there is high clinical suspicion despite negative findings on initial radiographs. The authors compared the ability of DT vs MRI to detect acute occult scaphoid fractures. This was an institutional review board-approved, prospective series. Adults for which clinical suspicion for acute scaphoid fracture (presenting within 96 hours of trauma) and negative findings on initial radiographs existed were included. Both a wrist tomogram and MRI were obtained. Wrists were immobilized and reevaluated at 10 to 14 days with repeat radiographs as a control. Studies were interpreted by a radiologist in a blinded fashion. Forty consecutive extremities in 39 patients met the inclusion criteria. Six (15%) of the 40 scaphoids were determined to be fractured on repeat radiographs. Digital tomogram yielded positive findings in 4 of these. Magnetic resonance imaging yielded positive findings in 8 (20%) of the 40 extremities. Sensitivities were 67% and 100% for digital tomogram and MRI, respectively (P=.0001). The positive predictive value was 100% for DT and MRI. The authors found that DT detects more occult scaphoid fractures than initial standard radiographs but is less sensitive than MRI. This is the first study to compare DT with MRI. Digital tomography can be used to augment radiographs and may increase diagnostic efficiency, minimize unnecessary immobilization, and reduce health care costs. [Orthopedics. 2017; 40(6):e1092-e1095.].

Should We Ignore What We Cannot Measure? How Non-Uniform Stretch, Non-Uniform Wall Thickness and Minor Side Branches Affect Computational Aortic Biomechanics in Mice

In order to advance the state-of-the-art in computational aortic biomechanics, we investigated the influence of (i) a non-uniform wall thickness, (ii) minor aortic side branches and (iii) a non-uniform axial stretch distribution on the location of predicted hotspots of principal strain in a mouse model for dissecting aneurysms. After 3 days of angiotensin II infusion, a murine abdominal aorta was scanned in vivo with contrast-enhanced micro-CT. The animal was subsequently sacrificed and its aorta was scanned ex vivo with phase-contrast X-ray tomographic microscopy (PCXTM). An automatic morphing framework was developed to map the non-pressurized, non-stretched PCXTM geometry onto the pressurized, stretched micro-CT geometry. The output of the morphing model was a structural FEM simulation where the output strain distribution represents an estimation of the wall deformation, not only due to the pressurization, but also due to the local axial stretch field. The morphing model also included minor branches and a mouse-specific wall thickness. A sensitivity study was then performed to assess the influence of each of these novel features on the outcome of the simulations. The results were supported by comparing the computed hotspots of principal strain to hotspots of early vascular damage as detected on PCXTM. Non-uniform axial stretch, non-uniform wall thickness and minor subcostal arteries significantly alter the locations of calculated hotspots of maximal principal strain. Even if experimental data on these features are often not available in clinical practice, one should be aware of the important implications that simplifications in the model might have on the final simulated result.

Biofilm imaging in porous media by laboratory X-Ray tomography: Combining a non-destructive contrast agent with propagation-based phase-contrast imaging tools

X-ray tomography is a powerful tool giving access to the morphology of biofilms, in 3D porous media, at the mesoscale. Due to the high water content of biofilms, the attenuation coefficient of biofilms and water are very close, hindering the distinction between biofilms and water without the use of contrast agents. Until now, the use of contrast agents such as barium sulfate, silver-coated micro-particles or 1-chloronaphtalene added to the liquid phase allowed imaging the biofilm 3D morphology. However, these contrast agents are not passive and potentially interact with the biofilm when injected into the sample. Here, we use a natural inorganic compound, namely iron sulfate, as a contrast agent progressively bounded in dilute or colloidal form into the EPS matrix during biofilm growth. By combining a very long source-to-detector distance on a X-ray laboratory source with a Lorentzian filter implemented prior to tomographic reconstruction, we substantially increase the contrast between the biofilm and the surrounding liquid, which allows revealing the 3D biofilm morphology. A comparison of this new method with the method proposed by Davit et al (Davit et al., 2011), which uses barium sulfate as a contrast agent to mark the liquid phase was performed. Quantitative evaluations between the methods revealed substantial differences for the volumetric fractions obtained from both methods. Namely, contrast agent—biofilm interactions (e.g. biofilm detachment) occurring during barium sulfate injection caused a reduction of the biofilm volumetric fraction of more than 50% and displacement of biofilm patches elsewhere in the column. Two key advantages of the newly proposed method are that passive addition of iron sulfate maintains the integrity of the biofilm prior to imaging, and that the biofilm itself is marked by the contrast agent, rather than the liquid phase as in other available methods. The iron sulfate method presented can be applied to understand biofilm development and bioclogging mechanisms in porous materials and the obtained biofilm morphology could be an ideal basis for 3D numerical calculations of hydrodynamic conditions to investigate biofilm-flow coupling.

Three-dimensional single-cell imaging with X-ray waveguides in the holographic regime

X-ray tomography at the level of single biological cells is possible in a low-dose regime, based on full-field holographic recordings, with phase contrast originating from free-space wave propagation. Building upon recent progress in cellular imaging based on the illumination by quasi-point sources provided by X-ray waveguides, here this approach is extended in several ways. First, the phase-retrieval algorithms are extended by an optimized deterministic inversion, based on a multi-distance recording. Second, different advanced forms of iterative phase retrieval are used, operational for single-distance and multi-distance recordings. Results are compared for several different preparations of macrophage cells, for different staining and labelling. As a result, it is shown that phase retrieval is no longer a bottleneck for holographic imaging of cells, and how advanced schemes can be implemented to cope also with high noise and inconsistencies in the data.

Characterisation of noise and sharpness of images from four digital breast tomosynthesis systems for simulation of images for virtual clinical trials

In-depth evaluation of the noise and sharpness characteristics of FujiFilm Innovality, GE SenoClaire, Hologic Selenia Dimensions and Siemens Inspiration digital breast tomosynthesis (DBT) systems was performed with the intention of improving image simulation for virtual clinical trials. Noise power spectra (NPS) and modulation transfer function curves (MTF) were measured for planar modes and for the first and central projections for DBT modes. In DBT mode, the x-ray beam was blocked for the projections before the central projection in order to remove the influence of lag and ghosting from the previous images. A quadratic fit between the NPS and linearised pixel value gave the noise coefficients for planar and DBT imaging modes. The spatial frequencies corresponding to an MTF of 0.5 (MTF0.5) were calculated from the MTF measurements made on the breast support and at 40 mm above the breast support. This was done for the first and the central projections. The percentage of signal carried over from the first projection to subsequent images (lag) was measured using a slit. The noise associated with lag was also evaluated. The DBT modes typically had lower electronic noise coefficients but higher structural noise coefficients compared to the respective planar mode MTF0.5 measured 40 mm above the table was between 6% and 47% lower for continuous scanning systems compared to 1% lower for step and shoot systems. For wide angle DBT, the MTF0.5 of the first projection was 18% (FujiFilm) and 28% (Siemens) lower than for the central projection. Lag in the second projection was 2.2%, 0.3%, 0.8% for the FujiFilm, GE and Hologic systems respectively. In all cases, the noise associated with lag was negligible. Current modelling frameworks for virtual clinical trials of breast DBT systems need to be adapted to account for signals from lag and variations in the MTF at wide angles.

The effect of system geometry and dose on the threshold detectable calcification diameter in 2D-mammography and digital breast tomosynthesis

Digital breast tomosynthesis (DBT) is under consideration to replace or to be used in combination with 2D-mammography in breast screening. The aim of this study was the comparison of the detection of microcalcification clusters by human observers in simulated breast images using 2D-mammography, narrow angle (15°/15 projections) and wide angle (50°/25 projections) DBT. The effects of the cluster height in the breast and the dose to the breast on calcification detection were also tested. Simulated images of 6 cm thick compressed breasts were produced with and without microcalcification clusters inserted, using a set of image modelling tools for 2D-mammography and DBT. Image processing and reconstruction were performed using commercial software. A series of 4-alternative forced choice (4AFC) experiments was conducted for signal detection with the microcalcification clusters as targets. Threshold detectable calcification diameter was found for each imaging modality with standard dose: 2D-mammography: 2D-mammography (165  ±  9 µm), narrow angle DBT (211  ±  11 µm) and wide angle DBT (257  ±  14 µm). Statistically significant differences were found when using different doses, but different geometries had a greater effect. No differences were found between the threshold detectable calcification diameters at different heights in the breast. Calcification clusters may have a lower detectability using DBT than 2D imaging.

[Comparison of a Radiation Dose During Standard Digital Radiography, Tomosynthesis, and Multislice Spiral Computed Tomography in an Experimental Study of Pediatric Anthropomorphic Phantom]

OBJECTIVE

To compare a radiation dose obtained during standard digital radiography, tomosynthesis, and multislice spiral computed tomography (MSCT).

MATERIAL AND METHODS

Life-size full body pediatric anthropomorphic mannequin phantom was examined with a Fujifilm FDR Ac Selerate 200 X-ray diagnostic apparatus and a Toshiba Aquilion Prime 64 computed scanner using the Piranha dosimetry equipment, as well as Gammex planar target, for comparison of the resolution of the apparatus. The effective radiation doses were calculated for different anatomical regions with the formulas specified in the methodical instructions, using the coefficients K and Kd.

RESULTS

The tables and graphs comparing the radiation dose when using different radiation diagnostic techniques were presented. The resolution of standard digital radiography versus that of tomosynthesis was analyzed. Fluctuations of the doses obtained were associated with the difference in the volume of irradiated tissue and in the presence of the doses in the irradiated volume of organs with high radiosensitivity. Optimal physical and technical parameters of photography were proposed, which could reduce a dose load on the patient, without significantly losing the quality of films.

CONCLUSION

The effective doses of tomosynthesis were significantly higher than those of standard digital radiography (p < 0.05) while those of (MSCT) were above those of both X-ray and tomosynthesis, and the resolution of the latter was slightly lower.

Absorption and Phase Contrast X-Ray Imaging in Paleontology Using Laboratory and Synchrotron Sources

X-ray micro-computed tomography (μCT) is commonly used for imaging of samples in biomedical or materials science research. Owing to the ability to visualize a sample in a nondestructive way, X-ray μCT is perfectly suited to inspect fossilized specimens, which are mostly unique or rare. In certain regions of the world where important sedimentation events occurred in the Precambrian geological time, several fossilized animals are studied to understand questions related to their origin, environment, and life evolution. This article demonstrates the advantages of applying absorption and phase-contrast CT on the enigmatic fossil Corumbella werneri, one of the oldest known animals capable of building hard parts, originally discovered in Corumbá (Brazil). Different tomographic setups were tested to visualize the fossilized inner structures: a commercial laboratory-based μCT device, two synchrotron-based imaging setups using conventional absorption and propagation-based phase contrast, and a commercial X-ray microscope with a lens-coupled detector system, dedicated for radiography and tomography. Based on our results we discuss the strengths and weaknesses of the different imaging setups for paleontological studies.

Imaging and characterizing cells using tomography

We can learn much about cell function by imaging and quantifying sub-cellular structures, especially if this is done non-destructively without altering said structures. Soft X-ray tomography (SXT) is a high-resolution imaging technique for visualizing cells and their interior structure in 3D. A tomogram of the cell, reconstructed from a series of 2D projection images, can be easily segmented and analyzed. SXT has a very high specimen throughput compared to other high-resolution structure imaging modalities; for example, tomographic data for reconstructing an entire eukaryotic cell is acquired in a matter of minutes. SXT visualizes cells without the need for chemical fixation, dehydration, or staining of the specimen. As a result, the SXT reconstructions are close representations of cells in their native state. SXT is applicable to most cell types. The deep penetration of soft X-rays allows cells, even mammalian cells, to be imaged without being sectioned. Image contrast in SXT is generated by the differential attenuation soft X-ray illumination as it passes through the specimen. Accordingly, each voxel in the tomographic reconstruction has a measured linear absorption coefficient (LAC) value. LAC values are quantitative and give rise to each sub-cellular component having a characteristic LAC profile, allowing organelles to be identified and segmented from the milieu of other cell contents. In this chapter, we describe the fundamentals of SXT imaging and how this technique can answer real world questions in the study of the nucleus. We also describe the development of correlative methods for the localization of specific molecules in a SXT reconstruction. The combination of fluorescence and SXT data acquired from the same specimen produces composite 3D images, rich with detailed information on the inner workings of cells.

Comparison of digital breast tomosynthesis and 2D digital mammography using a hybrid performance test

This paper introduces a hybrid method for performing detection studies in projection image based modalities, based on image acquisitions of target objects and patients. The method was used to compare 2D mammography and digital breast tomosynthesis (DBT) in terms of the detection performance of spherical densities and microcalcifications. The method starts with the acquisition of spheres of different glandular equivalent densities and microcalcifications of different sizes immersed in a homogeneous breast tissue simulating medium. These target objects are then segmented and the subsequent templates are fused in projection images of patients and processed or reconstructed. This results in hybrid images with true mammographic anatomy and clinically relevant target objects, ready for use in observer studies. The detection study of spherical densities used 108 normal and 178 hybrid 2D and DBT images; 156 normal and 321 hybrid images were used for the microcalcifications. Seven observers scored the presence/absence of the spheres/microcalcifications in a square region via a 5-point confidence rating scale. Detection performance in 2D and DBT was compared via ROC analysis with sub-analyses for the density of the spheres, microcalcification size, breast thickness and z-position. The study was performed on a Siemens Inspiration tomosynthesis system using patient acquisitions with an average age of 58 years and an average breast thickness of 53 mm providing mean glandular doses of 1.06 mGy (2D) and 2.39 mGy (DBT). Study results showed that breast tomosynthesis (AUC = 0.973) outperformed 2D (AUC = 0.831) for the detection of spheres (p  <  0.0001) and this applied for all spherical densities and breast thicknesses. By way of contrast, DBT was worse than 2D for microcalcification detection (AUC2D = 0.974, AUCDBT = 0.838, p  <  0.0001), with significant differences found for all sizes (150-354 µm), for breast thicknesses above 40 mm and for heights above the detector of 20 mm and above. In conclusion, the hybrid method was successfully used to produce images for a detection study; results showed breast tomosynthesis outperformed 2D for spherical densities while further optimization of DBT for microcalcifications is suggested.

Performance of one-view breast tomosynthesis as a stand-alone breast cancer screening modality: results from the Malmö Breast Tomosynthesis Screening Trial, a population-based study

OBJECTIVE

To assess the performance of one-view digital breast tomosynthesis (DBT) in breast cancer screening.

METHODS

The Malmö Breast Tomosynthesis Screening Trial is a prospective population-based one-arm study with a planned inclusion of 15000 participants; a random sample of women aged 40-74 years eligible for the screening programme. This is an explorative analysis of the first half of the study population (n = 7500). Participants underwent one-view DBT and two-view digital mammography (DM), with independent double reading and scoring. Primary outcome measures were detection rate, recall rate and positive predictive value (PPV). McNemar's test with 95 % confidence intervals was used.

RESULTS

Breast cancer was found in sixty-eight women. Of these, 46 cases were detected by both modalities, 21 by DBT alone and one by DM alone. The detection rate for one-view DBT was 8.9/1000 screens (95 % CI 6.9 to 11.3) and 6.3/1000 screens (4.6 to 8.3) for two-view DM (p < 0.0001). The recall rate after arbitration was 3.8 % (3.3 to 4.2) for DBT and 2.6 % (2.3 to 3.0) for DM (p < 0.0001). The PPV was 24 % for both DBT and DM.

CONCLUSION

Our results suggest that one-view DBT might be feasible as a stand-alone screening modality.

KEY POINTS

One-view DBT as a stand-alone breast cancer screening modality has not been investigated. One-view DBT increased the cancer detection rate significantly. The recall rate increased significantly but was still low. Breast cancer screening with one-view DBT as a stand-alone modality seems feasible.

Are human peripheral nerves sensitive to X-ray imaging?

Diagnostic imaging techniques play an important role in assessing the exact location, cause, and extent of a nerve lesion, thus allowing clinicians to diagnose and manage more effectively a variety of pathological conditions, such as entrapment syndromes, traumatic injuries, and space-occupying lesions. Ultrasound and nuclear magnetic resonance imaging are becoming useful methods for this purpose, but they still lack spatial resolution. In this regard, recent phase contrast x-ray imaging experiments of peripheral nerve allowed the visualization of each nerve fiber surrounded by its myelin sheath as clearly as optical microscopy. In the present study, we attempted to produce high-resolution x-ray phase contrast images of a human sciatic nerve by using synchrotron radiation propagation-based imaging. The images showed high contrast and high spatial resolution, allowing clear identification of each fascicle structure and surrounding connective tissue. The outstanding result is the detection of such structures by phase contrast x-ray tomography of a thick human sciatic nerve section. This may further enable the identification of diverse pathological patterns, such as Wallerian degeneration, hypertrophic neuropathy, inflammatory infiltration, leprosy neuropathy and amyloid deposits. To the best of our knowledge, this is the first successful phase contrast x-ray imaging experiment of a human peripheral nerve sample. Our long-term goal is to develop peripheral nerve imaging methods that could supersede biopsy procedures.

In vivo photoacoustic and fluorescence cystography using clinically relevant dual modal indocyanine green

Conventional X-ray-based cystography uses radio-opaque materials, but this method uses harmful ionizing radiation and is not sensitive. In this study, we demonstrate nonionizing and noninvasive photoacoustic (PA) and fluorescence (FL) cystography using clinically relevant indocyanine green (ICG) in vivo. After transurethral injection of ICG into rats through a catheter, their bladders were photoacoustically and fluorescently visualized. A deeply positioned bladder below the skin surface (i.e., ~1.5-5 mm) was clearly visible in the PA and FL image using a laser pulse energy of less than 2 mJ/cm2 (1/15 of the safety limit). Then, the in vivo imaging results were validated through in situ studies. Our results suggest that dual modal cystography can provide a nonionizing and noninvasive imaging tool for bladder mapping.

Ordered subsets convex algorithm for 3D terahertz transmission tomography

We investigate in this paper a new reconstruction method in order to perform 3D Terahertz (THz) tomography using a continuous wave acquisition setup in transmission mode. This method is based on the Maximum Likelihood for TRansmission tomography (ML-TR) first developed for X-ray imaging. We optimize the Ordered Subsets Convex (OSC) implementation of the ML-TR by including the Gaussian propagation model of THz waves and take into account the intensity distributions of both blank calibration scan and dark-field measured on THz detectors. THz ML-TR reconstruction quality and accuracy are discussed and compared to other tomographic reconstructions.

Synchrotron-based X-ray tomographic microscopy for visualization of three-dimensional collagen matrices

INTRODUCTION

Three-dimensional collagen matrices (3D-CMs) may be visualized by cumbersome reconstructions of serial sections. We report here on the method of synchrotron-based X-ray tomographic microscopy (SRXTM) to image 3D-CMs in native tissue probes.

MATERIAL AND METHODS

SRXTM of 3D-CMs (mucoderm®, mucograft®) was performed at the TOMCAT beamline of the Swiss Light Source (SLS) at the Paul Scherrer Institute (Villigen, Switzerland).

RESULTS

SRXTM combines the advantages of high-resolution scanning electron microscopy (SEM) imaging with the low-resolution reconstructions of micro-CT (μCT) imaging. It may be used to non-destructively visualize and analyze structures within the 3D-CMs without the need of serial sectioning and reconstruction.

CONCLUSION

High-resolution SRXTM is a useful tool in analyzing the topology and morphometry of structures in 3D-CMs. The outcome justifies the efforts in sophisticated data processing.

CLINICAL RELEVANCE

SRXTM may help to understand the clinical characteristics of 3D-CMs in more detail.

Three-dimensional study of poly(lactic co-glycolic acid) micro-porous microspheres using hard X-ray nano-tomography

Poly(lactic co-glycolic acid) (PLGA) is widely used in diverse fields, especially in delivering biologically active proteins and drugs. For these applications, the knowledge of morphology and microstructure of PLGA micro-porous microspheres is of great importance since they strongly influence the drug delivering efficiency. In this study, micro-porous PLGA microspheres loaded by bovine serum albumin are investigated by using a full-field Zernike phase contrast transmission hard X-ray microscope. From three-dimensional reconstructions and segmentations, fundamental microstructural parameters such as size, shape, distribution and volume ratio among pores and proteins inside PLGA microspheres were obtained. These parameters are useful to understand the relationship between the internal microstructure and drug encapsulation, as well as the drug release efficiency of PLGA microspheres. The presented results demonstrate the capability of hard X-ray nano-tomography to characterize porous microspheres loaded with proteins and drugs, and also open a way to analyse, optimize and design new PLGA microspheres for specific applications.

Linear fitting of multi-threshold counting data with a pixel-array detector for spectral X-ray imaging

Experiments and modeling are described to perform spectral fitting of multi-threshold counting measurements on a pixel-array detector. An analytical model was developed for describing the probability density function of detected voltage in X-ray photon-counting arrays, utilizing fractional photon counting to account for edge/corner effects from voltage plumes that spread across multiple pixels. Each pixel was mathematically calibrated by fitting the detected voltage distributions to the model at both 13.5 keV and 15.0 keV X-ray energies. The model and established pixel responses were then exploited to statistically recover images of X-ray intensity as a function of X-ray energy in a simulated multi-wavelength and multi-counting threshold experiment.

Estimation of scattered radiation in digital breast tomosynthesis

Digital breast tomosynthesis (DBT) is a promising technique to overcome the tissue superposition limitations found in planar 2D x-ray mammography. However, as most DBT systems do not employ an anti-scatter grid, the levels of scattered radiation recorded within the image receptor are significantly higher than that observed in planar 2D x-ray mammography. Knowledge of this field is necessary as part of any correction scheme and for computer modelling and optimisation of this examination. Monte Carlo (MC) simulations are often used for this purpose, however they are computationally expensive and a more rapid method of calculation is desirable. This issue is addressed in this work by the development of a fast kernel-based methodology for scatter field estimation using a detailed realistic DBT geometry. Thickness-dependent scatter kernels, which were validated against the literature with a maximum discrepancy of 4% for an idealised geometry, have been calculated and a new physical parameter (air gap distance) was used to estimate more accurately the distribution of scattered radiation for a series of anthropomorphic breast phantom models. The proposed methodology considers, for the first time, the effects of scattered radiation from the compression paddle and breast support plate, which can represent more than 30% of the total scattered radiation recorded within the image receptor. The results show that the scatter field estimator can calculate scattered radiation images in an average of 80 min for projection angles up to 25° with equal to or less than a 10% error across most of the breast area when compared with direct MC simulations.