Mark Müller

Latest developments in microtomography and nanotomography at PETRA III

Due to the extraordinary beam characteristics of the new PETRA III synchrotron, i.e., the high brilliance, the extremely low emittance of 1 nm rad, and the high fraction of coherent photons even in the hard X-ray range, the imaging beamline (IBL) at PETRA III will provide state of the art imaging and tomography capabilities with resolution well into the nanometer range. Novel applications of tomographic techniques allow for high speed in situ measurements as well as highest spatial and density resolutions. Additionally, the highly coherent beam enables the application of phase contrast methods in an exceptional way. Since the focus is on the energy range between 5 and 50 keV, the IBL will among others be ideally suited for microtomography and nanotomography on small engineering materials science samples as well as for studying soft matter, bones, medical implants, and biomatter.

Segmentation-Based Attenuation Correction in Positron Emission Tomography/Magnetic Resonance Erroneous Tissue Identification and Its Impact on Positron Emission Tomography Interpretation

ObjectivesThe objective of this study was to evaluate the frequency and characteristics of artifacts in segmentation-based attenuation correction maps (&mgr;-maps) of positron emission tomography/magnetic resonance (PET/MR) and their impact on PET interpretation and the standardized uptake value (SUV) quantification in normal tissue and lesions. Materials and MethodsThe study was approved by the local institutional review board. Attenuation maps of 100 patients with PET/MR and preceding PET/computed tomography examination were retrospectively inspected for artifacts (tracers: 2-deoxy-2-[18F]fluoro-D-glucose (18F-FDG), 11C-Choline, 68Ga-DOTATOC, 68Ga-DOTATATE, 11C-Methionine). The artifacts were subdivided into 9 different groups on the basis of their localization and appearance. The impact of &mgr;-map artifacts in normal tissue and lesions on PET interpretation was evaluated qualitatively via visual analysis in synopsis with the non-attenuation-corrected (NAC) PET as well as quantitatively by comparing the SUV in artifact regions to reference regions. ResultsAttenuation map artifacts were found in 72% of the head/neck data sets, 61% of the thoracic data sets, 25% of the upper abdominal data sets, and 26% of the pelvic data sets. The most frequent localizations of the overall 276 artifacts were around metal implants (16%), in the lungs (19%), and outer body contours (31%). Twenty-one percent of all PET-avid lesions (38 of 184 lesions) were affected by artifacts in the majority without further consequences for visual PET interpretation. However, 9 PET-avid lung lesions were masked owing to &mgr;-map artifacts and, thus, were only detectable on the NAC PET or additional MR imaging sequences. Quantitatively, &mgr;-map artifacts led to significant SUV changes in areas with erroneous assignment of air instead of soft tissue (ie, metal artifacts) and of soft tissue instead of lung. Nevertheless, no change in diagnosis would have been caused by &mgr;-map artifacts. ConclusionsAttenuation map artifacts that occur in a considerable percentage of PET/MR data sets have the potential to falsify PET quantification and visual PET interpretation. Nevertheless, on the basis of the present data, in the clinical interpretation setup, no changes in diagnosis due to &mgr;-map artifacts may occur, especially when the &mgr;-maps are checked for artifacts and PET/MR is read in synopsis with the NAC PET, if artifacts are present.

Grating-based X-ray Dark-field Computed Tomography of Living Mice

Changes in x-ray attenuating tissue caused by lung disorders like emphysema or fibrosis are subtle and thus only resolved by high-resolution computed tomography (CT). The structural reorganization, however, is of strong influence for lung function. Dark-field CT (DFCT), based on small-angle scattering of x-rays, reveals such structural changes even at resolutions coarser than the pulmonary network and thus provides access to their anatomical distribution. In this proof-of-concept study we present x-ray in vivo DFCTs of lungs of a healthy, an emphysematous and a fibrotic mouse. The tomographies show excellent depiction of the distribution of structural – and thus indirectly functional – changes in lung parenchyma, on single-modality slices in dark field as well as on multimodal fusion images. Therefore, we anticipate numerous applications of DFCT in diagnostic lung imaging. We introduce a scatter-based Hounsfield Unit (sHU) scale to facilitate comparability of scans. In this newly defined sHU scale, the pathophysiological changes by emphysema and fibrosis cause a shift towards lower numbers, compared to healthy lung tissue.

Myoanatomy of the velvet worm leg revealed by laboratory-based nanofocus X-ray source tomography

Significance X-ray computed tomography (CT) imaging has become popular for investigating, nondestructively and three-dimensionally, both external and internal structures of various specimens. However, the limited resolution of conventional laboratory-based CT systems (≥500 nm) still hampers the detailed visualization of features on the low nanometer level. We present a laboratory CT device and data processing pipeline to routinely and efficiently generate high-resolution 3D data (≈100 nm) without requiring synchrotron radiation facilities. Our setup is especially relevant for conducting detailed analysis of very small biological samples, as demonstrated for a walking appendage of a velvet worm. Comparative analyses of our CT data with those obtained from other popular imaging methods highlight the advantages and future applicability of the nanoCT setup. X-ray computed tomography (CT) is a powerful noninvasive technique for investigating the inner structure of objects and organisms. However, the resolution of laboratory CT systems is typically limited to the micrometer range. In this paper, we present a table-top nanoCT system in conjunction with standard processing tools that is able to routinely reach resolutions down to 100 nm without using X-ray optics. We demonstrate its potential for biological investigations by imaging a walking appendage of Euperipatoides rowelli, a representative of Onychophora—an invertebrate group pivotal for understanding animal evolution. Comparative analyses proved that the nanoCT can depict the external morphology of the limb with an image quality similar to scanning electron microscopy, while simultaneously visualizing internal muscular structures at higher resolutions than confocal laser scanning microscopy. The obtained nanoCT data revealed hitherto unknown aspects of the onychophoran limb musculature, enabling the 3D reconstruction of individual muscle fibers, which was previously impossible using any laboratory-based imaging technique.

Ex Vivo Perfusion-Simulation Measurements of Microbubbles as a Scattering Contrast Agent for Grating-Based X-Ray Dark-Field Imaging.

The investigation of dedicated contrast agents for x-ray dark-field imaging, which exploits small-angle scattering at microstructures for contrast generation, is of strong interest in analogy to the common clinical use of high-atomic number contrast media in conventional attenuation-based imaging, since dark-field imaging has proven to provide complementary information. Therefore, agents consisting of gas bubbles, as used in ultrasound imaging for example, are of particular interest. In this work, we investigate an experimental contrast agent based on microbubbles consisting of a polyvinyl-alcohol shell with an iron oxide coating, which was originally developed for multimodal imaging and drug delivery. Its performance as a possible contrast medium for small-animal angiography was examined using a mouse carcass to realistically consider attenuating and scattering background signal. Subtraction images of dark field, phase contrast and attenuation were acquired for a concentration series of 100%, 10% and 1.3% to mimic different stages of dilution in the contrast agent in the blood vessel system. The images were compared to the gold-standard iodine-based contrast agent Solutrast, showing a good contrast improvement by microbubbles in dark-field imaging. This study proves the feasibility of microbubble-based dark-field contrast-enhancement in presence of scattering and attenuating mouse body structures like bone and fur. Therefore, it suggests a strong potential of the use of polymer-based microbubbles for small-animal dark-field angiography.

Three-dimensional virtual histology enabled through cytoplasm-specific X-ray stain for microscopic and nanoscopic computed tomography

Significance Three-dimensional histology of soft-tissue samples has proven to provide crucial benefits for the understanding of tissue structure. Nevertheless, the low attenuation of soft tissue has impaired the use of computed tomography (CT) as a tool for the nondestructive and 3D visualization of external and internal structural details. We present a cytoplasm-specific staining method tailored for X-ray CT that enables a routine and efficient 3D volume screening at high resolutions. Our technique is fully compatible with conventional histology and allows further histological investigations, as demonstrated for a mouse kidney. The comparative analysis of our CT data with conventional 2D histology highlights the future applicability of the cytoplasm-specific X-ray staining method for modern histological and histopathological investigations using laboratory X-ray CT devices. Many histological methods require staining of the cytoplasm, which provides instrumental details for diagnosis. One major limitation is the production of 2D images obtained by destructive preparation of 3D tissue samples. X-ray absorption micro- and nanocomputed tomography (microCT and nanoCT) allows for a nondestructive investigation of a 3D tissue sample, and thus aids to determine regions of interest for further histological examinations. However, application of microCT and nanoCT to biological samples (e.g., biopsies) is limited by the missing contrast within soft tissue, which is important to visualize morphological details. We describe an eosin-based preparation overcoming the challenges of contrast enhancement and selectivity for certain tissues. The eosin-based staining protocol is suitable for whole-organ staining, which then enables high-resolution microCT imaging of whole organs and nanoCT imaging of smaller tissue pieces retrieved from the original sample. Our results demonstrate suitability of the eosin-based staining method for diagnostic screening of 3D tissue samples without impeding further diagnostics through histological methods.

Contrast-to-noise ratio optimization for a prototype phase-contrast computed tomography scanner.

In the field of biomedical X-ray imaging, novel techniques, such as phase-contrast and dark-field imaging, have the potential to enhance the contrast and provide complementary structural information about a specimen. In this paper, a first prototype of a preclinical X-ray phase-contrast CT scanner based on a Talbot-Lau interferometer is characterized. We present a study of the contrast-to-noise ratios for attenuation and phase-contrast images acquired with the prototype scanner. The shown results are based on a series of projection images and tomographic data sets of a plastic phantom in phase and attenuation-contrast recorded with varying acquisition settings. Subsequently, the signal and noise distribution of different regions in the phantom were determined. We present a novel method for estimation of contrast-to-noise ratios for projection images based on the cylindrical geometry of the phantom. Analytical functions, representing the expected signal in phase and attenuation-contrast for a circular object, are fitted to individual line profiles of the projection data. The free parameter of the fit function is used to estimate the contrast and the goodness of the fit is determined to assess the noise in the respective signal. The results depict the dependence of the contrast-to-noise ratios on the applied source voltages, the number of steps of the phase stepping routine, and the exposure times for an individual step. Moreover, the influence of the number of projection angles on the image quality of CT slices is investigated. Finally, the implications for future imaging purposes with the scanner are discussed.

Small-animal dark-field radiography for pulmonary emphysema evaluation

Chronic obstructive pulmonary disease (COPD) is one of the leading causes of morbidity and mortality worldwide and emphysema is one of its main components. The disorder is characterized by irreversible destruction of the alveolar walls and enlargement of distal airspaces. Despite the severe changes in the lung tissue morphology, conventional chest radiographs have only a limited sensitivity for the detection of mild to moderate emphysema. X-ray dark-field is an imaging modality that can significantly increase the visibility of lung tissue on radiographic images. The dark-field signal is generated by coherent, small-angle scattering of x-rays on the air-tissue interfaces in the lung. Therefore, morphological changes in the lung can be clearly visualized on dark-field images. This is demonstrated by a preclinical study with a small-animal emphysema model. To generate a murine model of pulmonary emphysema, a female C57BL/6N mouse was treated with a single orotracheal application of porcine pancreatic elastase (80 U/kg body weight) dissolved in phosphate-buffered saline (PBS). Control mouse received PBS. The mice were imaged using a small-animal dark-field scanner. While conventional x-ray transmission radiography images revealed only subtle indirect signs of the pulmonary disorder, the difference between healthy and emphysematous lungs could be clearly directly visualized on the dark-field images. The dose applied to the animals is compatible with longitudinal studies. The imaging results correlate well with histology. The results of this study reveal the high potential of dark-field radiography for clinical lung imaging.

Lab-based x-ray nanoCT imaging

Due to the recent development of transmission X-ray tubes with very small focal spot sizes, laboratory-based CT imaging with sub-micron resolutions is nowadays possible. We recently developed a novel X-ray nanoCT setup featuring a prototype nanofocus X-ray source and a single-photon counting detector. The system is based on mere geometrical magnification and can reach resolutions of 200 nm. To demonstrate the potential of the nanoCT system for biomedical applications we show high resolution nanoCT data of a small piece of human tooth comprising coronal dentin. The reconstructed CT data clearly visualize the dentin tubules within the tooth piece.

Preclinical x-ray dark-field radiography for pulmonary emphysema evaluation

Pulmonary emphysema is a widespread disorder characterized by irreversible destruction of alveolar walls. The spatial distribution of the disease, so far, could only be obtained using an X-ray CT scan, implying a high patient dose. X-ray scattering on alveolar structures is measured in the dark-field signal. The signal is dependent on the size of alveoli and therefore, a combination of absorption and darkfield signal is explored for mapping the distribution of emphysema in the lung on x-ray projection images. In this study three excised murine lungs with pulmonary emphysema and three control samples were imaged using a compact, cone-beam, small-animal x-ray dark-field scanner with a polychromatic source. Statistical analysis of the results, based on a combination of transmission and darkfield signals, revealed a distinct difference between emphysematous and control samples. Subsequently, the distribution of emphysema was mapped out per-pixel for the lungs and showed good agreement with histological findings.