Dietary specializations and diversity in feeding ecology of the earliest stem mammals.

The origin and radiation of mammals are key events in the history of life, with fossils placing the origin at 220 million years ago, in the Late Triassic period. The earliest mammals, representing the first 50 million years of their evolution and including the most basal taxa, are widely considered to be generalized insectivores. This implies that the first phase of the mammalian radiation--associated with the appearance in the fossil record of important innovations such as heterodont dentition, diphyodonty and the dentary-squamosal jaw joint--was decoupled from ecomorphological diversification. Finds of exceptionally complete specimens of later Mesozoic mammals have revealed greater ecomorphological diversity than previously suspected, including adaptations for swimming, burrowing, digging and even gliding, but such well-preserved fossils of earlier mammals do not exist, and robust analysis of their ecomorphological diversity has previously been lacking. Here we present the results of an integrated analysis, using synchrotron X-ray tomography and analyses of biomechanics, finite element models and tooth microwear textures. We find significant differences in function and dietary ecology between two of the earliest mammaliaform taxa, Morganucodon and Kuehneotherium--taxa that are central to the debate on mammalian evolution. Morganucodon possessed comparatively more forceful and robust jaws and consumed 'harder' prey, comparable to extant small-bodied mammals that eat considerable amounts of coleopterans. Kuehneotherium ingested a diet comparable to extant mixed feeders and specialists on 'soft' prey such as lepidopterans. Our results reveal previously hidden trophic specialization at the base of the mammalian radiation; hence even the earliest mammaliaforms were beginning to diversify--morphologically, functionally and ecologically. In contrast to the prevailing view, this pattern suggests that lineage splitting during the earliest stages of mammalian evolution was associated with ecomorphological specialization and niche partitioning.

Fast iterative reconstruction of data in full interior tomography.

This paper introduces two novel strategies for iterative reconstruction of full interior tomography (FINT) data, i.e. when the field of view is entirely inside the object support and knowledge of the object support itself or the attenuation coefficients inside specific regions of interest are not available. The first approach is based on data edge-padding. The second technique creates an intermediate virtual sinogram, which is, then, reconstructed by a standard iterative algorithm. Both strategies are validated in the framework of the alternate direction method of multipliers plug-and-play with gridding projectors that provide a speed-up of three orders of magnitude with respect to standard operators implemented in real space. The proposed methods are benchmarked on synchrotron-based X-ray tomographic microscopy datasets of mouse lung alveoli. Compared with analytical techniques, the proposed methods substantially improve the reconstruction quality for FINT underconstrained datasets, facilitating subsequent post-processing steps.

Stimulated scintillation emission depletion X-ray imaging.

X-ray microtomography is a widely applied tool for noninvasive structure investigations. The related detectors are usually based on a scintillator screen for the fast in situ conversion of an X-ray image into an optical image. Spatial resolution of the latter is fundamentally diffraction limited. In this work, we introduce stimulated scintillation emission depletion (SSED) X-ray imaging where, similar to stimulated emission depletion (STED) microscopy, a depletion beam is applied to the scintillator screen to overcome the diffraction limit. The requirements for the X-ray source, the X-ray flux, the scintillator screen, and the STED beam were evaluated. Fundamental spatial resolution limits due to the spread of absorbed X-ray energy were estimated with Monte Carlo simulations. The SSED proof-of-concept experiments demonstrated 1) depletion of X-ray excited scintillation, 2) partial confinement of scintillating regions to sub-diffraction sized volumes, and 3) improvement of the imaging contrast by applying SSED.

STED properties of Ce3+, Tb3+, and Eu3+ doped inorganic scintillators.

Scintillator-based X-ray imaging is a powerful technique for noninvasive real-space microscopic structural investigation such as synchrotron-based computed tomography. The resolution of an optical image formed by scintillation emission is fundamentally diffraction limited. To overcome this limit, stimulated scintillation emission depletion (SSED) X-ray imaging, based on stimulated emission depletion (STED) microscopy, has been recently developed. This technique imposes new requirements on the scintillator material: efficient de-excitation by the STED-laser and negligible STED-laser excited luminescence. In this work, luminescence depletion was measured in several commonly-used Ce3+, Tb3+, and Eu3+ - doped scintillators using various STED lasers. The depletion of Tb3+ and Eu3+ via 4f-4f transitions was more efficient (Ps = 8…19 mW) than Ce3+ depletion via 5d-4f transitions (Ps = 43…45 mW). Main origins of STED-laser excited luminescence were one- and two-photon excitation, and scintillator impurities. LSO:Tb scintillator and a 628 nm cw STED-laser is the most promising combination for SSED satisfying the above-mentioned requirements.

Ancient administrative handwritten documents: X-ray analysis and imaging.

Handwritten characters in administrative antique documents from three centuries have been detected using different synchrotron X-ray imaging techniques. Heavy elements in ancient inks, present even for everyday administrative manuscripts as shown by X-ray fluorescence spectra, produce attenuation contrast. In most cases the image quality is good enough for tomography reconstruction in view of future applications to virtual page-by-page `reading'. When attenuation is too low, differential phase contrast imaging can reveal the characters from refractive index effects. The results are potentially important for new information harvesting strategies, for example from the huge Archivio di Stato collection, objective of the Venice Time Machine project.

Quantifying phosphoric acid in high-temperature polymer electrolyte fuel cell components by X-ray tomographic microscopy.

Synchrotron-based X-ray tomographic microscopy is investigated for imaging the local distribution and concentration of phosphoric acid in high-temperature polymer electrolyte fuel cells. Phosphoric acid fills the pores of the macro- and microporous fuel cell components. Its concentration in the fuel cell varies over a wide range (40-100 wt% H3PO4). This renders the quantification and concentration determination challenging. The problem is solved by using propagation-based phase contrast imaging and a referencing method. Fuel cell components with known acid concentrations were used to correlate greyscale values and acid concentrations. Thus calibration curves were established for the gas diffusion layer, catalyst layer and membrane in a non-operating fuel cell. The non-destructive imaging methodology was verified by comparing image-based values for acid content and concentration in the gas diffusion layer with those from chemical analysis.

Simple merging technique for improving resolution in qualitative single image phase contrast tomography.

For dynamic samples and/or for simple ease-of-use experiments, single-image phase contrast tomography is a very effective method for the 3D visualization of materials which would otherwise be indiscernible in attenuation based x-ray imaging. With binary samples (e.g. air-material) and monochromatic wavefields a transport-of-intensity (TIE)-based phase retrieval algorithm is known to retrieve accurate quantitative maps of the phase distribution. For mixed material samples and/or white beam radiation the algorithm can still produce useful qualitative tomographic reconstructions with significantly improved area contrast. The stability of the algorithm comes with a recognized associated loss of spatial resolution due to its essential behaviour as a low-pass filter. One possible answer to this is an image fusion technique that merges the slices reconstructed from raw phase contrast images and those after phase retrieval, where the improved contrast may be acquired without the associated loss of high-frequency information. We present this technique as a simple few-parameter Fourier method, which is easily tunable and highly compatible with current reconstruction steps.

Comparison of two x-ray phase-contrast imaging methods with a microfocus source.

We present a comparison for high-resolution imaging with a laboratory source between grating-based (GBI) and propagation-based (PBI) x-ray phase-contrast imaging. The comparison is done through simulations and experiments using a liquid-metal-jet x-ray microfocus source. Radiation doses required for detection in projection images are simulated as a function of the diameter of a cylindrical sample. Using monochromatic radiation, simulations show a lower dose requirement for PBI for small object features and a lower dose for GBI for larger object features. Using polychromatic radiation, such as that from a laboratory microfocus source, experiments and simulations show a lower dose requirement for PBI for a large range of feature sizes. Tested on a biological sample, GBI shows higher noise levels than PBI, but its advantage of quantitative refractive index reconstruction for multi-material samples becomes apparent.

Towards virtual histology with X-ray grating interferometry.

Breast cancer is the most common type of cancer worldwide. Diagnosing breast cancer relies on clinical examination, imaging and biopsy. A core-needle biopsy enables a morphological and biochemical characterization of the cancer and is considered the gold standard for breast cancer diagnosis. A histopathological examination uses high-resolution microscopes with outstanding contrast in the 2D plane, but the spatial resolution in the third, Z-direction, is reduced. In the present paper, we propose two high-resolution table-top systems for phase-contrast X-ray tomography of soft-tissue samples. The first system implements a classical Talbot-Lau interferometer and allows to perform ex-vivo imaging of human breast samples with a voxel size of 5.57 µm. The second system with a comparable voxel size relies on a Sigray MAAST X-ray source with structured anode. For the first time, we demonstrate the applicability of the latter to perform X-ray imaging of human breast specimens with ductal carcinoma in-situ. We assessed image quality of both setups and compared it to histology. We showed that both setups made it possible to target internal features of breast specimens with better resolution and contrast than previously achieved, demonstrating that grating-based phase-contrast X-ray CT could be a complementary tool for clinical histopathology.

X-ray mosaic nanotomography of large microorganisms.

Full-field X-ray microscopy is a valuable tool for 3D observation of biological systems. In the soft X-ray domain organelles can be visualized in individual cells while hard X-ray microscopes excel in imaging of larger complex biological tissue. The field of view of these instruments is typically 10(3) times the spatial resolution. We exploit the assets of the hard X-ray sub-micrometer imaging and extend the standard approach by widening the effective field of view to match the size of the sample. We show that global tomography of biological systems exceeding several times the field of view is feasible also at the nanoscale with moderate radiation dose. We address the performance issues and limitations of the TOMCAT full-field microscope and more generally for Zernike phase contrast imaging. Two biologically relevant systems were investigated. The first being the largest known bacteria (Thiomargarita namibiensis), the second is a small myriapod species (Pauropoda sp.). Both examples illustrate the capacity of the unique, structured condenser based broad-band full-field microscope to access the 3D structural details of biological systems at the nanoscale while avoiding complicated sample preparation, or even keeping the sample environment close to the natural state.

Imaging brain amyloid deposition using grating-based differential phase contrast tomography.

One of the core pathological features of Alzheimer's disease (AD) is the accumulation of amyloid plaques in the brain. Current efforts of medical imaging research aim at visualizing amyloid plaques in living patients in order to evaluate the progression of the pathology, but also to facilitate the diagnosis of AD at the prodromal stage. In this study, we evaluated the capabilities of a new experimental imaging setup to image amyloid plaques in the brain of a transgenic mouse model of Alzheimer's disease. This imaging setup relies on a grating interferometer at a synchrotron X-ray source to measure the differential phase contrast between brain tissue and amyloid plaques. It provides high-resolution images with a large field of view, making it possible to scan an entire mouse brain. Here, we showed that this setup yields sufficient contrast to detect amyloid plaques and to quantify automatically several important structural parameters, such as their size and their regional density in 3D, on the scale of a whole mouse brain. Whilst future developments are required to apply this technique in vivo, this grating-based setup already gives the possibility to perform powerful studies aiming at quantifying the amyloid pathology in mouse models of AD and might accelerate the evaluation of anti-amyloid compounds. In addition, this technique may also facilitate the development of other amyloid imaging methods such as positron emission tomography (PET) by providing convenient high-resolution 3D data of the plaque distribution for multimodal comparison.

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils.

The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a three-dimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains.

Regridding reconstruction algorithm for real-time tomographic imaging.

Sub-second temporal-resolution tomographic microscopy is becoming a reality at third-generation synchrotron sources. Efficient data handling and post-processing is, however, difficult when the data rates are close to 10 GB s(-1). This bottleneck still hinders exploitation of the full potential inherent in the ultrafast acquisition speed. In this paper the fast reconstruction algorithm gridrec, highly optimized for conventional CPU technology, is presented. It is shown that gridrec is a valuable alternative to standard filtered back-projection routines, despite being based on the Fourier transform method. In fact, the regridding procedure used for resampling the Fourier space from polar to Cartesian coordinates couples excellent performance with negligible accuracy degradation. The stronger dependence of the observed signal-to-noise ratio for gridrec reconstructions on the number of angular views makes the presented algorithm even superior to filtered back-projection when the tomographic problem is well sampled. Gridrec not only guarantees high-quality results but it provides up to 20-fold performance increase, making real-time monitoring of the sub-second acquisition process a reality.

Imaging the ultrasmall-angle x-ray scattering distribution with grating interferometry.

X-ray imaging with grating interferometry has previously been regarded as a technique providing information only in direct space. It delivers absorption, phase, and dark-field contrast, which can be viewed as parameters of the underlying but unresolved scattering distribution. Here, we present a method that provides the ultrasmall-angle x-ray scattering distribution and, thus, allows simultaneous access to direct and reciprocal space information.

A hybrid column generation and simulated annealing algorithm for direct aperture optimization.

The purpose of this work was to develop a hybrid column generation (CG) and simulated annealing (SA) algorithm for direct aperture optimization (H-DAO) and to show its effectiveness in generating high quality treatment plans for intensity modulated radiation therapy (IMRT) and mixed photon-electron beam radiotherapy (MBRT). The H-DAO overcomes limitations of the CG-DAO with two features improving aperture selection (branch-feature) and enabling aperture shape changes during optimization (SA-feature). The H-DAO algorithm iteratively adds apertures to the plan. At each iteration, a branch is created for each field provided. First, each branch determines the most promising aperture of its assigned field and adds it to a copy of the current apertures. Afterwards, the apertures of each branch undergo an MU-weight optimization followed by an SA-based simultaneous shape and MU-weight optimization and a second MU-weight optimization. The next H-DAO iteration continues the branch with the lowest objective function value. IMRT and MBRT treatment plans for an academic, a brain and a head and neck case generated using the CG-DAO and H-DAO were compared. For every investigated case and both IMRT and MBRT, the H-DAO leads to a faster convergence of the objective function value with number of apertures compared to the CG-DAO. In particular, the H-DAO needs about half the apertures to reach the same objective function value as the CG-DAO. The average aperture areas are 27% smaller for H-DAO than for CG-DAO leading to a slightly larger discrepancy between optimized and final dose. However, a dosimetric benefit remains. The H-DAO was successfully developed and applied to IMRT and MBRT. The faster convergence with number of apertures of the H-DAO compared to the CG-DAO allows to select a better compromise between plan quality and number of apertures.

Sensitivity of X-ray grating interferometry.

It is known that the sensitivity of X-ray phase-contrast grating interferometry with regard to electron density variations present in the sample is related to the minimum detectable refraction angle. In this article a numerical framework is developed that allows for a realistic and quantitative determination of the sensitivity. The framework is validated by comparisons with experimental results and then used for the quantification of several influences on the sensitivity, such as spatial coherence or the number of phase step images. In particular, we identify the ideal inter-grating distance with respect to the highest sensitivity for parallel beam geometry. This knowledge will help to optimize existing synchrotron-based grating interferometry setups.

TriB-RT: Simultaneous optimization of photon, electron and proton beams.

PURPOSE: To develop a novel treatment planning process (TPP) with simultaneous optimization of modulated photon, electron and proton beams for improved treatment plan quality in radiotherapy. METHODS: A framework for fluence map optimization of Monte Carlo (MC) calculated beamlet dose distributions is developed to generate treatment plans consisting of photon, electron and spot scanning proton fields. Initially, in-house intensity modulated proton therapy (IMPT) plans are compared to proton plans created by a commercial treatment planning system (TPS). A triple beam radiotherapy (TriB-RT) plan is generated for an exemplary academic case and the dose contributions of the three particle types are investigated. To investigate the dosimetric potential, a TriB-RT plan is compared to an in-house IMPT plan for two clinically motivated cases. Benefits of TriB-RT for a fixed proton beam line with a single proton field are investigated. RESULTS: In-house optimized IMPT are of at least equal or better quality than TPS-generated proton plans, and MC-based optimization shows dosimetric advantages for inhomogeneous situations. Concerning TriB-RT, for the academic case, the resulting plan shows substantial contribution of all particle types. For the clinically motivated case, improved sparing of organs at risk close to the target volume is achieved compared to IMPT (e.g. myelon and brainstem [Formula: see text] -37%) at cost of an increased low dose bath (healthy tissue V 10% +22%). In the scenario of a fixed proton beam line, TriB-RT plans are able to compensate the loss in degrees of freedom to substantially improve plan quality compared to a single field proton plan. CONCLUSION: A novel TPP which simultaneously optimizes photon, electron and proton beams was successfully developed. TriB-RT shows the potential for improved treatment plan quality and is especially promising for cost-effective single-room proton solutions with a fixed beamline in combination with a conventional linac delivering photon and electron fields.

Image processing pipeline for synchrotron-radiation-based tomographic microscopy.

With synchrotron-radiation-based tomographic microscopy, three-dimensional structures down to the micrometer level can be visualized. Tomographic data sets typically consist of 1000 to 1500 projections of 1024 x 1024 to 2048 x 2048 pixels and are acquired in 5-15 min. A processing pipeline has been developed to handle this large amount of data efficiently and to reconstruct the tomographic volume within a few minutes after the end of a scan. Just a few seconds after the raw data have been acquired, a selection of reconstructed slices is accessible through a web interface for preview and to fine tune the reconstruction parameters. The same interface allows initiation and control of the reconstruction process on the computer cluster. By integrating all programs and tools, required for tomographic reconstruction into the pipeline, the necessary user interaction is reduced to a minimum. The modularity of the pipeline allows functionality for new scan protocols to be added, such as an extended field of view, or new physical signals such as phase-contrast or dark-field imaging etc.

Development of an extended Macro Monte Carlo method for efficient and accurate dose calculation in magnetic fields.

MOTIVATION: Progress in the field of magnetic resonance (MR)-guided radiotherapy has triggered the need for fast and accurate dose calculation in presence of magnetic fields. The aim of this work is to satisfy this need by extending the macro Monte Carlo (MMC) method to enable dose calculation for photon, electron, and proton beams in a magnetic field. METHODS: The MMC method is based on the transport of particles in macroscopic steps through an absorber by sampling the relevant physical quantities from a precalculated database containing probability distribution functions. To enable MMC particle transport in a magnetic field, a transformation accounting for the Lorentz force is applied for each macro step by rotating the sampled position and direction around the magnetic field vector. The transformed position and direction distributions on local geometries are validated against full MC for electron and proton pencil beams. To enable photon dose calculation, an in-house MC algorithm is used for photon transport and interaction. Emerging secondary charged particles are passed to MMC for transport and energy deposition. The extended MMC dose calculation accuracy and efficiency is assessed by comparison with EGSnrc (photon and electron beams) and Geant4 (proton beam) calculated dose distributions of different energies and homogeneous magnetic fields for broad beams impinging on water phantoms with bone and lung inhomogeneities. RESULTS: The geometric transformation on the local geometries is able to reproduce the results of full MC for all investigated settings (difference in mean value and standard deviation <1%). Macro Monte Carlo calculated dose distributions in a homogeneous magnetic field are in agreement with EGSnrc and Geant4, respectively, with gamma passing rates >99.6% (global 2%, 2 mm and 10% threshold criteria) for all situations. MMC achieves a substantial efficiency gain of up to a factor of 21 (photon beam), 66 (electron beam), and 356 (proton beam) compared to EGSnrc or Geant4. CONCLUSION: Efficient and accurate dose calculation in magnetic fields was successfully enabled by utilizing the developed extended MMC transport method for photon, electron, and proton beams.

Towards MR-guided electron therapy: Measurement and simulation of clinical electron beams in magnetic fields.

PURPOSE: In the current era of MRI-linac radiotherapy, dose optimization with arbitrary dose distributions is a reality. For the first time, we present new and targeted experiments and modeling to aid in evaluating the potential dose improvements offered with an electron beam mode during MRI-linac radiotherapy. METHODS: Small collimated (1 cm diameter and 1.5 × 1.5 cm2 square) electron beams (6, 12 and 20 MeV) from a clinical linear accelerator (Varian Clinac 2100C) are incident perpendicular and parallel to the strong and localized magnetic fields (0-0.7 T) generated by a permanent magnet device. Gafchromic EBT3 film is placed inside a slab phantom to measure two-dimensional dose distributions. A benchmarked and comprehensive Monte Carlo model (Geant4) is established to directly compare with experiments. RESULTS: With perpendicular fields a 5% narrowing of the beam FWHM and a 10 mm reduction in the 15% isodose penetration is seen for the 20 MeV beam. In the inline setup the penumbral width is reduced by up to 20%, and a local central dose enhancement of 100% is observed. Monte Carlo simulations are in agreement with the measured dose distributions (2% or 2 mm). CONCLUSION: A new range of experiments have been performed to offer insight into how an electron beam mode could offer additional choices in MRI-linac radiotherapy. The work extends on historic studies to bring a successful unified experimental and Monte Carlo modeling approach for studying small field electron beam dosimetry inside magnetic fields. The results suggest further work, particularly on the inline magnetic field scenario.