SyncMRT: a solution to image-guided synchrotron radiotherapy for quality assurance and pre-clinical trials.

In this work, a new image guidance system and protocols for delivering image-guided radiotherapy (IGRT) on the Imaging and Medical Beamline (IMBL) at the ANSTO Australian Synchrotron are introduced. The image guidance methods used and the resulting accuracy of tumour alignment in in vivo experiments are often under-reported. Image guidance tasks are often complex, time-consuming and prone to errors. If unchecked, they may result in potential mis-treatments. We introduce SyncMRT, a software package that provides a simple, image guidance tool-kit for aligning samples to the synchrotron beam. We have demonstrated sub-millimetre alignment using SyncMRT and the small-animal irradiation platform (the DynamicMRT system) on the IMBL. SyncMRT has become the standard for carrying out IGRT treatments on the IMBL and has been used in all pre-clinical radiotherapy experiments since 2017. Further, we introduce two quality assurance (QA) protocols to synchrotron radiotherapy on the IMBL: the Winston-Lutz test and hidden target test. It is shown that the presented QA tests are appropriate for picking up geometrical setup errors and assessing the end-to-end accuracy of the image guidance process. Together, these tools make image guidance easier and provide a mechanism for reporting the geometric accuracy of synchrotron-based IGRT treatments. Importantly, this work is scalable to other delivery systems, and is in continual development to support the upcoming veterinary radiotherapy trials on the IMBL.

Laboratory-based multi-modal X-ray microscopy and micro-CT with Bragg magnifiers.

We report on the successful demonstration of X-ray phase contrast microscopy and micro computed tomography (CT) with a Bragg magnifier microscope (BMM) in a laboratory setup. The Bragg magnifiers, constituted by two channel-cut crystals in asymmetric diffraction, produced a 15X magnification of the X-ray beam, thus enabling high resolution imaging to be attained. The angular sensitivity of the crystals was used to implement analyzer-based phase contrast imaging: acquiring images at different angular positions and the three parametric images (apparent absorption, differential phase and scattering) have been obtained. Micro-CT, with resolution of about 5 µm is demonstrated with the same system. The main limitations, as well as the ways to mitigate them, are discussed with the aid of the experimental data. The technique demonstrated herein extends high-resolution, multi-modal, x-ray imaging and micro-CT to compact laboratory setups, with the potential of broadening the reach of these techniques outside the community of synchrotron users.

X-ray Bragg magnifier microscope as a linear shift invariant imaging system: image formation and phase retrieval.

We present the theoretical description of the image formation with the in-line germanium Bragg Magnifier Microscope (BMM) and the first successful phase retrieval of X-ray holograms recorded with this imaging system. The conditions under which the BMM acts as a linear shift invariant system are theoretically explained and supported by the experiment. Such an approach simplifies the mathematical treatment of the image formation and reconstruction as complicated propagation of the wavefront onto inclined planes can be avoided. Quantitative phase retrieval is demonstrated using a test sample and a proof of concept phase imaging of a spider leg is also presented.

Analytical description of partially coherent propagation and absorption losses in x-ray planar waveguides.

We present an analytical approach to describe field propagation along a planar x-ray waveguide (WG) in the presence of absorption losses. The method utilizes the complete expression for the complex index of refraction in solving the Helmholtz equation describing the guided modes. In this way, the propagation modes for the WG are no longer imposed to be standing waves and the energy flow from the core to the cladding, a consequence of the absorption in the cladding, can be calculated. In addition, the method accurately describes the field coupling between a plane wave and the WG, reproducing the self-imaging phenomenon. The case of partially coherent illumination has also been calculated for a realistic laboratory x-ray source.

Using coherent X-ray ptychography to probe medium-range order.

Characterization of microscopic structural order and in particular medium range order (MRO) in amorphous materials is challenging. A new technique is demonstrated that allows analysis of MRO using X-rays. Diffraction data were collected from a sample consisting of densely packed polystyrene-latex micro-spheres. Ptychography is used to reconstruct the sample transmission function and fluctuation microscopy applied to characterize structural order producing a detailed `fluctuation map' allowing analysis of the sample at two distinct length scales. Independent verification is provided via X-ray diffractometry. Simulations of dense random packing of spheres have also been used to explore the origin of the structural order measured.

Simultaneous X-ray fluorescence and ptychographic microscopy of Cyclotella meneghiniana.

Scanning X-ray fluorescence microscopy (XFM) is a particularly useful method for studying the spatial distribution of trace metals in biological samples. Here we demonstrate the utility of combining coherent diffractive imaging (CDI) with XFM for imaging biological samples to simultaneously produce high-resolution and high-contrast transmission images and quantitative elemental maps. The reconstructed transmission function yields morphological details which contextualise the elemental maps. We report enhancement of the spatial resolution in both the transmission and fluorescence images beyond that of the X-ray optics. The freshwater diatom Cyclotella meneghiniana was imaged to demonstrate the benefits of combining these techniques that have complementary contrast mechanisms.

Iterative retrieval of one-dimensional x ray wave field using a single intensity measurement.

The problem of retrieving a complex function from the modulus of its Fourier transform has non-unique solutions in one dimension. Therefore iterative phase retrieval methods cannot in general be confidently applied to one-dimensional problems, due to the presence of ambiguities. We present a method for a posteriori reduction of the ambiguities based on the correlation analysis of the solution of a large number of runs of an iterative phase retrieval algorithm with different random starting phases. The method is applied to experimentally measured diffraction patterns from an x ray waveguide illuminated by hard x rays. We demonstrate the possibility of retrieving the complex wave field at the exit face of the waveguide and compare the result with theoretical prediction.

Wave-field formation in a hollow x-ray waveguide.

Diffraction and refraction phenomena at the entrance of a hollow x-ray waveguide with weakly absorbing dielectric cladding layers are investigated using two independent approaches: (a) analytical and (b) numerical solutions of the wave equation in the paraxial (parabolic) approximation. It is shown that the wave penetrating through the cladding material substantially modifies the wave field near the waveguide entrance. It results in a significant increase of the total energy flux inside the guiding layer and in additional spatial modulation of the electromagnetic field.

Dispersion properties of x-ray waveguides.

We study the propagation of ultrashort pulses in x-ray waveguides (WGs) by addressing the problem of the temporal dispersion. Starting from basic equations, by means of numerical calculation we demonstrate that far from the absorption edges of the WGs the cladding's material dispersion is negligible. However, close to the absorption edge significant dispersion can take place. This behavior could in principle be exploited to manipulate incoming chirped beams. Moreover, using the two coherent beams produced by the WG in the second (and higher) order of resonance suggests the use of the WC as a dispersion-free beam splitter, which can facilitate x-ray pump-probe experiments in the femtosecond temporal range without the need for external sources.

Comparison of human trichinellosis caused by Trichinella spiralis and by Trichinella britovi.

The first documented report of an outbreak of human trichinellosis caused by Trichinella spiralis in Italy is described. Two family groups were involved. The source was wild boar meat products. The principal clinical features were fever (60%), myalgia (50%), and diarrhea (40%). The most useful laboratory indicators were eosinophilia (100%), elevated levels of creatine phosphokinase (CPK) (90%) and other muscle enzymes, parasite-specific IgG titers (100%), and anti-newborn larvae antibodies (30%). The levels of these responses correlated with the number of infective muscle larvae ingested, which was influenced by the length of time the ingested meat was cured. The clinical and biological features observed during human infection with T. spiralis appear to have been different from those reported during two outbreaks due to T. britovi, which occurred in southern Italy. The main distinctions between the two types of infections were a longer duration of parasite-specific IgG, increased CPK levels, and a more severe intestinal symptomatology in T. spiralis-infected patients than in those infected with T. britovi.