Tim Gureyev

Optimization of propagation-based x-ray phase-contrast tomography for breast cancer imaging

The aim of this study was to optimise the experimental protocol and data analysis for in-vivo breast cancer x-ray imaging. Results are presented of the experiment at the SYRMEP beamline of Elettra Synchrotron using the propagation-based phase-contrast mammographic tomography method, which incorporates not only absorption, but also x-ray phase information. In this study the images of breast tissue samples, of a size corresponding to a full human breast, with radiologically acceptable x-ray doses were obtained, and the degree of improvement of the image quality (from the diagnostic point of view) achievable using propagation-based phase-contrast image acquisition protocols with proper incorporation of x-ray phase retrieval into the reconstruction pipeline was investigated. Parameters such as the x-ray energy, sample-to-detector distance and data processing methods were tested, evaluated and optimized with respect to the estimated diagnostic value using a mastectomy sample with a malignant lesion. The results of quantitative evaluation of images were obtained by means of radiological assessment carried out by 13 experienced specialists. A comparative analysis was performed between the x-ray and the histological images of the specimen. The results of the analysis indicate that, within the investigated range of parameters, both the objective image quality characteristics and the subjective radiological scores of propagation-based phase-contrast images of breast tissues monotonically increase with the strength of phase contrast which in turn is directly proportional to the product of the radiation wavelength and the sample-to-detector distance. The outcomes of this study serve to define the practical imaging conditions and the CT reconstruction procedures appropriate for low-dose phase-contrast mammographic imaging of live patients at specially designed synchrotron beamlines.

X-ray ultramicroscopy using integrated sample cells.

The X-ray ultramicroscope (XuM), based on using a scanning electron microscope as host, provides a new approach to X-ray projection microscopy. The right-angle-type integrated sample cells described here expand the capabilities of the XuM technique. The integrated sample cell combines a target, a spacer, a sample chamber, and an exit window in one physical unit, thereby simplifying the instrumentation and providing increased mechanical stability. The XuM imaging results presented here, obtained using such right-angle integrated sample cells, clearly demonstrate the ability to characterize very small features in objects, down to of order 100nm, including their use for dry, wet and even liquid samples.

New Methods of X-Ray Imaging based on Phase Contrast

Phase-contrast X-ray images can be produced in various ways. Some aspects of the relatively simple “in-line” method are presented which may be implemented using a quasi-spherical X-ray wave with high spatial but not chromatic coherence. Appropriate sources can be found in commercially-available microfocus tubes or at synchrotrons. Compared to previous phase-contrast methods, the present one offers relatively simple implementation, relatively high intensity and a large field of view, making it potentially suitable for clinical applications.

Soft tissue small avascular tumor imaging with x-ray phase-contrast micro-CT in-line holography

To assess the feasibility of small soft tissue avascular tumor micro-CT imaging with x-ray phase-contrast in-line holography, we have studied micro-CT imaging with in-line geometry of small spheroidal avascular tumor models with quiescent cell core (< 250 μm) and various distributions of the proliferating cell density (PCD) forming the outer shell. We have simulated imaging with an ultrafast laser-based x-ray source with a Mo target. We observe phase-contrast enhancement of the tumor boundaries in the reconstructed transaxial images, resulting in improved detection of small soft tissue tumors, providing that the PCD density gradient is sufficiently large.

Biomedical image analysis and processing in clouds

Cloud-based Image Analysis and Processing Toolbox project runs on the Australian National eResearch Collaboration Tools and Resources (NeCTAR) cloud infrastructure and allows access to biomedical image processing and analysis services to researchers via remotely accessible user interfaces. By providing user-friendly access to cloud computing resources and new workflow-based interfaces, our solution enables researchers to carry out various challenging image analysis and reconstruction tasks. Several case studies will be presented during the conference.

X‐ray phase‐contrast imaging with an Inverse Compton Scattering source

Single‐shot in‐line phase‐contrast imaging with the Inverse Compton Scattering X‐ray source available at ATF (Accelerator Test Facility) at Brookhaven National Laboratory is experimentally demonstrated. Phase‐contrast images of polymer wires are obtained with a single X‐ray pulse whose time length is about 1 picosecond. The edge‐enhancement effect is clearly visible in the images and simulations show a quantitative agreement with experimental data. A phase‐retrieval step in the image processing leads to a accurate estimation of the projected thickness of our samples. Finally, a single‐shot image of a wasp is presented as an example of a biological sample.

Cloud based toolbox for image analysis, processing and reconstruction tasks.

This chapter describes a novel way of carrying out image analysis, reconstruction and processing tasks using cloud based service provided on the Australian National eResearch Collaboration Tools and Resources (NeCTAR) infrastructure. The toolbox allows users free access to a wide range of useful blocks of functionalities (imaging functions) that can be connected together in workflows allowing creation of even more complex algorithms that can be re-run on different data sets, shared with others or additionally adjusted. The functions given are in the area of cellular imaging, advanced X-ray image analysis, computed tomography and 3D medical imaging and visualisation. The service is currently available on the website www.cloudimaging.net.au .

Applications of Heterogeneous Computing in Computational and Simulation Science

As the size and complexity of scientific problems and datasets grow, scientists from a broad range of discipline areas are relying more and more on computational methods and simulations to help solve their problems. This paper presents a summary of heterogeneous algorithms and applications that have been developed by a large research organization (CSIRO) for solving practical and challenging science problems faster than is possible with conventional multi-core CPUs alone. The problem domains discussed include biological image analysis, computed tomography reconstruction, marine biogeochemical models, fluid dynamics, and bioinformatics. The algorithms utilize GPUs and multi-core CPUs on a scale ranging from single workstation installations through to large GPU clusters. Results demonstrate that large GPU clusters can be used to accelerate a variety of practical science applications, and justify the significant financial investment and interest being placed into such systems.

Mean absorbed dose to mouse in micro-CT imaging with an ultrafast laser-based x-ray source

We have investigated theoretically the mean absorbed dose to the mouse in our newly constructed, in-line holography, x-ray phase-contrast, in-vivo, micro-CT system with an ultrafast laser-based x-ray (ULX) source. We assumed that the effective mouse diameter was 30 mm and the x-ray detector required minimum 30 μGy per frame to produce high quality images. The following laser target-filter combinations were considered: Ag-Ag, Mo-Mo, Sn- Sn. In addition, we considered narrow-pass multilayer x-ray mirrors. The corresponding ULX spectra were obtained using a CZT solid-state spectrometer. The approach used for dose computation was similar to human dose estimation. The mouse was modeled as a tissue-equivalent cylinder located at the isocenter with diameter 30 mm and density 1g/cm3. A layer of dermis (skin and fur) with 1 mm thickness was also modeled. Imparted energy per volume was estimated for 1 keV wide x-ray energy intervals in the 6-100 keV range. Monte Carlo simulations were performed using the SIERRA code previously validated using 30 mm diameter PMMA phantom. The results obtained indicate that: a) the mean absorbed dose for ULX is less than or equal to that from a W-anode micro-CT tube operating at 30-40 kVp with 0.5 or 1.0 mm Al; b) for filter thickness above 100 μm, Sn-Sn results in the highest dose, followed by Ag-Ag and Mo-Mo; c) the multilayer x-ray mirror with FWHM ≤ 10 keV produces significantly lower dose than metallic foil filters. We conclude that ULX can provide better dose utilization than a microfocal x-ray tube for in vivo microtomography applications.

Laboratory-based x-ray micro-tomography with submicron resolution

X-ray Microtomography bridges the 3D analysis gap between conventional x-ray tomography and TEM tomography. The use of a laboratory-based microfocus source opens up the opportunity to gain additional benefits from in-line phase contrast for enhancing the visibility of fine features, cracks, voids and boundaries in individual views. Coupled with phase retrieval methods, such images can be used as input to conventional reconstruction algorithms for three dimensional visualization. Working at high resolution brings challenges of physical stability of the system. Software approaches to overcoming these difficulties have enabled submicron resolution 3D reconstructions.