Particle Induced X-ray Emission Tomography Research Articles

Application of silicon drift detector in PIXE tomography system of Fudan University

In the Nuclear Microprobe Laboratory of Fudan University, particle induced X-ray emission (PIXE) has invariably used the Si(Li) detector. Although it is a widely used X-ray detector, the Si(Li) detector has a low counting rate. In recent years, high-counting rate detectors such as the silicon drift detector (SDD) have developed rapidly. This paper demonstrates the feasibility of applying the SDD to PIXE tomography (PIXE-T) for the first time. We placed the Si(Li) detector and the SDD in symmetrical positions to collect X-rays emitted from a Cl-doped inertial confinement fusion (ICF) target simultaneously. The counting rate of the SDD is about 5 times that of the Si(Li) detector. The maximum likelihood expectation maximization (MLEM) algorithm was used to reconstruct the projection slice by slice. The quality of the projections and the reconstructed images is improved using the SDD thanks to the higher number of events collected in the detector.

A dual-PIXE tomography setup for reconstruction of Germanium in ICF target

Inertial Confinement Fusion (ICF) is one type of fusion energy research which could initiate nuclear fusion reactions through heating and compressing thermonuclear fuel. Compared to a pure plastic target, Germanium doping into the CH ablator layer by Glow Discharge Polymer (GDP) technique can increase the ablation velocity and the standoff distance between the ablation front and laser-deposition region. During target fabrication process, quantitative doping of Ge should be accurately controlled. Particle Induced X-ray Emission Tomography (PIXE-T) can make not only quantification of the concentration, but also reconstruction of the spatial distribution of doped element. The Si (Li) detector for PIXE tomography technique had a disadvantage of low counting rate. To make up this deficiency, another detector of Si (Li) with the same configuration positioned at the opposite side with the same detective angle 135° have been implemented. Simultaneously acquired elemental maps of Ge obtained using two detectors may be different because of the X-ray absorption along the X-ray exit route in the target. In this paper, the X-ray detection efficiency is drastically improved by this dual-PIXE tomography system.

Reconstruction of Ge spatial distribution in ICF target using PIXE-T

Inertial confinement fusion (ICF) target is a microsphere with diameter at millimeter scale and shell thickness at micrometer scale. Ge-doped glow discharge polymer (GDP) is an ideal material for the target. The homogeneity of dopant is vital for uniform compression and minimization of Rayleigh-Taylor (RT) instabilities in ignition. However, the method of quantitative measurement of dopants’ spatial distribution is still not mature. Quantitation is not accurate and image resolution is low. Particle induced X-ray emission tomography (PIXE-T) is a suitable technique for measuring trace elements’ spatial distribution in small sample at micrometer scale. This paper demonstrates the capabilities of PIXE-T to obtain quantitative spatial distribution of dopant (Germanium) in ICF target for the first time. We also developed a program run in MATLAB to reconstruct Ge spatial distribution 3D image using Filtered Back Projection (FBP) algorithm. When ion beam is transmitted through the target, its energy is attenuated due to collisions. This energy attenuation causes decrease of X-ray emission cross section. For X-ray emitted from target inside, it will be absorbed by target itself before being collected by detector. Both effects cause loss of X-ray counts, especially at the rear of target toward beam. The program can compensate the loss of X-ray counts caused by these two effects, non-linear X-ray production (NLXP) along the path of the beam and X-ray attenuation (XA). This correction is based on a uniform mass density (1.08g/cm3) and a uniform major composition (stoichiometric ratio C:H=5:7 for GDP material) within the sample. Corrections are applied before tomographic reconstruction, producing a more accurate Ge spatial distribution image. After converting X-ray counts in every voxel to Ge concentration using standard reference material (SRM), the image shows quantitative spatial distribution.

Quantitative reconstruction of PIXE-tomography data for thin samples using GUPIX X-ray emission yields

We present here a new development of the TomoRebuild software package, to perform quantitative Particle Induced X-ray Emission Tomography (PIXET) reconstruction. X-ray yields are obtained from the GUPIX code. The GUPIX data base is available for protons up to 5MeV and also in the 20–100MeV energy range, deuterons up to 6MeV, 3He and alphas up to 12MeV. In this version, X-ray yields are calculated for thin samples, i.e. without simulating X-ray attenuation. PIXET data reconstruction is kept as long as possible independent from Scanning Transmission Ion Microscopy Tomography (STIMT). In this way, the local mass distribution (in g/cm3) of each X-ray emitting element is reconstructed in all voxels of the analyzed volume, only from PIXET data, without the need of associated STIMT data. Only the very last step of data analysis requires STIMT data, in order to normalize PIXET data to obtain concentration distributions, in terms of normalized mass fractions (in μg/g). For this, a noise correction procedure has been designed in ImageJ. Moreover sinogram or image misalignment can be corrected, as well as the difference in beam size between the two experiments. The main features of the TomoRebuild code, user friendly design and modular C++ implementation, were kept. The software package is portable and can run on Windows and Linux operating systems. An optional user-friendly graphic interface was designed in Java, as a plugin for the ImageJ graphic software package. Reconstruction examples are presented from biological specimens of Caenorhabditis elegans – a small nematode constituting a reference model for biology studies. The reconstruction results are compared between the different codes TomoRebuild, DISRA and JPIXET, and different reconstruction methods: Filtered BackProjection (FBP) and Maximum Likelihood Expectation Maximization (MLEM).

Beyond filtered backprojection: A reconstruction software package for ion beam microtomography data

A new version of the TomoRebuild data reduction software package is presented, for the reconstruction of scanning transmission ion microscopy tomography (STIMT) and particle induced X-ray emission tomography (PIXET) images. First, we present a state of the art of the reconstruction codes available for ion beam microtomography. The algorithm proposed here brings several advantages. It is a portable, multi-platform code, designed in C++ with well-separated classes for easier use and evolution. Data reduction is separated in different steps and the intermediate results may be checked if necessary. Although no additional graphic library or numerical tool is required to run the program as a command line, a user friendly interface was designed in Java, as an ImageJ plugin. All experimental and reconstruction parameters may be entered either through this plugin or directly in text format files. A simple standard format is proposed for the input of experimental data. Optional graphic applications using the ROOT interface may be used separately to display and fit energy spectra. Regarding the reconstruction process, the filtered backprojection (FBP) algorithm, already present in the previous version of the code, was optimized so that it is about 10 times as fast. In addition, Maximum Likelihood Expectation Maximization (MLEM) and its accelerated version Ordered Subsets Expectation Maximization (OSEM) algorithms were implemented. A detailed user guide in English is available. A reconstruction example of experimental data from a biological sample is given. It shows the capability of the code to reduce noise in the sinograms and to deal with incomplete data, which puts a new perspective on tomography using low number of projections or limited angle.

3D ANALYSIS OF AN INDUCED ATHEROSCLEROTIC LESION IN A MURINE ARTERY BY PIXE STACKING

Quantitative three dimensional analysis is possible, in principle, by PIXE tomography. But, the inherent problems in quantitation, restrictions on the sample geometry and preparation, and specimen damage due to high fluences make this method unsuitable for many biological samples. The specimen under investigation, a murine artery, was around a millimeter in diameter and the induced atherosclerotic lesion was spread few hundreds of micrometers across the length of the artery. Since no tomographic experiments were possible, we chose to do the 3D quantitative analysis by means of PIXE Stacking. Herein, thin serial sections of the specimen are prepared and measured by conventional ion beam techniques. The resultant two dimensional quantitative element maps are stacked and aligned to reconstruct a quantitative volume of the specimen. Although the reconstructed dimension has poorer spatial resolution as compared with the measured dimensions, new information can still be gained from it. The three dimensional element distribution of the atherosclerotic lesion shows calcification on the outer surface of the artery, which otherwise would not have been easily visible in the two dimensional analysis.

First results on ion micro-tomography at LIPSION

Abstract At the nanoprobe LIPSION ion micro-tomography can be used to determine the 3D distribution information of a sample’s mass density and elemental composition. For ion micro-tomography the two analytical techniques scanning transmission ion microscopy tomography (STIM-T) and particle induced X-ray emission tomography (PIXE-T) are combined. The required data are collected in two consecutive series of measurements, during which the sample is rotated by 180°/360° in small steps. Because all ions have to traverse the sample, the upper limit of the sample size is given by the range of the ions in the material. The tomogram is obtained using the discrete image space reconstruction algorithm (DISRA) by Sakellariou (1997) [1] . This algorithm iteratively corrects a sketchy initial tomogram estimated from the experimental reconstruction – obtained by backprojection of filtered projections (BFP) – and an a priori elemental composition. The necessary correction factors are calculated comparing the reconstruction of the experimental data with the reconstruction of simulated data. For the simulated data sets of STIM projections and PIXE maps are computed from the tomogram. These data sets are proceeded with the BFP algorithm to get simulated reconstruction data. Using the DISRA for ion micro-tomography, one can benefit from the high resolution of STIM-T by transferring it to the elemental distribution given by PIXE-T. This article presents first results of this technique applied on a phantom at the LIPSION facility.

Limited angle STIM and PIXE tomography of single cells

Abstract STIM (scanning transmission ion microscopy) tomography has been shown to be a valuable method for the three-dimensional characterization of microsamples. It has, however, rarely been employed for the study of single cells, since a free-standing sample is needed for an ordinary tomography experiment. This requirement places high demands on sample preparation techniques. In this study cells fixated on a substrate rather than free-standing were used for tomography. Since the substrate prevented a full rotation of the sample an algorithm for limited-angle tomography was devised. STIM projections covering only a limited angular range of ca. 120° were supplemented with simulated projections generated from a back and forth iteration between real space and Radon space. The energy loss caused by the substrate was subtracted from each projection. The cells were reconstructed using filtered backprojection. The surface of the cells as well as some interior structures could be reconstructed. Following the STIM projections a lesser number of PIXE (particle induced X-ray emission) projections were taken in order to obtain information about the elemental distribution of the sample. From the PIXE projections the three-dimensional phosphorus distribution within the cell was reconstructed using limited-angle tomography. Superimposition of the STIM and PIXE tomograms revealed the location of intracellular structures. Whereas STIM tomography is sensitive to density contrast, which are greatest at the surface, PIXE tomography is sensitive to changes in elemental concentration. Hence, the combination of the two methods can be very fruitful, while the limited angle approach can compensate some of the difficulties associated with tomography of single cells, namely preparation difficulties and excessive sample damage.

Reconstruction of 3D ion beam micro-tomography data for applications in Cell Biology

The DISRA (Discrete Image Space Reconstruction Algorithm) reconstruction code, created by A. Sakellariou, was conceived for the ideal case of complete three-dimensional (3D) PIXET (Particle Induced X-ray Emission Tomography) data. This implies two major difficulties for biological samples: first, the long duration of such experiments and second, the subsequent damage that occurs on such fragile specimens. For this reason, the DISRA code was extended at CENBG in order to probe isolated PIXET slices, taking into account the sample structure and mass density provided by 3D STIMT (Scanning Transmission Ion Microscopy Tomography) in the volume of interest. This modified version was tested on a phantom sample and first results on human cancer cells are also presented.

At the Tip of an MeV Beam: Provoking Cells and Performing Tomographic Imaging

Biological applications of ion beams have recently become a new important research field using single ion hit facilities to study individual living cells and their response to the hit of a counted number of ions. One motivation is the search for a better understanding of the fundamental processes taking place in cells and organs as a result of irradiation. Another comes from the increasing interest in using high energy protons and heavy ions as a modality for radiotherapy of deep seated tumours. In the view of treatment efficiency, study of cell culture behaviour under controlled radiation experiments, and in different chemical environments at single ion hit facilities, is a first step towards a better understanding of the processes. Tomographic techniques are applicable to situations where you need information of the inside of an object but do not want to section it into thin slices or cannot do it. Using focused MeV ion beams for tomography restricts the sample size to the order of 10-100 mu m, depending of the initial energy. On the other hand, the ability to focus at a sub-micrometer level makes ion beams well suited for analyses of small sized objects as cells, spores, etc. The scanning transmission ion microscopy mode of tomography gives the mass density and corresponding morphological structure of holes and pores. It can then be used to correct the results from the other mode, particle induced X-ray emission tomography. Here is discussed a porosity analysis of bentonite clay that is planned to form an important buffer zone around canisters filled with spent nuclear reactor fuel waste deposited 500 m underground in Sweden. (Less)

Radioanalytical and imaging techniques: Challenges and opportunities in biomedical applications

Where human health worldwide is under threat, radioanalytical and imaging scientists are expected to make significant difference and contribution. Diabetes, malnutrition, Alzheimer’s and cardiovascular diseases can be better understood by probing elemental distributions to nano-scales and quantifying elemental compositions to ultratrace levels. As we aim towards personalized medicine, cancer management awaits new diagnostic and therapy methods which account, for example, for tissue oxygenation. In the context of such biomedical issues, recent trends and future developments are presented taking into consideration the availability of research reactors and ion beam facilities, as well as alternative and emerging techniques such as PIXE tomography (PIXE-T) and two-and three-gamma PET.

Development of a microtomography system at the Lund sub-micron beamline

A system for ion beam tomography has been implemented in conjunction with the new sub-micron beamline at the Lund Nuclear Microprobe laboratory. The first version of the system is dedicated to STIM (scanning transmission ion microscopy) tomography for three-dimensional mass density analysis, but future development will allow also PIXE (particle induced X-ray emission) tomography for elemental analysis of micrometer-sized samples. The PIXE tomography will gain from the 8-element large area HPGe X-ray detector (100mm2 for each element) at the low beam currents inherited with a sub-micrometer beam spot size.In this work, the first results are presented together with a detailed description of the developed system, including computer control of the sample rotation. The reconstruction technique, as well as potential tomography applications is briefly discussed.

Density and composition analysis using focused MeV ion mubeam techniques

Nuclear muscopy uses focused MeV ion mubeams to non-destructively characterize materials and components with mun scale spatial resolution. Although a number of accelerator-based mubeam methods are available for materials analysis, this paper centers on the techniques of Ion mutomography (IMT) and Particle-Induced X-ray Emission (PIXE). IMT provides quantitative three-dimensional density information with mun-scale spatial resolution and 1% density variation sensitivity. Recently, IMT has become more versatile because greater emphasis has been placed on understanding the effects of reconstruction artifacts, beam spatial broadening, and limited projection data sets. PIXE provides quantitative elemental information with detection sensitivities to 1 μg/g or below in some instances. By scanning the beam, two-dimensional maps of elemental concentration can also be recorded. However, since X-rays are produced along the entire path of the ion beam as it penetrates the sample, these measurements only give depth-averaged information in general. PIXE tomography (PIXET) is the natural extension from conventional PIXE analysis to the full three-dimensional measurement and forms the bridge linking the complementary techniques of PIXE and IMT. This paper presents recent developments and applications of these ion beam techniques in a diverse range of fields including characterizing metal-matrix composites, biological specimens and inertial confinement fusion targets.

PIXE tomography

PIXE is recognised as a very sensitive quantitative tool for multielement analysis. If PIXE is coupled with a scanning ion microprobe it provides two-dimensional mapping of a sample to resolutions of 1 μm or better. The higher resolution imaging technique of scanning transmission ion microscopy STIM, developed over the last decade, has led to the development of STIM tomography for quantitative (density) three-dimensional imaging of microscopic objects. STIM offers a spatial resolution an order of magnitude better than that of PIXE. However, STIM is not directly sensitive to changes in elemental composition. In this paper we describe the new technique of PIXE tomography (PIXET) and its ability to provide three-dimensional images of the elemental content of samples. Early results are presented and we discuss the requirements and possibilities for further progress, including the possibilities for higher resolution.