Search

Quantification and imaging of chemical elements at the cellular level requires the use of a combination of techniques such as micro-PIXE, micro-RBS, STIM, secondary electron imaging associated with optical and fluorescence microscopy techniques employed prior to irradiation. Such a numerous set of methods generates an important amount of data per experiment. Typically for each acquisition the following data has to be processed: chemical map for each element present with a concentration above the detection limit, density and backscattered maps, mean and local spectra corresponding to relevant region of interest such as whole cell, intracellular compartment, or nanoparticles. These operations are time consuming, repetitive and as such could be source of errors in data manipulation. In order to optimize data processing, we have developed a new tool for batch data processing and imaging. This tool has been developed as a plugin for ImageJ, a versatile software for image processing that is suitable for the treatment of basic IBA data operations. Because ImageJ is written in Java, the plugin can be used under Linux, Mas OS X and Windows in both 32-bits and 64-bits modes, which may interest developers working on open-access ion beam facilities like AIFIRA. The main features of this plugin are presented here: listfile processing, spectroscopic imaging, local information extraction, quantitative density maps and database management using OMERO.

International audience; In combination with nuclear microprobes, STIM and PIXE tomography offer non-destructive quantitative three-dimensional characterization of microscopic samples. STIM tomography provides 3D density maps of the analyzed sample with sub-micrometer resolution and PIXE tomography is one of the only methods allowing a quantification of trace elements in three dimensions. These tomography techniques have been developed in several microbeam laboratories around the world since the 80’s. Nevertheless, despite a huge interest in mapping the inner content of a sample without destroying it, the use of ion beam tomography has been limited to a few studies up to now. This comes from the specific requirements of this kind of experiments, i.e. specific experimental set-up (rotation of the sample during analysis) and reconstruction software, making this type of experiments difficult to handle and relatively long. For a few years, efforts have been made to facilitate the implementation of these techniques and reduce the duration of data acquisition: new detectors and new algorithms were proposed. After an introduction to ion beam tomography techniques and to the first developments made in that field, the experimental and data processing specificities of this 3D imaging approach will be discussed. Finally, examples of recent applications to biology and material science are presented, as well as related techniques developed in the field of microbeam 3D imaging.

International audience; The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans - a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

International audience; 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 Xray 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.

During the past two decades, front-wheel-drive architecture has grown enormously in Europe. This trend can be explained by the need to provide compactness, large inside space, and good road holding. The paper describes technical problems that arise when designing a front-wheel- drive car and quotes the various technical solutions in current use. The authors conclude that a preference for front-wheel-drive will last for a long time. /GMRL/

17ème conférence internationale "Ion Beam Analysis"- Séville - 26 juin 1er juillet 2005; International audience; Scanning transmission ion microscopy tomography (STIM-T) was carried out on diatom cells with the aim of displaying their 3D structure and performing density measurements on their silica skeleton. Two software packages were compared for data reduction: TomoRebuild, based on a simple filtered backprojection algorithm, and DISRA, an iterative program. Silicon carbide microfibres of known density were also analysed as reference specimens. Similar results were obtained with both algorithms, demonstrating the ability of STIM-T to provide density measurements at the cell level without requiring any standard calibration samples. This unique feature stresses the interest of STIM-T to accurately normalise X ray emission micro-tomography data from synchrotron radiation (SXRF: synchrotron radiation X-ray fluorescence) or ion beam sources (PIXE: particle induced X-ray emission). Possible enhancements of the DISRA code are discussed in order to facilitate its use for the reconstruction of future PIXE/STIM tomography data. A “nanoprobe” coupled to a Singletron® accelerator, allowing a spatial resolution of a few tens of nanometers, is going to be built in the coming months at the Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG). This new facility will bring promising applications in imaging and analysis at the sub-cellular level.

Charged particle microbeams provide unique features to study targeted and non-targeted radiation response and have recently emerged as a powerful tool to investigate radiation-induced DNA damage and repair. We have developed a charged particle microbeam delivering protons and alpha particles in the MeV energy range equipped with online time-lapse imaging capabilities. The beam is focused to a sub-micrometer beam spot under vacuum by means of a triplet of magnetic quadrupoles and extracted in air through a 200 nm Si 3 N 4 window. The end-station is equipped with an automated fluorescence microscope used for single cell targeting and online time-lapse imaging. Cells are kept in their medium during the irradiation procedure and the sample temperature is regulated to 37 °C. An overall targeting accuracy of 2.0 ± 0.7 μm has been measured by tracking the re-localization of the XRCC1 protein. First measurements of this re-localization shows the ability of our system to follow online the radiation-induced re-localization of proteins in the first minutes after irradiation.