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An implementation of the NiftyRec medical imaging library for PIXE-tomography reconstruction

hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorMICHELET, Claire
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorBARBERET, Philippe
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
dc.contributor.authorDESBARATS, Pascal
hal.structure.identifierLaboratoire de l'intégration, du matériau au système [IMS]
dc.contributor.authorGIOVANNELLI, Jean-François
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorSCHOU, C.
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorCHEBIL, I.
hal.structure.identifierInstitut de Chimie de la Matière Condensée de Bordeaux [ICMCB]
dc.contributor.authorDELVILLE, Marie-Hélène
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorGORDILLO, Nuria
hal.structure.identifierCentre for Medical Image Computing [CMIC]
dc.contributor.authorBEASLEY, Daniel G.
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorDEVÈS, Guillaume
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorMORETTO, Philippe
hal.structure.identifierCentre d'Etudes Nucléaires de Bordeaux Gradignan [CENBG]
dc.contributor.authorSEZNEC, Hervé
dc.date.issued2017
dc.identifier.issn0168-583X
dc.description.abstractEnA new development of the TomoRebuild software package is presented, including “thick sample” correction for non linear X-ray production (NLXP) and X-ray absorption (XA). As in the previous versions, C++ programming with standard libraries was used for easier portability. Data reduction requires different steps which may be run either from a command line instruction or via a user friendly interface, developed as a portable Java plugin in ImageJ. All experimental and reconstruction parameters can be easily modified, either directly in the ASCII parameter files or via the ImageJ interface. A detailed user guide in English is provided. Sinograms and final reconstructed images are generated in usual binary formats that can be read by most public domain graphic softwares. New MLEM and OSEM methods are proposed, using optimized methods from the NiftyRec medical imaging library. An overview of the different medical imaging methods that have been used for ion beam microtomography applications is presented. In TomoRebuild, PIXET data reduction is performed for each chemical element independently and separately from STIMT, except for two steps where the fusion of STIMT and PIXET data is required: the calculation of the correction matrix and the normalization of PIXET data to obtain mass fraction distributions. Correction matrices for NLXP and XA are calculated using procedures extracted from the DISRA code, taking into account a large X-ray detection solid angle. For this, the 3D STIMT mass density distribution is used, considering a homogeneous global composition. A first example of PIXET experiment using two detectors is presented. Reconstruction results are compared and found in good agreement between different codes: FBP, NiftyRec MLEM and OSEM of the TomoRebuild software package, the original DISRA, its accelerated version provided in JPIXET and the accelerated MLEM version of JPIXET, with or without correction.
dc.language.isoen
dc.publisherElsevier
dc.subject.enPIXE tomography
dc.subject.enQuantitative imaging
dc.subject.enFiltered backprojection
dc.subject.enMLEM
dc.subject.enOSEM
dc.subject.enImageJ
dc.subject.enCaenorhabditis elegans
dc.title.enAn implementation of the NiftyRec medical imaging library for PIXE-tomography reconstruction
dc.typeArticle de revue
dc.identifier.doi10.1016/j.nimb.2017.01.067
dc.subject.halChimie/Matériaux
bordeaux.journalNuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms
bordeaux.page131-139
bordeaux.volume404
bordeaux.peerReviewedoui
hal.identifierhal-01544227
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01544227v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Nuclear%20Instruments%20and%20Methods%20in%20Physics%20Research%20Section%20B:%20Beam%20Interactions%20with%20Materials%20and%20Atoms&rft.date=2017&rft.volume=404&rft.spage=131-139&rft.epage=131-139&rft.eissn=0168-583X&rft.issn=0168-583X&rft.au=MICHELET,%20Claire&BARBERET,%20Philippe&DESBARATS,%20Pascal&GIOVANNELLI,%20Jean-Fran%C3%A7ois&SCHOU,%20C.&rft.genre=article


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