Enhanced and Flexible Software Tools for X-ray Computed Tomography at the Italian Synchrotron Radiation Facility Elettra

Brun, Francesco; Pacilè, Serena; Accardo, Agostino; Kourousias, Georgios; Dreossi, Diego; Mancini, Lucia; Tromba, Giuliana; Pugliese, Roberto

doi:10.3233/fi-2015-1273

Cited by 103 publications

(67 citation statements)

References 17 publications

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“…However, iterative approaches typically require more computational throughput (Sidky et al, 2006;Agulleiro & Fernandez, 2011;Treibig et al, 2013;Beister et al, 2012). Accelerators, such as GPUs, have been used to improve performance of iterative algorithms (Chilingaryan et al, 2010;Mirone et al, 2014;Brun et al, 2015;Vogelgesang et al, 2012), but memory limitations of these accelerators can introduce significant overheads due to the data movement from host to device memory. The TomoPy framework provides a complete set of tools for the portable analysis of tomography datasets, which can run on workstations (Gü rsoy et al, 2014).…”

Section: Related Workmentioning

confidence: 99%

Optimization of tomographic reconstruction workflows on geographically distributed resources

Biçer

Gürsoy

Kettimuthu

et al. 2016

J Synchrotron Radiat

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New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modeling of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can provide up to 3.13Â speedup (on experimented resources). Moreover, the error rates of the models range between 2.1 and 23.3% (considering workflow execution times), where the accuracy of the model estimations increases with higher computational demands in reconstruction tasks.

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Section: Related Workmentioning

confidence: 99%

Optimization of tomographic reconstruction workflows on geographically distributed resources

Biçer

Gürsoy

Kettimuthu

et al. 2016

J Synchrotron Radiat

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“…During this period of 24 min, the secondary liquid is moving and this needs to be taken into account when analysing the results. All the acquired data sets were phase-retrieved and then reconstructed using the custom developed software SYRMEP Tomo Project (Brun et al, 2015) using the filtered back projection reconstruction algorithm (Kak and Slaney, 1988). The optimized value for phase retrieval was set to 400.…”

Section: Image Analysismentioning

confidence: 99%

Studying model suspensions using high resolution synchrotron X-ray microtomography

Islam

Mancini

Sundara

et al. 2017

Chemical Engineering Research and Design

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Please note that changes made in the online proofing system will be added to the article before publication but are not reflected in this PDF.We also ask that this file not be used for submitting corrections. ARTICLE IN PRESSCHERD 2506 1-17 chemical engineering research and design x x x ( 2 0 1 6 ) xxx-xxx Contents lists available at ScienceDirectChemical Engineering Research and Design j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / c h e r dStudying model suspensions using high resolution synchrotron X-ray microtomography The addition of minor quantities of secondary liquids to suspensions may lead to a transition from a fluid-like structure to paste-like structure for the system. Previous studies haveshown how rheological properties such as viscosity and yield stress are affected, however, qualitative visual observation on the micro-scale during both short and long term storage has yet to be achieved or reported.This research focuses on the movement of a secondary immiscible liquid (water or saturated sucrose solution) when added to a model food system. The model food system used in this study is a suspension of sucrose particles in a continuous oil phase to better understand the interactions between the particles and the liquid phases present. This was accomplished using dynamic X-ray computer tomography to study the behaviour of the sample. This nondestructive approach allowed the movement of the secondary liquid as well as the solid particles from the bulk suspension to be monitored through a time lapse of scans. This was achieved by observing the changes in the grey scale range of the droplet with time, which was then correlated to the uptake and movement of sucrose into the secondary liquid using an innovative method. This movement was due to the hydrophilicity and solubility of sucrose Q4with gravity/sedimentation playing a minimal role. IntroductionSeveral food products comprise of suspensions in which solid Q5 hydrophilic particles are suspended as a disperse phase throughout a continuous hydrophobic liquid phase. When a small proportion of a secondary immiscible liquid such as water or glycerol is added to a suspension of this kind, it can lead to behavioural changes from a fluid-like material to a paste-like material (Koos and Willenbacher, 2011;Johansson and Bergenståhl, 1992). This transformation has been ascribed to the formation of liquid bridges between the solid particles by the secondary liquid thereby modifying the rheological properties of the suspension such as its yield stress and viscosity which can increase several-fold Willenbacher, 2011, 2012; Koos et al., * Corresponding author. Q3E-mail address: sfislam1@sheffield.ac.uk (S.F. Islam). Negreiros et al., 2015). The secondary liquid in this case has a greater affinity to the primary particles in comparison to the continuous phase because of their hydrophilic nature. Q6 In food systems, the movement of moisture is generally considered from the view point of molecular diffusion. Moisture can enter from ...

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“…In this work, the same algorithm 345 was applied to synchrotron X-μCT data of garnets, acquired in phase-contrast mode, also with 346 polychromatic light (see Meyers et al 2007; Arzilli et al 2016). Phase-retrieval pre-processing was 347 carried out using the STP software (Brun et al 2015(Brun et al , 2017 employed also for tomographic 348 reconstruction. For the investigated garnet samples, a δ/β ratio equal to 100 was selected for phase-349 retrieval reconstructions (where δ is the refractive index decrement, proportional to the electron density 350 of a material, and β is called extinction coefficient, related to the absorption coefficient and 351 wavelength).…”

Section: Image Processing Of X-μct Data 326mentioning

confidence: 99%

“…The use of phase-contrast effects allows to detect very small details and to 265 highlight the interfaces between the different phases compared to the pure absorption mode. The 266 reconstruction of tomographic slices was carried out using the SYRMEP Tomo Project (STP) software 267 developed at Elettra (Brun et al 2015(Brun et al , 2017. 268…”

Section: Garnets and Their Anatectic Melt Inclusions 199mentioning

confidence: 99%

Three-dimensional distribution of primary melt inclusions in garnets by X-ray microtomography

Parisatto

Turina

Cruciani

et al. 2018

American Mineralogist

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14 X-ray computed microtomography (X-μCT) is applied here to investigate in a non-invasive way the 15 three-dimensional (3D) spatial distribution of primary melt and fluid inclusions in garnets from the 16 metapelitic enclaves of El Hoyazo and from the migmatites of Sierra Alpujata, Spain. The attention is 17 focused on a particular case of inhomogeneous distribution of inclusions, characterized by inclusion-18 rich cores and almost inclusion-free rims (i.e. zonal arrangement), that has been previously investigated

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Enhanced and Flexible Software Tools for X-ray Computed Tomography at the Italian Synchrotron Radiation Facility Elettra

Cited by 103 publications

References 17 publications

Optimization of tomographic reconstruction workflows on geographically distributed resources

Optimization of tomographic reconstruction workflows on geographically distributed resources

Studying model suspensions using high resolution synchrotron X-ray microtomography

Three-dimensional distribution of primary melt inclusions in garnets by X-ray microtomography

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