<i>PITRE</i>: software for phase-sensitive X-ray image processing and tomography reconstruction

Chen, Rong Chang; Dreossi, Diego; Mancini, Lucia; Menk, R.H.; Rigon, Luigi; Xiao, Ti Qiao; Longo, Renata

doi:10.1107/s0909049512029731

Cited by 223 publications

(124 citation statements)

References 52 publications

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“…In the framework of our research of cultural heritage objects, and in the case of a full set of neutron tomography projections, the use of the conventional Filtered Backprojection (FBP) algorithm [26] seems reasonable and sufficient for our study aims. The H-PITRE software [27] was used for the tomography reconstruction . An algorithm [28] for reducing ring-shaped artifacts was applied.…”

Section: Methodsmentioning

confidence: 99%

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Studies of Ancient Russian Cultural Objects Using the Neutron Tomography Method

et al. 2018

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Neutron radiography and tomography is a non-destructive method that provides detailed information about the internal structure of cultural heritage objects. The differences in the neutron attenuation coefficients of constituent elements of the studied objects, as well as the application of modern mathematical algorithms to carry out three-dimensional imaging data analysis, allow one to obtain unique information about the spatial distribution of different phases, the presence of internal defects, or the degree of structural degradation inside valuable cultural objects. The results of the neutron studies of several archaeological objects related to different epochs of the Russian history are reported in order to demonstrate the opportunities provided by the neutron tomography method. The obtained 3D structural volume data, as well as the results of the corresponding data analysis, are presented.

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Section: Methodsmentioning

confidence: 99%

“…In addition, specialized plug-ins for the ImageJ software, like Segmentation3D [29], Local Thickness [30] and Skeletonize3D [31] were used for quantitative analysis of the obtained 3D volume data. The H-PITRE software [27] was used for the tomography reconstruction . An algorithm [28] for reducing ring-shaped artifacts was applied.…”

Section: Methodsmentioning

confidence: 99%

Studies of Ancient Russian Cultural Objects Using the Neutron Tomography Method

et al. 2018

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“…Tomography is a widely used imaging technique at synchrotron light sources (Gü rsoy et al, 2015a,b;Mohan et al, 2015;Qi & Leahy, 2006;Duke et al, 2015;Chen et al, 2012;Pelt et al, 2016). Iterative tomographic reconstruction typically provides higher-quality images than the filtered-back projection method does, because of the better reduction in noise and in missing wedge artifacts.…”

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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“…Burvall et al also provide a scheme for choosing which reconstruction method to use based on the characteristics of the data set. Phase retrieval is recognized as an important aspect of phase-contrast imaging, but was not considered a main focus of this study for two reasons: (i) of the four programs assessed, only two (PITRE, H-PITRE) are capable of performing phase retrieval, and (ii) Mohammadi et al (2013) provide a comparison of the free software programs ANKAPhase (Weitkamp et al, 2011(Weitkamp et al, , 2014 and PITRE (Chen et al, 2012a(Chen et al, , 2013a for implementing phase-retrieval algorithms with propagation-based X-ray tomography. As such this work only reviews the performance of the three-dimensional reconstruction software.…”

Section: Background Information 21 Phase-contrast Ctmentioning

confidence: 99%

“…One way to represent the projection data for filtering is by using sinograms which are plots of the absorption data for the reconstruction of a single slice (Stock, 2009). Sinograms are produced by collecting the linear signal along a specific detector row in the imaging plane for all the angular views along the 180 rotation and arranging them side by side (Chen et al, 2012a). FBP approximates the inverse Radon transform by a single convolution followed by a back projection of the data thus producing the cross-section image of the sample (Herman, 2010).…”

Section: Tomography Algorithmmentioning

confidence: 99%

Assessment of freeware programs for the reconstruction of tomography datasets obtained with a monochromatic synchrotron-based X-ray source

Wolkowski

Snead

Wesolowski

et al. 2015

J Synchrotron Radiat

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Synchrotron-based in-line phase-contrast computed tomography (PC-CT) allows soft tissue to be imaged with sub-gross resolution and has potential to be used as a diagnostic tool. The reconstruction and processing of in-line PC-CT datasets is a computationally demanding task; thus, an efficient and user-friendly software program is desirable. Four freeware programs (NRecon, PITRE, H-PITRE and Athabasca Recon) were compared for the availability of features such as dark-and flat-field calibration, beam power normalization, ring artifact removal, and alignment tools for optimizing image quality. An in-line PC-CT projection dataset (3751 projections, 180 rotation, 10.13 mm Â 0.54 mm) was collected from a formalin-fixed canine prostate at the Biomedical Imaging and Therapy Bending Magnet (BMIT-BM) beamline of the Canadian Light Source. This dataset was processed with each of the four software programs and usability of the program was evaluated. Efficiency was assessed by how each program maximized computer processing power during computation. Athabasca Recon had the least-efficient memory usage, least user-friendly interface, and lacked a ring artifact removal feature. NRecon, PITRE and H-PITRE produced similar quality images, but the Athabasca Recon reconstruction suffered from the lack of a native ring remover algorithm. The 64-bit version of NRecon uses GPU (graphics processor unit) memory for accelerated processing and is userfriendly, but does not provide necessary parameters for in-line PC-CT data, such as dark-field and flat-field correction and beam power normalization. PITRE has many helpful features and tools, but lacks a comprehensive user manual and help section. H-PITRE is a condensed version of PITRE and maximizes computer memory for efficiency. To conclude, NRecon has fewer imaging processing tools than PITRE and H-PITRE, but is ideal for less experienced users due to a simple user interface. Based on the quality of reconstructed images, efficient use of computer memory and parameter availability, H-PITRE was the preferred of the four programs compared.

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PITRE: software for phase-sensitive X-ray image processing and tomography reconstruction

Cited by 223 publications

References 52 publications

Studies of Ancient Russian Cultural Objects Using the Neutron Tomography Method

Studies of Ancient Russian Cultural Objects Using the Neutron Tomography Method

Optimization of tomographic reconstruction workflows on geographically distributed resources

Assessment of freeware programs for the reconstruction of tomography datasets obtained with a monochromatic synchrotron-based X-ray source

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