XDesign: An open-source software package for designing X-ray imaging phantoms and experiments

Ching, Daniel J.; Gursoy, Dogˇa

doi:10.1107/S1600577517001928

Title: XDesign: An open-source software package for designing X-ray imaging phantoms and experiments

Journal Article · 20 February 2017 · Journal of Synchrotron Radiation (Online)

DOI: https://doi.org/10.1107/S1600577517001928 · OSTI ID:1372695

Ching, Daniel J. ^[1]; Gursoy, Dogˇa ^[2]

Oregon State Univ., Corvallis, OR (United States)
Argonne National Lab. (ANL),Lemont, IL (United States)

Here, the development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Lab. (ANL), Lemont, IL (United States)

Sponsoring Organization:: U.S. Department of Energy (Office not specified); USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1372695

Journal Information:: Journal of Synchrotron Radiation (Online), Journal Name: Journal of Synchrotron Radiation (Online) Journal Issue: 2 Vol. 24; ISSN 1600-5775; ISSN JSYRES

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

References (21)

Image processing of multiphase images obtained via X-ray microtomography: A review Schlüter, Steffen; Sheppard, Adrian; Brown, Kendra Water Resources Research, Vol. 50, Issue 4 https://doi.org/10.1002/2014WR015256	journal	April 2014
X-Ray Interactions: Photoabsorption, Scattering, Transmission, and Reflection at E = 50-30,000 eV, Z = 1-92 Henke, B. L.; Gullikson, E. M.; Davis, J. C. Atomic Data and Nuclear Data Tables, Vol. 54, Issue 2, p. 181-342 https://doi.org/10.1006/adnd.1993.1013	journal	July 1993
In situ X-ray synchrotron tomographic imaging during the compression of hyper-elastic polymeric materials Patterson, Brian M.; Cordes, Nikolaus L.; Henderson, Kevin Journal of Materials Science, Vol. 51, Issue 1 https://doi.org/10.1007/s10853-015-9355-8	journal	September 2015
Comparison of interfacial partitioning tracer test and high-resolution microtomography measurements of fluid-fluid interfacial areas for an ideal porous medium: MEASUREMENTS OF FLUID-FLUID INTERFACIAL Narter, Matt; Brusseau, Mark L. Water Resources Research, Vol. 46, Issue 8 https://doi.org/10.1029/2009WR008375	journal	August 2010
Quantitative 3D analysis of huge nanoparticle assemblies Zanaga, Daniele; Bleichrodt, Folkert; Altantzis, Thomas Nanoscale, Vol. 8, Issue 1 https://doi.org/10.1039/C5NR06962A	journal	January 2016
GATE: a simulation toolkit for PET and SPECT Jan, S.; Santin, G.; Strul, D. Physics in Medicine and Biology, Vol. 49, Issue 19 https://doi.org/10.1088/0031-9155/49/19/007	journal	September 2004
The effect of respiratory induced density variations on non-TOF PET quantitation in the lung Holman, Beverley F.; Cuplov, Vesna; Hutton, Brian F. Physics in Medicine and Biology, Vol. 61, Issue 8 https://doi.org/10.1088/0031-9155/61/8/3148	journal	March 2016
TXM-Wizard : a program for advanced data collection and evaluation in full-field transmission X-ray microscopy Liu, Yijin; Meirer, Florian; Williams, Phillip A. Journal of Synchrotron Radiation, Vol. 19, Issue 2 https://doi.org/10.1107/S0909049511049144	journal	January 2012
TomoPy: a framework for the analysis of synchrotron tomographic data Gürsoy, Dogˇa; De Carlo, Francesco; Xiao, Xianghui Journal of Synchrotron Radiation, Vol. 21, Issue 5 https://doi.org/10.1107/S1600577514013939	journal	August 2014
MMX-I : data-processing software for multimodal X-ray imaging and tomography Bergamaschi, Antoine; Medjoubi, Kadda; Messaoudi, Cédric Journal of Synchrotron Radiation, Vol. 23, Issue 3 https://doi.org/10.1107/S1600577516003052	journal	April 2016
Real-time image-content-based beamline control for smart 4D X-ray imaging Vogelgesang, Matthias; Farago, Tomas; Morgeneyer, Thilo F. Journal of Synchrotron Radiation, Vol. 23, Issue 5 https://doi.org/10.1107/S1600577516010195	journal	July 2016
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Image information and visual quality Sheikh, H. R.; Bovik, A. C. IEEE Transactions on Image Processing, Vol. 15, Issue 2 https://doi.org/10.1109/TIP.2005.859378	journal	February 2006
FSIM: A Feature Similarity Index for Image Quality Assessment IEEE Transactions on Image Processing, Vol. 20, Issue 8 https://doi.org/10.1109/TIP.2011.2109730	journal	August 2011
The Fourier reconstruction of a head section Shepp, L. A.; Logan, B. F. IEEE Transactions on Nuclear Science, Vol. 21, Issue 3 https://doi.org/10.1109/TNS.1974.6499235	journal	June 1974
Image information and visual quality Sheikh, H. R.; Bovik, A. C. 2004 IEEE International Conference on Acoustics, Speech, and Signal Processing https://doi.org/10.1109/icassp.2004.1326643	conference	January 2004
k-Wave: MATLAB toolbox for the simulation and reconstruction of photoacoustic wave fields Treeby, Bradley E.; Cox, B. T. Journal of Biomedical Optics, Vol. 15, Issue 2 https://doi.org/10.1117/1.3360308	journal	January 2010
TomoPy: A framework for the analysis of synchrotron tomographic data Gürsoy, Doğa; De Carlo, Francesco; Xiao, Xianghui SPIE Optical Engineering + Applications, SPIE Proceedings https://doi.org/10.1117/12.2061373	conference	September 2014
Step-and-shoot data acquisition and reconstruction for cardiac x-ray computed tomography: Step-and-shoot data acquisition and reconstruction for cardiac Hsieh, Jiang; Londt, John; Vass, Melissa Medical Physics, Vol. 33, Issue 11 https://doi.org/10.1118/1.2361078	journal	October 2006
A simple approach to measure computed tomography (CT) modulation transfer function (MTF) and noise-power spectrum (NPS) using the American College of Radiology (ACR) accreditation phantom: CT MTF/NPS calculation using an ACR phantom Friedman, Saul N.; Fung, George S. K.; Siewerdsen, Jeffrey H. Medical Physics, Vol. 40, Issue 5 https://doi.org/10.1118/1.4800795	journal	April 2013
GATE : a simulation toolkit for PET and SPECT Jan, S.; Santin, G.; Strul, D. arXiv https://doi.org/10.48550/arxiv.physics/0408109	text	January 2004

Cited By (8)

Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection Gürsoy, Doğa; Hong, Young P.; He, Kuan Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-12141-9	journal	September 2017
Rotation-as-fast-axis scanning-probe x-ray tomography: the importance of angular diversity for fly-scan modes Ching, Daniel J.; Hidayetoğlu, Mert; Biçer, Tekin Applied Optics, Vol. 57, Issue 30 https://doi.org/10.1364/ao.57.008780	journal	January 2018
X-ray tomography of extended objects: a comparison of data acquisition approaches Du, Ming; Vescovi, Rafael; Fezzaa, Kamel Journal of the Optical Society of America A, Vol. 35, Issue 11 https://doi.org/10.1364/josaa.35.001871	journal	January 2018
Joint ptycho-tomography reconstruction through alternating direction method of multipliers Aslan, Selin; Nikitin, Viktor; Ching, Daniel J. Optics Express, Vol. 27, Issue 6 https://doi.org/10.1364/oe.27.009128	journal	January 2019
Direct coupling of tomography and ptychography Gürsoy, Doğa Optics Letters, Vol. 42, Issue 16 https://doi.org/10.1364/ol.42.003169	journal	January 2017
Analytical registration of vertical image drifts in parallel beam tomographic data Storm, Malte; Beckmann, Felix; Rau, Christoph Optics Letters, Vol. 42, Issue 23 https://doi.org/10.1364/ol.42.004982	journal	January 2017
3D x-ray imaging of continuous objects beyond the depth of focus limit Gilles, M. A.; Nashed, Y. S. G.; Du, M. Optica, Vol. 5, Issue 9 https://doi.org/10.1364/optica.5.001078	journal	January 2018
Analytical registration of vertical image drifts in parallel beam tomographic data Storm, Malte; Beckmann, Felix; Rau, Christoph Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2018-01126	text	January 2017

Similar Records

Incorporation of correlated structural images in PET image reconstruction

Journal Article · 1994 · IEEE Transactions on Medical Imaging (Institute of Electrical and Electronics Engineers); (United States) · OSTI ID:6873650

Ouyang, X; Wong, W H; Chen, C T; +2 more

SU-F-I-14: 3D Breast Digital Phantom for XACT Imaging

Journal Article · 2016 · Medical Physics · OSTI ID:22626786

Tang, S; Laaroussi, R; Chen, J; +5 more

A software-based x-ray scatter correction method for breast tomosynthesis

Journal Article · 2011 · Medical Physics · OSTI ID:22098699

Jia Feng, Steve Si; Sechopoulos, Ioannis

Related Subjects

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND TECHNOLOGY
97 MATHEMATICS AND COMPUTING
Python
data acquisition
experiment design
open-source
phantom
quality
reconstruction
scanning X-ray probe
simulation
tomography

Title: XDesign: An open-source software package for designing X-ray imaging phantoms and experiments

Citation Formats

References (21)

Cited By (8)

Similar Records

Related Subjects