syris: a flexible and efficient framework for X-ray imaging experiments simulation

被引:17
作者
Farago, Tomas [1 ,2 ]
Mikulik, Petr [3 ,4 ]
Ershov, Alexey [1 ,2 ]
Vogelgesang, Matthias [5 ]
Haenschke, Daniel [1 ,2 ]
Baumbach, Tilo [1 ,2 ]
机构
[1] KIT, Inst Photon Sci & Synchrotron Radiat, Herrmann von Helmholtz Pl 1, D-76344 Eggenstein Leopoldshafen, Germany
[2] KIT, Lab Applicat Synchrotron Radiat, D-76131 Karlsruhe, Germany
[3] Masaryk Univ, Fac Sci, Dept Condensed Matter Phys, Kotlarska 2, CS-61137 Brno, Czech Republic
[4] MU, CEITEC Cent European Inst Technol, Kamenice 753-5, Brno 62500, Czech Republic
[5] KIT, Inst Data Proc & Elect, Herrmann von Helmholtz Pl 1, D-76344 Eggenstein Leopoldshafen, Germany
关键词
simulation; high-speed imaging; parallelization; free-space propagation; coherence; X-ray imaging; synchrotron radiation; SYNCHROTRON-RADIATION; OPTICAL-FLOW; PHASE-CONTRAST; TOMOGRAPHY; SEGMENTATION; COMPUTATION; PACKAGE;
D O I
10.1107/S1600577517012255
中图分类号
TH7 [仪器、仪表];
学科分类号
0804 ; 080401 ; 081102 ;
摘要
An open-source framework for conducting a broad range of virtual X-ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time-dependent, which enables simulations of dynamic experiments, e.g. four-dimensional time-resolved tomography and laminography. The high-level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high-speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.
引用
收藏
页码:1283 / 1295
页数:13
相关论文
共 44 条
[1]  
[Anonymous], 2000, Principles of optics: electromagnetic theory of propagation, interference and diffraction of light
[2]  
[Anonymous], INT J COMP VISION
[3]   Crowdsourcing the creation of image segmentation algorithms for connectomics [J].
Arganda-Carreras, Ignacio ;
Turaga, Srinivas C. ;
Berger, Daniel P. ;
Ciresan, Dan ;
Giusti, Alessandro ;
Gambardella, Luca M. ;
Schmidhuber, Juergen ;
Laptev, Dmitry ;
Dwivedi, Sarvesh ;
Buhmann, Joachim M. ;
Liu, Ting ;
Seyedhosseini, Mojtaba ;
Tasdizen, Tolga ;
Kamentsky, Lee ;
Burget, Radim ;
Uher, Vaclav ;
Tan, Xiao ;
Sun, Changming ;
Pham, Tuan D. ;
Bas, Erhan ;
Uzunbas, Mustafa G. ;
Cardona, Albert ;
Schindelin, Johannes ;
Seung, H. Sebastian .
FRONTIERS IN NEUROANATOMY, 2015, 9 :1-13
[4]   A Database and Evaluation Methodology for Optical Flow [J].
Baker, Simon ;
Scharstein, Daniel ;
Lewis, J. P. ;
Roth, Stefan ;
Black, Michael J. ;
Szeliski, Richard .
INTERNATIONAL JOURNAL OF COMPUTER VISION, 2011, 92 (01) :1-31
[5]  
Blinn J. F., 1982, Computer Graphics, V16, DOI 10.1145/965145.801290
[6]  
Chubar O., 1998, P 6 EUR PART ACC C S, P1177
[7]  
Cloetens P., 1999, THESIS
[8]   THE ILL-CONDITIONED NATURE OF THE LIMITED ANGLE TOMOGRAPHY PROBLEM [J].
DAVISON, ME .
SIAM JOURNAL ON APPLIED MATHEMATICS, 1983, 43 (02) :428-448
[9]  
De Boor C., 1978, PRACTICAL GUIDE SPLI, V27, P2
[10]   SHADOW3: a new version of the synchrotron X-ray optics modelling package [J].
del Rio, Manuel Sanchez ;
Canestrari, Niccolo ;
Jiang, Fan ;
Cerrina, Franco .
JOURNAL OF SYNCHROTRON RADIATION, 2011, 18 :708-716