ScatterX: A software for fast processing of high-throughput small-angle scattering data

doi:10.1088/1674-1056/ad8b36

Abstract Scattering experiments become increasingly popular in modern scientific research, including the areas of materials, biology, chemistry, physics, etc. Besides, various types of scattering facilities have been developed recently, such as lab-based x-ray scattering equipment, national synchrotron facilities and large neutron facilities. These above-mentioned trends bring up fast-increasing data amounts of scattering data, as well as different scattering types (x-ray, neutron, laser and even microwaves). To help researchers process and analyze scattering data more efficiently, we developed a general and model-free scattering data analysis software based on matrix operation, which has the unique advantage of high throughput scattering data processing, analysis and visualization. To maximize generality and efficiency, data processing is performed based on a three-dimensional matrix, where scattering curves are saved as matrices or vectors, rather than the traditional definition of paired values. It can not only realize image batch processing, background subtraction and correction, but also analyze data according to scattering theory and model, such as radius of gyration, fractal dimension and other physical quantities. In the aspect of visualization, the software allows the modify the color maps of two-dimensional scattering images and the gradual color variation of one-dimensional curves to suit efficient data communications. In all, this new software can work as a stand-alone platform for researchers to process, analyze and visualize scattering data from different research facilities without considering different file types or formats. All codes in this manuscript are open-sourced and can be easily implemented in matrix-based software, such as MATLAB, Python and Igor.

Keywords: scatter fractal correlation function high-throughput SVD

Received: 30 July 2024
Revised: 09 October 2024
Accepted manuscript online: 25 October 2024

PACS:	01.50.hv	(Computer software and software reviews)
	13.85.Dz	(Elastic scattering)
	98.35.Ce	(Mass and mass distribution)
	87.14.E-	(Proteins)

Fund: Project supported by School Project Cultivation Fund (Grant No. WK2310000101).

Corresponding Authors: Fei Xie
E-mail: xjiao@ustc.edu.cn

Cite this article:

Fei Xie(谢飞), Mei Xie(解梅), Baoyu Song(宋宝玉), Qiaoyu Guo(郭桥雨), and Xuechen Jiao(焦学琛) ScatterX: A software for fast processing of high-throughput small-angle scattering data 2024 Chin. Phys. B 33 120101

[1] Cowieson N P, Edwards-Gayle C J C, Inoue K, Khunti N S, Doutch J, Williams E, Daniels S, Preece G, Krumpa N A, Sutter J P, Tully M D, Terrill N J and Rambo R P 2020 J. Synchrotron Radiat. 27 1438
[2] Peters G S, Zakharchenko O A, Konarev P V, Karmazikov Y V, Smirnov M A, Zabelin A V, Mukhamedzhanov E H, Veligzhanin A A, Blagov A E and Kovalchuk M V 2019 Nucl. Instrum. Meth. A 945 162616
[3] Takagi H, Igarashi N, Nagatani Y, Ohta H, Mori T, Kosuge T and Shimizu N 2019 AIP Conf. Proc. 2054 060038
[4] Zhang Y P, Mo C J, Zhang P and Kang W 2023 Chin. Phys. Lett. 41 017801
[5] Lyngso J and Pedersen J S 2021 J. Appl. Crystallogr. 54 295
[6] Ushakov A, Velthuis H, Koster N and Janssen J 2021 IEEE Trans. Plasma Sci. 49 770
[7] Heller W T, Cuneo M, Debeer-Schmitt L, Do C, He L L, Heroux L, Littrell K, Pingali S V, Qian S, Stanley C, Urban V S, Wu B and Bras W 2018 J. Appl. Crystallogr. 51 242
[8] Ke Y, He C, Zheng H, Geng Y, Fu J, Zhang S, Hu H, Wang S, Zhou B, Wang F and Tao J 2018 Neutron News 29 14
[9] Wang T, Sun L, Chen L, Wang Y, Sun G and Liu D 2018 J. Instrument. 13 T10008
[10] Sokolova A, Whitten A E, de Campo L, Christoforidis J, Eltobaji A, Barnes J, Darmann F and Berry A 2019 J. Appl. Crystallogr. 52 1
[11] Wang Y X, Li Z H, Kong J, Chang L P, Li D F and Lv B L 2021 Phil. Mag. Lett. 101 320
[12] Hu J Y, Zhang J L, Tan X N, Cheng X Y, Su Z Z, Qian L X, Xu M Z, Sha Y F, Wang Y Y, Yang Y S, Liu Y P, Mo G, Xing X Q and Wu Z H 2023 Nano Res. 16 3703
[13] Xie F, Li Z H, Wang W J, Li D F, Li Z Z, Lv B L and Hou B 2020 Fuel 262 116547
[14] Mao Z N, Bi X W, Ye F, Shu X, Sun L, Guan J, Ritchie R O and Wu S J 2020 ACS Biomater. Sci. Eng. 6 4512
[15] Zhang B X, Zhang J L, Zhang F Y, Zheng L R, Mo G, Han B X and Yang G Y 2020 Adv. Funct. Mater. 30 1906194
[16] Meng X, Meng L, Gong Y, Li Z, Mo G and Zhang J 2021 RSC Adv. 11 37528
[17] Xiao P, Gong Y J, Li D F and Li Z H 2021 Microporous Mesoporous Mater. 323 111201
[18] Xiao P, Zhang S J, Gong Y J, Liu Y, Li Z H and Li D F 2023 Chem. Phys. Lett. 811 140239
[19] Wu T, Lu C, Sun T, Li Y, Yuan S, Li D, Wang G and Ren X 2022 Microporous Mesoporous Mater. 330 111584
[20] Spinozzi F, Ortore M G, Nava G, Bomboi F, Carducci F, Amenitsch H, Bellini T, Sciortino F and Mariani P 2020 Langmuir 36 10387
[21] Baker M A B, Tuckwell A J, Berengut J F, Bath J, Benn F, Duff A P, Whitten A E, Dunn K E, Hynson R M, Turberfield A J and Lee L K 2018 Acs Nano 12 5791
[22] Bernetti M, Hall K B and Bussi G 2021 Nucleic Acids Res. 49 e84
[23] Chen Y L, Lee T, Elber R and Pollack L 2019 Biophys. J. 116 19
[24] Hermann M R and Hub J S 2019 J. Chem. Theory Comput. 15 5103
[25] Ivanovic M T, Bruetzel L K, Shevchuk R, Lipfert J and Hub J S 2018 Phys. Chem. Chem. Phys. 20 26351
[26] Khaykelson D and Raviv U 2020 Biophys. Rev. 12 41
[27] Konishi T, Okamoto D, Tadokoro D, Kawahara Y, Fukao K and Miyamoto Y 2018 Phys. Rev. Mater. 2 105602
[28] Ballauff M 2001 Curr. Opin. Colloid Interface Sci. 6 132
[29] Xuan W, Zhu C, Liu Y and Cui Y 2012 Chem. Soc. Rev. 41 1677
[30] Du D Y, Qin J S, Li S L, Su Z M and Lan Y Q 2014 Chem. Soc. Rev. 43 4615
[31] Hirst A R, Smith D K, Feiters M C and Geurts H P M 2004 Chem. Eur. J. 10 5901
[32] Yu G C, Yan X Z, Han C Y and Huang F H 2013 Chem. Soc. Rev. 42 6697
[33] Radlinski A P, Mastalerz M, Hinde A L, Hainbuchner A, Rauch H, Baron M, Lin J S, Fan L and Thiyagarajan P 2004 Int. J. Coal Geol. 59 245
[34] Coppens M O 1999 Catal. Today 53 225
[35] Kikhney A G and Svergun D I 2015 Febs. Lett. 589 2570
[36] Meek N and Penumadu D 2021 Carbon 178 133
[37] Ryan A J, Bras W, Mant G R and Derbyshire G E 1994 Polymer 35 4537
[38] Michael S 2021 Zenodo 1.024 5825707
[39] Hopkins J B, Gillilan R E and Skou S 2017 J. Appl. Crystallogr. 50 1545
[40] Tan L X, Elkins J G, Davison B H, Kelley E G and Nickels J 2021 J. Appl. Crystallogr. 54 363
[41] Cookson D, Kirby N, Knott R, Lee M and Schultz D 2006 J. Synchrotron Rad. 13 440
[42] Hammersley A P 2016 J. Appl. Crystallogr. 49 646
[43] Ilavsky J 2012 J. Appl. Crystallogr. 45 324
[44] Boesecke P 2007 J. Appl. Crystallogr. 40 S423
[45] Kieffer J and Karkoulis D 2013 J. Phys. Conf. Ser. 425 202012
[46] Ilavsky J and Jemian P R 2009 J. Appl. Crystallogr. 42 347
[47] Konarev P V, Petoukhov M V, Volkov V V and Svergun D I 2006 J. Appl. Crystallogr.. 39 277
[48] Bressler I, Pauw B R and Thünemann A F 2015 J. Appl. Crystallogr. 48 962
[49] Bressler I, Kohlbrecher J and Thunemann A F 2015 J. Appl. Crystallogr. 48 1587
[50] Hossain E 2022 Introduction to MATLAB
[51] Tomsic M, Jamnik A, Fritz-Popovski G, Glatter O and Vlcek L 2007 J. Phys. Chem. B 111 1738
[52] Michot L J, Bihannic I, Maddi S, Baravian C, Levitz P and Davidson P 2008 Langmuir 24 3127
[53] Page K A, Landis F A, Phillips A K and Moore R B 2006 Macromolecules 39 3939
[54] Lemaire B J, Panine P, Gabriel J C P and Davidson P 2002 Europhys. Lett. 59 55
[55] Pauw B R 2013 J. Phys. Condensed Matter 25 383201
[56] Orthaber D, Bergmann A and Glatter O 2000 J. Appl. Crystallogr. 33 218
[57] Dreiss C A, Jack K S and Parker A P 2006 J. Appl. Crystallogr. 39 32
[58] Russell T P 1983 J. Appl. Crystallogr. 16 473
[59] Russell T P, Lin J S, Spooner S and Wignall G D 1988 J. Appl. Crystallogr. 21 629
[60] Hermans P H, Heikens D and Weidinger A 1959 J. Polym. Sci. 35 145
[61] Kratky O, Pilz I and Schmitz P J 1966 J. Colloid Interface Sci. 21 24
[62] Pilz I and Kratky O 1967 J. Colloid Interface Sci. 24 211
[63] Pilz I 1969 J. Colloid Interface Sci. 30 140
[64] Shaffer L B and Hendrick R W 1974 J. Appl. Crystallogr. 7 159
[65] Endres A, Lode U, vonKrosigk G, Bark M, Cunis S, Gehrke R and Wilke W 1997 Rev. Sci. Instrum. 68 4009
[66] Haubold H G, Vad T, Jungbluth H and Hiller P 2001 Electrochim. Acta 46 1559
[67] Xie F, Li Z H, Li Z Z, Li D F, Gao Y X and Wang B 2018 Nucl. Instrum. Meth. A 900 64
[68] Affholter K A, Henderson S J, Wignall G D, Bunick G J, Haufler R E and Compton R N 1993 J. Chem. Phys. 99 9224
[69] Vollet D R, Donatti D A and Ruiz A I 2001 J. Non-Cryst. Solids 288 81
[70] Osamura K, Shibue K, Suzuki R and Murakami Y 1980 Sci. Rep. Res. Inst. Tohoku Univ. Ser. A 28 65
[71] Debye P and Bueche A M 1949 J. Appl. Phys. 20 518
[72] Goderis B, Reynaers H, Koch M H J and Mathot V B F 1999 J. Polym. Sci. Part B Polym. Phys. 37 1715
[73] Liu H G and Zwart P H 2012 J. Struct. Biol. 180 226
[74] Franke D and Svergun D I 2009 J. Appl. Crystallogr. 42 342
[75] Liu J, Pancera S, Boyko V, Shukla A, Narayanan T and Huber K 2010 Langmuir 26 17405
[76] Hammons J A, Ilavsky J and Zhang F 2015 Electrochemistry in Ionic Liquids pp. 169-213
[77] Gao P L, Gong J, Tian Q, Sun G A, Yan H Y, Chen L, Bai L F, Guo Z M and Ju X 2022 Chin. Phys. B 31 056102
[78] Berryman J G 1987 J. Math. Phys. 28 244

[1]	Induced magneto-conductivity in a two-node Weyl semimetal under Gaussian random disorder Chuanxiong Xu(徐川雄), Haoping Yu(于昊平), Mei Zhou(周梅), and Xuanting Ji(吉轩廷). Chin. Phys. B, 2024, 33(9): 097502.
[2]	Riemann-Hilbert problem for the defocusing Lakshmanan-Porsezian-Daniel equation with fully asymmetric nonzero boundary conditions Jianying Ji(纪建英) and Xiyang Xie(解西阳). Chin. Phys. B, 2024, 33(9): 090201.
[3]	Acoustic radiation force on a cylindrical composite particle with an elastic thin shell and an internal eccentric liquid column in a plane ultrasonic wave field Rui-Qi Pan(潘瑞琪), Zhi-Wei Du(杜芷玮), Cheng-Hui Wang(王成会), Jing Hu(胡静), and Run-Yang Mo(莫润阳). Chin. Phys. B, 2024, 33(9): 094302.
[4]	Observation of parabolic electron bands on superconductor LaRu₂As₂ Xingtai Zhou(周兴泰), Geng Li(李更), Lulu Pan(潘禄禄), Zichao Chen(陈子超), Meng Li(李萌), Yanhao Shi(时延昊), Haitao Yang(杨海涛), and Hong-Jun Gao(高鸿钧). Chin. Phys. B, 2024, 33(7): 077401.
[5]	Entangling two levitated charged nanospheres through Coulomb interaction Guoyao Li(李国耀) and Zhangqi Yin(尹璋琦). Chin. Phys. B, 2024, 33(7): 074205.
[6]	Wavelength-interval switchable Brillouin-Raman random fiber laser through Brillouin pump manipulation Yang Li(李阳), En-Ming Xu(徐恩明), Rui-Jia Chen(陈睿佳), Yu-Gang Shee, and Zu-Xing Zhang(张祖兴). Chin. Phys. B, 2024, 33(7): 074209.
[7]	Frequency-tunable single-photon router based on a microresonator containing a driven three-level emitter Jin-Song Huang(黄劲松), Jing-Lan Hu(胡菁兰), Yan-Ling Li(李艳玲), and Zhong-Hui Xu(徐中辉). Chin. Phys. B, 2024, 33(6): 064202.
[8]	Design and implementation of the monochromator shielding for the cold neutron spectrometers XINGZHI and BOYA Jinchen Wang(汪晋辰), Juanjuan Liu(刘娟娟), Daye Xu(徐大业), Florian Grünauer, Lijie Hao(郝丽杰), Yuntao Liu(刘蕴韬), Hongxia Zhang(张红霞), Peng Cheng(程鹏), and Wei Bao(鲍威). Chin. Phys. B, 2024, 33(5): 057801.
[9]	Experimental realization of fractal fretwork metasurface for sound anomalous modulation Jiajie He(何佳杰), Shumeng Yu(于书萌), Xue Jiang(江雪), and Dean Ta(他得安). Chin. Phys. B, 2024, 33(5): 054301.
[10]	Single-photon scattering and quantum entanglement of two giant atoms with azimuthal angle differences in a waveguide system Jin-Song Huang(黄劲松), Hong-Wu Huang(黄红武), Yan-Ling Li(李艳玲), and Zhong-Hui Xu(徐中辉). Chin. Phys. B, 2024, 33(5): 050506.
[11]	High-order Bragg forward scattering and frequency shift of low-frequency underwater acoustic field by moving rough sea surface Ya-Xiao Mo(莫亚枭), Chao-Jin Zhang(张朝金), Li-Cheng Lu(鹿力成), Qi-Hang Sun(孙启航), and Li Ma(马力). Chin. Phys. B, 2024, 33(3): 034301.
[12]	Broadband bidirectional Brillouin-Raman random fiber laser with ultra-narrow linewidth Qian Yang(杨茜), Yang Li(李阳), Hui Zou(邹辉), Jie Mei(梅杰), En-Ming Xu(徐恩明), and Zu-Xing Zhang(张祖兴). Chin. Phys. B, 2024, 33(2): 024206.
[13]	Imaging through scattering layers using a near-infrared low-spatial-coherence fiber random laser Anda Shi(史安达), Zeyu Wang(王泽宇), Chenxi Duan(段辰锡), Zhao Wang(王昭), and Weili Zhang(张伟利). Chin. Phys. B, 2024, 33(10): 104202.
[14]	Suppression of stimulated Brillouin and Raman scatterings using an alternating frequency laser and transverse magnetic fields Rui-Jin Cheng(程瑞锦), Xiao-Xun Li(李晓旬), Qing Wang(王清), De-Ji Liu(刘德基), Zhuo-Ming Huang(黄卓明), Shuai-Yu Lv(吕帅宇), Yuan-Zhi Zhou(周远志), Shu-Tong Zhang(张舒童), Xue-Ming Li(李雪铭), Zu-Jie Chen(陈祖杰), Qiang Wang(王强), Zhan-Jun Liu(刘占军), Li-Hua Cao(曹莉华), and Chun-Yang Zheng(郑春阳). Chin. Phys. B, 2024, 33(1): 015206.
[15]	Collision off-axis position dependence of relativistic nonlinear Thomson inverse scattering of an excited electron in a tightly focused circular polarized laser pulse Yubo Wang(王禹博), Qingyu Yang(杨青屿), Yifan Chang(常一凡), Zongyi Lin(林宗熠), and Youwei Tian(田友伟). Chin. Phys. B, 2024, 33(1): 013301.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Metrics
Related Articles

ScatterX: A software for fast processing of high-throughput small-angle scattering data

Cite this article:

Online attention