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Currently, the machine learning (ML)-based scanning transmission electron microscopy (STEM) analysis is limited in the simulative stage, its application in experimental STEM is needed but challenging. Herein, we built up a universal model to analyze the vacancy defects and single atoms accurately and rapidly in experimental STEM images using a full convolution network. In our model, the unavoidable interference factors of noise, aberration, and carbon contamination were fully considered during the training, which were difficult to be considered in the past. Even toward the simultaneous identification of various vacancy types and low-contrast single atoms in the low-quality STEM images, our model showed rapid process speed (45 images per second) and high accuracy (> 95%). This work represents an improvement in experimental STEM image analysis by ML.


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Accurate atomic scanning transmission electron microscopy analysis enabled by deep learning

Show Author's information Tianshu Chu1,2,3,§Lei Zhou1,2,3,§Bowei Zhang1,2,3( )Fu-Zhen Xuan1,2,3( )
Shanghai Key Laboratory of Intelligent Sensing and Detection Technology, East China University of Science and Technology, Shanghai 200237, China
School of Mechanical and Power Engineering, East China University of Science and Technology, Shanghai 200237, China
Key Laboratory of Pressure Systems and Safety of Ministry of Education, East China University of Science and Technology, Shanghai 200237, China

§ Tianshu Chu and Lei Zhou contributed equally to this work.

Abstract

Currently, the machine learning (ML)-based scanning transmission electron microscopy (STEM) analysis is limited in the simulative stage, its application in experimental STEM is needed but challenging. Herein, we built up a universal model to analyze the vacancy defects and single atoms accurately and rapidly in experimental STEM images using a full convolution network. In our model, the unavoidable interference factors of noise, aberration, and carbon contamination were fully considered during the training, which were difficult to be considered in the past. Even toward the simultaneous identification of various vacancy types and low-contrast single atoms in the low-quality STEM images, our model showed rapid process speed (45 images per second) and high accuracy (> 95%). This work represents an improvement in experimental STEM image analysis by ML.

Keywords: deep learning, single atoms, low-dimensional materials, atomic defects

References(58)

[1]

Chu, T. S.; Rong, C.; Zhou, L.; Mao, X. Y.; Zhang, B. W.; Xuan, F. Z. Progress and perspectives of single-atom catalysts for gas sensing. Adv. Mater. 2023, 35, 2206783.

[2]

Mitterreiter, E.; Schuler, B.; Micevic, A.; Hernangómez-Pérez, D.; Barthelmi, K.; Cochrane, K. A.; Kiemle, J.; Sigger, F.; Klein, J.; Wong, E. et al. The role of chalcogen vacancies for atomic defect emission in MoS2. Nat. Commun. 2021, 12, 3822.

[3]

Hong, J. H.; Hu, Z. X.; Probert, M.; Li, K.; Lv, D. H.; Yang, X. N.; Gu, L.; Mao, N. N.; Feng, Q. L.; Xie, L. M. et al. Exploring atomic defects in molybdenum disulphide monolayers. Nat. Commun. 2015, 6, 6293.

[4]

Sun, H. M.; Yan, Z. H.; Liu, F. M.; Xu, W. C.; Cheng, F. Y.; Chen, J. Self-supported transition-metal-based electrocatalysts for hydrogen and oxygen evolution. Adv. Mater. 2020, 32, 1806326.

[5]

Zhang, N. Q.; Ye, C. L.; Yan, H.; Li, L. C.; He, H.; Wang, D. S.; Li, Y. D. Single-atom site catalysts for environmental catalysis. Nano Res. 2020, 13, 3165–3182.

[6]

Zhang, Q. Q.; Guan, J. Q. Applications of single-atom catalysts. Nano Res. 2022, 15, 38–70.

[7]

Zhang, J. Q.; Zhao, Y. F.; Guo, X.; Chen, C.; Dong, C. L.; Liu, R. S.; Han, C. P.; Li, Y. D.; Gogotsi, Y.; Wang, G. X. Single platinum atoms immobilized on an MXene as an efficient catalyst for the hydrogen evolution reaction. Nat. Catal. 2018, 1, 985–992.

[8]

Du, Q. H.; Wu, L. J.; Cao, H. B.; Kang, C. J.; Nelson, C.; Pascut, G. L.; Besara, T.; Siegrist, T.; Haule, K.; Kotliar, G. et al. Vacancy defect control of colossal thermopower in FeSb2. npj Quantum Mater. 2021, 6, 13.

[9]

Gao, W.; Li, S.; He, H. C.; Li, X. N.; Cheng, Z. X.; Yang, Y.; Wang, J. L.; Shen, Q.; Wang, X. Y.; Xiong, Y. J. et al. Vacancy-defect modulated pathway of photoreduction of CO2 on single atomically thin AgInP2S6 sheets into olefiant gas. Nat. Commun. 2021, 12, 4747.

[10]

Dou, Y. H.; He, C. T.; Zhang, L.; Yin, H. J.; Al-Mamun, M.; Ma, J. M.; Zhao, H. J. Approaching the activity limit of CoSe2 for oxygen evolution via Fe doping and Co vacancy. Nat. Commun. 2020, 11, 1664.

[11]

Sun, Y. H.; Zhao, H. F.; Zhou, D.; Zhu, Y. C.; Ye, H. Y.; Moe, Y. A.; Wang, R. M. Direct observation of epitaxial alignment of Au on MoS2 at atomic resolution. Nano Res. 2019, 12, 947–954.

[12]

Gu, H. Y.; Liu, X.; Liu, X. F.; Ling, C. C.; Wei, K.; Zhan, G. M.; Guo, Y. B.; Zhang, L. Z. Adjacent single-atom irons boosting molecular oxygen activation on MnO2. Nat. Commun. 2021, 12, 5422.

[13]

Hobbs, C.; Downing, C.; Jaskaniec, S.; Nicolosi, V. TEM and EELS characterization of Ni-Fe layered double hydroxide decompositions caused by electron beam irradiation. npj 2D Mater. Appl. 2021, 5, 29.

[14]

Zhai, P. L.; Xia, M. Y.; Wu, Y. Z.; Zhang, G. H.; Gao, J. F.; Zhang, B.; Cao, S. Y.; Zhang, Y. T.; Li, Z. W.; Fan, Z. Z. et al. Engineering single-atomic ruthenium catalytic sites on defective nickel-iron layered double hydroxide for overall water splitting. Nat. Commun. 2021, 12, 4587.

[15]

Cui, W. J.; Hu, Z. Y.; Unocic, R. R.; Van Tendeloo, G.; Sang, X. H. Atomic defects, functional groups and properties in MXenes. Chin. Chem. Lett. 2021, 32, 339–344.

[16]

Zhang, B. W.; Zhu, C. Q.; Wu, Z. S.; Stavitski, E.; Lui, Y. H.; Kim, T. H.; Liu, H.; Huang, L.; Luan, X. C.; Zhou, L. et al. Integrating Rh species with NiFe-layered double hydroxide for overall water splitting. Nano Lett. 2020, 20, 136–144.

[17]

Pattengale, B.; Huang, Y. C.; Yan, X. X.; Yang, S. Z.; Younan, S.; Hu, W. H.; Li, Z. D.; Lee, S.; Pan, X. Q.; Gu, J. et al. Dynamic evolution and reversibility of single-atom Ni(II) active site in 1T-MoS2 electrocatalysts for hydrogen evolution. Nat. Commun. 2020, 11, 4114.

[18]

Kalinin, S. V.; Ophus, C.; Voyles, P. M.; Erni, R.; Kepaptsoglou, D.; Grillo, V.; Lupini, A. R.; Oxley, M. P.; Schwenker, E.; Chan, M. K. Y. et al. Machine learning in scanning transmission electron microscopy. Nat. Rev. Methods Primers 2022, 2, 11.

[19]
Jimenez-Del-Toro, O.; Otálora, S.; Andersson, M.; Eurén, K.; Hedlund, M.; Rousson, M.; Müller, H.; Atzori, M. Analysis of histopathology images: From traditional machine learning to deep learning. In Biomedical Texture Analysis. Depeursinge, A.; Al-Kadi, A. S.; Mitchell, J. R., Eds.; Elsevier: Amsterdam, 2017; pp 281–314.
[20]

Castiglioni, I.; Rundo, L.; Codari, M.; Di Leo, G.; Salvatore, C.; Interlenghi, M.; Gallivanone, F.; Cozzi, A.; D’Amico, N. C.; Sardanelli, F. AI applications to medical images: From machine learning to deep learning. Phys. Medica 2021, 83, 9–24.

[21]

Lecun, Y.; Bottou, L.; Bengio, Y.; Haffner, P. Gradient-based learning applied to document recognition. Proc. IEEE 1998, 86, 2278–2324.

[22]
Simonyan, K.; Zisserman, A. Very deep convolutional networks for large-scale image recognition. In 3rd International Conference on Learning Representations, San Diego, USA, 2015, pp 1–14.
[23]
Liu, J. J.; Hou, Q. B.; Cheng, M. M.; Feng, J. S.; Jiang, J. M. A simple pooling-based design for real-time salient object detection. In 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Long Beach, USA, 2019, pp 3912–3921.
[24]

Vaisman, R.; Kroese, D. P.; Gertsbakh, I. B. Improved sampling plans for combinatorial invariants of coherent systems. IEEE Trans. Reliab. 2016, 65, 410–424.

[25]
Wang, T. T.; Borji, A.; Zhang, L. H.; Zhang, P. P.; Lu, H. C. A stagewise refinement model for detecting salient objects in images. In 2017 IEEE International Conference on Computer Vision, Venice, Italy, 2017, pp 4039–4048.
[26]

Cheng, M. M.; Fan, D. P. Structure-measure: A new way to evaluate foreground maps. Int. J. Comput. Vis. 2021, 129, 2622–2638.

[27]
Zhang, P. P.; Wang, D.; Lu, H. C.; Wang, H. Y.; Yin, B. C. Learning uncertain convolutional features for accurate saliency detection. In 2017 IEEE International Conference on Computer Vision, Venice, Italy, 2017, pp 212–221.
[28]
Chen, S. H.; Tan, X. L.; Wang, B.; Hu, X. L. Reverse attention for salient object detection. In 15th European Conference on Computer Vision, Munich, Germany, 2018, pp 236–252.
[29]

Zhang, Z. X.; Liu, Q. J.; Wang, Y. H. Road extraction by deep residual U-Net. IEEE Geosci. Remote Sens. Lett. 2018, 15, 749–753.

[30]

Qin, X. B.; Zhang, Z. C.; Huang, C. Y.; Dehghan, M.; Zaiane, O. R.; Jagersand, M. U2-Net: Going deeper with nested U-structure for salient object detection. Pattern Recognit. 2020, 106, 107404.

[31]

Lee, C. H.; Khan, A.; Luo, D.; Santos, T. P.; Shi, C. Q.; Janicek, B. E.; Kang, S. M.; Zhu, W. J.; Sobh, N. A.; Schleife, A. et al. Deep learning enabled strain mapping of single-atom defects in two-dimensional transition metal dichalcogenides with sub-picometer precision. Nano Lett. 2020, 20, 3369–3377.

[32]

Yang, S. H.; Choi, W.; Cho, B. W.; Agyapong-Fordjour, F. O. T.; Park, S.; Yun, S. J.; Kim, H. J.; Han, Y. K.; Lee, Y. H.; Kim, K. K. et al. Deep learning-assisted quantification of atomic dopants and defects in 2D materials. Adv. Sci. 2021, 8, 2101099.

[33]

Lin, R. Q.; Zhang, R.; Wang, C. Y.; Yang, X. Q.; Xin, H. L. TEMImageNet training library and AtomSegNet deep-learning models for high-precision atom segmentation, localization, denoising, and deblurring of atomic-resolution images. Sci. Rep. 2021, 11, 5386.

[34]

Aguiar, J. A.; Gong, M. L.; Unocic, R. R.; Tasdizen, T.; Miller, B. D. Decoding crystallography from high-resolution electron imaging and diffraction datasets with deep learning. Sci. Adv. 2019, 5, eaaw1949.

[35]

Sang, X. H.; Xie, Y.; Lin, M. W.; Alhabeb, M.; Van Aken, K. L.; Gogotsi, Y.; Kent, P. R. C.; Xiao, K.; Unocic, R. R. Atomic defects in monolayer titanium carbide (Ti3C2Tx) MXene. ACS Nano 2016, 10, 9193–9200.

[36]

Trentino, A.; Madsen, J.; Mittelberger, A.; Mangler, C.; Susi, T.; Mustonen, K.; Kotakoski, J. Atomic-level structural engineering of graphene on a mesoscopic scale. Nano Lett. 2021, 21, 5179–5185.

[37]

Ziatdinov, M.; Dyck, O.; Maksov, A.; Li, X. F.; Sang, X. H.; Xiao, K.; Unocic, R. R.; Vasudevan, R.; Jesse, S.; Kalinin, S. V. Deep learning of atomically resolved scanning transmission electron microscopy images: Chemical identification and tracking local transformations. ACS Nano 2017, 11, 12742–12752.

[38]

Zhao, L.; Pan, Y. L.; Wang, S.; Zhang, L.; Islam, M. S. A hybrid crack detection approach for scanning electron microscope image using deep learning method. Scanning 2021, 2021, 5558668.

[39]

Mitchell, S.; Parés, F.; Faust Akl, D.; Collins, S. M.; Kepaptsoglou, D. M.; Ramasse, Q. M.; Garcia-Gasulla, D.; Pérez-Ramírez, J.; López, N. Automated image analysis for single-atom detection in catalytic materials by transmission electron microscopy. J. Am. Chem. Soc. 2022, 144, 8018–8029.

[40]

Qi, K.; Cui, X. Q.; Gu, L.; Yu, S. S.; Fan, X. F.; Luo, M. C.; Xu, S.; Li, N. B.; Zheng, L. R.; Zhang, Q. H. et al. Single-atom cobalt array bound to distorted 1T MoS2 with ensemble effect for hydrogen evolution catalysis. Nat. Commun. 2019, 10, 5231.

[41]

Addou, R.; Colombo, L.; Wallace, R. M. Surface defects on natural MoS2. ACS Appl. Mater. Interfaces 2015, 7, 11921–11929.

[42]

Rasool, H. I.; Ophus, C.; Zettl, A. Atomic defects in two dimensional materials. Adv. Mater. 2015, 27, 5771–5777.

[43]

Stobinski, L.; Lesiak, B.; Malolepszy, A.; Mazurkiewicz, M.; Mierzwa, B.; Zemek, J.; Jiricek, P.; Bieloshapka, I. Graphene oxide and reduced graphene oxide studied by the XRD, TEM and electron spectroscopy methods. J. Electron Spectros. Relat. Phenomena 2014, 195, 145–154.

[44]

Peng, W.; Han, J. H.; Lu, Y. R.; Luo, M.; Chan, T. S.; Peng, M.; Tan, Y. W. A general strategy for engineering single-metal sites on 3D porous N, P Co-doped Ti3C2Tx MXene. ACS Nano 2022, 16, 4116–4125.

[45]

Zhao, D.; Chen, Z.; Yang, W. J.; Liu, S. J.; Zhang, X.; Yu, Y.; Cheong, W. C.; Zheng, L. R.; Ren, F. Q.; Ying, G. B. et al. MXene (Ti3C2) vacancy-confined single-atom catalyst for efficient functionalization of CO2. J. Am. Chem. Soc. 2019, 141, 4086–4093.

[46]

Cheng, Y. W.; Dai, J. H.; Zhang, Y. M.; Song, Y. Transition metal modification and carbon vacancy promoted Cr2CO2 (MXenes): A new opportunity for a highly active catalyst for the hydrogen evolution reaction. J. Mater. Chem. A 2018, 6, 20956–20965.

[47]

Wan, Q.; Li, S. N.; Liu, J. B. First-principle study of Li-ion storage of functionalized Ti2C monolayer with vacancies. ACS Appl. Mater. Interfaces 2018, 10, 6369–6377.

[48]

Wu, H.; Guo, Z. L.; Zhou, J.; Sun, Z. M. Vacancy-mediated lithium adsorption and diffusion on MXene. Appl. Surf. Sci. 2019, 488, 578–585.

[49]

Hao, J. C.; Zhuang, Z. C.; Cao, K. C.; Gao, G. H.; Wang, C.; Lai, F. L.; Lu, S. L.; Ma, P. M.; Dong, W. F.; Liu, T. X. et al. Unraveling the electronegativity-dominated intermediate adsorption on high-entropy alloy electrocatalysts. Nat. Commun. 2022, 13, 2662.

[50]

Chu, C. H.; Huang, D. H.; Gupta, S.; Weon, S.; Niu, J. F.; Stavitski, E.; Muhich, C.; Kim, J. H. Neighboring Pd single atoms surpass isolated single atoms for selective hydrodehalogenation catalysis. Nat. Commun. 2021, 12, 5179.

[51]

Zhang, C. Y.; Liang, S. X.; Liu, W.; Eickemeyer, F. T.; Cai, X. B.; Zhou, K.; Bian, J. M.; Zhu, H. W.; Zhu, C.; Wang, N. et al. Ti1-graphene single-atom material for improved energy level alignment in perovskite solar cells. Nat. Energy 2021, 6, 1154–1163.

[52]

Li, Z.; Xiao, Y.; Chowdhury, P. R.; Wu, Z. W.; Ma, T.; Chen, J. Z.; Wan, G.; Kim, T. H.; Jing, D. P.; He, P. L. et al. Direct methane activation by atomically thin platinum nanolayers on two-dimensional metal carbides. Nat. Catal. 2021, 4, 882–891.

[53]

Bao, H. H.; Qiu, Y.; Peng, X. Y.; Wang, J. A.; Mi, Y. Y.; Zhao, S. Z.; Liu, X. J.; Liu, Y. F.; Cao, R.; Zhuo, L. C. et al. Isolated copper single sites for high-performance electroreduction of carbon monoxide to multicarbon products. Nat. Commun. 2021, 12, 238.

[54]

Madsen, J.; Liu, P.; Kling, J.; Wagner, J. B.; Hansen, T. W.; Winther, O.; Schiøtz, J. A deep learning approach to identify local structures in atomic-resolution transmission electron microscopy images. Adv. Theory Simul. 2018, 1, 1800037.

[55]

Seo, S. Y.; Yang, D. H.; Moon, G.; Okello, O. F. N.; Park, M. Y.; Lee, S. H.; Choi, S. Y.; Jo, M. H. Identification of point defects in atomically thin transition-metal dichalcogenide semiconductors as active dopants. Nano Lett. 2021, 21, 3341–3354.

[56]

Maksov, A.; Dyck, O.; Wang, K.; Xiao, K.; Geohegan, D. B.; Sumpter, B. G.; Vasudevan, R. K.; Jesse, S.; Kalinin, S. V.; Ziatdinov, M. Deep learning analysis of defect and phase evolution during electron beam-induced transformations in WS2. npj Comput. Mater. 2019, 5, 12.

[57]
PyTorch. https://pytorch.org/docs/stable/generated/torch.nn.BCELoss.
[58]
Kirkland, E. J. Advanced Computing in Electron Microscopy; 2nd ed. Springer: New York, 2010; pp 1–351.
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Publication history
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Acknowledgements

Publication history

Received: 11 July 2023
Revised: 14 August 2023
Accepted: 16 August 2023
Published: 23 September 2023
Issue date: April 2024

Copyright

© Tsinghua University Press 2023

Acknowledgements

Acknowledgements

This work was supported by the National Natural Science Foundation of China (Nos. 52105145 and 12274124), the Shanghai Pilot Program for Basic Research (No. 22TQ1400100-6), and the Fundamental Research Funds for the Central Universities. Additional support was provided by the Feringa Nobel Prize Scientist Joint Research Center of the East China University of Science and Technology.

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