Simulation Study of Low-Dose 4D-STEM Phase Contrast Techniques at the Nanoscale in SEM
Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
21-13541S
Czech Science Foundation
PubMed
39791828
PubMed Central
PMC11722761
DOI
10.3390/nano15010070
PII: nano15010070
Knihovny.cz E-zdroje
- Klíčová slova
- 4D-STEM, SEM, STEM, carbon nanotubes, ePIE, electron microscopy, iCOM, low dose, phase contrast, ptychography,
- Publikační typ
- časopisecké články MeSH
Phase contrast imaging is well-suited for studying weakly scattering samples. Its strength lies in its ability to measure how the phase of the electron beam is affected by the sample, even when other imaging techniques yield low contrast. In this study, we explore via simulations two phase contrast techniques: integrated center of mass (iCOM) and ptychography, specifically using the extended ptychographical iterative engine (ePIE). We simulate the four-dimensional scanning transmission electron microscopy (4D-STEM) datasets for specific parameters corresponding to a scanning electron microscope (SEM) with an immersive objective and a given pixelated detector. The performance of these phase contrast techniques is analyzed using a contrast transfer function. Simulated datasets from a sample consisting of graphene sheets and carbon nanotubes are used for iCOM and ePIE reconstructions for two aperture sizes and two electron doses. We highlight the influence of aperture size, showing that for a smaller aperture, the radiation dose is spent mostly on larger sample features, which may aid in imaging sensitive samples while minimizing radiation damage.
Zobrazit více v PubMed
Reimer L. Scanning Electron Microscopy: Physics of Image Formation and Microanalysis. Springer; Berlin/Heidelberg, Germany: 1998. DOI
Erdman N., Bell D.C., Reichelt R. Springer Handbook of Microscopy. Springer International Publishing; Cham, Switzerland: 2019. Scanning Electron Microscopy; pp. 229–318. DOI
Botton G., Prabhudev S. Springer Handbook of Microscopy. Springer International Publishing; Cham, Switzerland: 2019. Analytical Electron Microscopy; pp. 345–453. DOI
Paras, Yadav K., Kumar P., Teja D.R., Chakraborty S., Chakraborty M., Mohapatra S.S., Sahoo A., Chou M.M.C., Liang C.T., et al. A Review on Low-Dimensional Nanomaterials: Nanofabrication, Characterization and Applications. Nanomaterials. 2022;13:160. doi: 10.3390/nano13010160. PubMed DOI PMC
Pauly N., Yubero F., Tougaard S. Determination of the Primary Excitation Spectra in XPS and AES. Nanomaterials. 2023;13:339. doi: 10.3390/nano13020339. PubMed DOI PMC
Magazzù A., Marcuello C. Investigation of Soft Matter Nanomechanics by Atomic Force Microscopy and Optical Tweezers: A Comprehensive Review. Nanomaterials. 2023;13:963. doi: 10.3390/nano13060963. PubMed DOI PMC
Ishikawa R., Okunishi E., Sawada H., Kondo Y., Hosokawa F., Abe E. Direct imaging of hydrogen-atom columns in a crystal by annular bright-field electron microscopy. Nat. Mater. 2011;10:278–281. doi: 10.1038/nmat2957. PubMed DOI
Zhou L., Song J., Kim J.S., Pei X., Huang C., Boyce M., Mendonça L., Clare D., Siebert A., Allen C.S., et al. Low-dose phase retrieval of biological specimens using cryo-electron ptychography. Nat. Commun. 2020;11:2773. doi: 10.1038/s41467-020-16391-6. PubMed DOI PMC
Bosch E.G., Lazić I. Analysis of HR-STEM theory for thin specimen. Ultramicroscopy. 2015;156:59–72. doi: 10.1016/j.ultramic.2015.02.004. PubMed DOI
Martis J., Susarla S., Rayabharam A., Su C., Paule T., Pelz P., Huff C., Xu X., Li H.K., Jaikissoon M., et al. Imaging the electron charge density in monolayer MoS2 at the Ångstrom scale. Nat. Commun. 2023;14:4363. doi: 10.1038/s41467-023-39304-9. PubMed DOI PMC
Rodenburg J., McCallum B., Nellist P. Experimental tests on double-resolution coherent imaging via STEM. Ultramicroscopy. 1993;48:304–314. doi: 10.1016/0304-3991(93)90105-7. DOI
Nellist P.D., McCallum B.C., Rodenburg J.M. Resolution beyond the “information limit” in transmission electron microscopy. Nature. 1995;374:630–632. doi: 10.1038/374630a0. DOI
Taylor K.A., Glaeser R.M. Electron Diffraction of Frozen, Hydrated Protein Crystals. Science. 1974;186:1036–1037. doi: 10.1126/science.186.4168.1036. PubMed DOI
Levin B.D.A. Direct detectors and their applications in electron microscopy for materials science. J. Phys. Mater. 2021;4:042005. doi: 10.1088/2515-7639/ac0ff9. DOI
Pennycook T.J., Lupini A.R., Yang H., Murfitt M.F., Jones L., Nellist P.D. Efficient phase contrast imaging in STEM using a pixelated detector. Part 1: Experimental demonstration at atomic resolution. Ultramicroscopy. 2015;151:160–167. doi: 10.1016/j.ultramic.2014.09.013. PubMed DOI
Lei D., Marras A.E., Liu J., Huang C.M., Zhou L., Castro C.E., Su H.J., Ren G. Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography. Nat. Commun. 2018;9:592. doi: 10.1038/s41467-018-03018-0. PubMed DOI PMC
Mrazova K., Bacovsky J., Sedrlova Z., Slaninova E., Obruca S., Fritz I., Krzyzanek V. Urany-Less Low Voltage Transmission Electron Microscopy: A Powerful Tool for Ultrastructural Studying of Cyanobacterial Cells. Microorganisms. 2023;11:888. doi: 10.3390/microorganisms11040888. PubMed DOI PMC
Oliveira S., Corduneanu O., Oliveira-Brett A. In situ evaluation of heavy metal–DNA interactions using an electrochemical DNA biosensor. Bioelectrochemistry. 2008;72:53–58. doi: 10.1016/j.bioelechem.2007.11.004. PubMed DOI
Ding Z., Gao S., Fang W., Huang C., Zhou L., Pei X., Liu X., Pan X., Fan C., Kirkland A.I., et al. Three-dimensional electron ptychography of organic–inorganic hybrid nanostructures. Nat. Commun. 2022;13:4787. doi: 10.1038/s41467-022-32548-x. PubMed DOI PMC
Kirkland E.J. Advanced Computing in Electron Microscopy. Springer; New York, NY, USA: 2010. DOI
Seki T., Ikuhara Y., Shibata N. Theoretical framework of statistical noise in scanning transmission electron microscopy. Ultramicroscopy. 2018;193:118–125. doi: 10.1016/j.ultramic.2018.06.014. PubMed DOI
Frojdh E., Campbell M., Gaspari M.D., Kulis S., Llopart X., Poikela T., Tlustos L. Timepix3: First measurements and characterization of a hybrid-pixel detector working in event driven mode. J. Instrum. 2015;10:C01039. doi: 10.1088/1748-0221/10/01/C01039. DOI
Madsen J., Susi T. The abTEM code: Transmission electron microscopy from first principles. Open Res. Eur. 2021;1:24. doi: 10.12688/openreseurope.13015.1. PubMed DOI PMC
Lazić I., Bosch E.G., Lazar S. Phase contrast STEM for thin samples: Integrated differential phase contrast. Ultramicroscopy. 2016;160:265–280. doi: 10.1016/j.ultramic.2015.10.011. PubMed DOI
Yücelen E., Lazić I., Bosch E.G.T. Phase contrast scanning transmission electron microscopy imaging of light and heavy atoms at the limit of contrast and resolution. Sci. Rep. 2018;8:2676. doi: 10.1038/s41598-018-20377-2. PubMed DOI PMC
Wang H., Liu L., Wang J., Li C., Hou J., Zheng K. The Development of iDPC-STEM and Its Application in Electron Beam Sensitive Materials. Molecules. 2022;27:3829. doi: 10.3390/molecules27123829. PubMed DOI PMC
Chapman H.N. Phase-retrieval X-ray microscopy by Wigner-distribution deconvolution. Ultramicroscopy. 1996;66:153–172. doi: 10.1016/S0304-3991(96)00084-8. DOI
Maiden A.M., Humphry M.J., Rodenburg J.M. Ptychographic transmission microscopy in three dimensions using a multi-slice approach. J. Opt. Soc. Am. 2012;29:1606. doi: 10.1364/JOSAA.29.001606. PubMed DOI
Thibault P., Menzel A. Reconstructing state mixtures from diffraction measurements. Nature. 2013;494:68–71. doi: 10.1038/nature11806. PubMed DOI
Maiden A.M., Rodenburg J.M. An improved ptychographical phase retrieval algorithm for diffractive imaging. Ultramicroscopy. 2009;109:1256–1262. doi: 10.1016/j.ultramic.2009.05.012. PubMed DOI
Humphry M., Kraus B., Hurst A., Maiden A., Rodenburg J. Ptychographic electron microscopy using high-angle dark-field scattering for sub-nanometre resolution imaging. Nat. Commun. 2012;3:730. doi: 10.1038/ncomms1733. PubMed DOI PMC
Rodenburg J., Maiden A. Springer Handbook of Microscopy. Springer International Publishing; Cham, Switzerland: 2019. Ptychography; pp. 833–853. DOI
Batey D.J., Edo T.B., Rau C., Wagner U., Pešić Z.D., Waigh T.A., Rodenburg J.M. Reciprocal-space up-sampling from real-space oversampling in x-ray ptychography. Phys. Rev. A. 2014;89:043812. doi: 10.1103/PhysRevA.89.043812. DOI
de Graaf S., Ahmadi M., Lazić I., Bosch E.G.T., Kooi B.J. Imaging atomic motion of light elements in 2D materials with 30 kV electron microscopy. Nanoscale. 2021;13:20683–20691. doi: 10.1039/D1NR06614E. PubMed DOI
Jiang Y., Chen Z., Han Y., Deb P., Gao H., Xie S., Purohit P., Tate M.W., Park J., Gruner S.M., et al. Electron ptychography of 2D materials to deep sub-ångström resolution. Nature. 2018;559:343–349. doi: 10.1038/s41586-018-0298-5. PubMed DOI
Pennycook T.J., Martinez G.T., Nellist P.D., Meyer J.C. High dose efficiency atomic resolution imaging via electron ptychography. Ultramicroscopy. 2019;196:131–135. doi: 10.1016/j.ultramic.2018.10.005. PubMed DOI
Hofer C., Pennycook T.J. Reliable phase quantification in focused probe electron ptychography of thin materials. Ultramicroscopy. 2023;254:113829. doi: 10.1016/j.ultramic.2023.113829. PubMed DOI
O’Leary C.M., Martinez G.T., Liberti E., Humphry M.J., Kirkland A.I., Nellist P.D. Contrast transfer and noise considerations in focused-probe electron ptychography. Ultramicroscopy. 2021;221:113189. doi: 10.1016/j.ultramic.2020.113189. PubMed DOI
van Heel M., Schatz M. Fourier shell correlation threshold criteria. J. Struct. Biol. 2005;151:250–262. doi: 10.1016/j.jsb.2005.05.009. PubMed DOI
Rosenthal P.B., Henderson R. Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy. J. Mol. Biol. 2003;333:721–745. doi: 10.1016/j.jmb.2003.07.013. PubMed DOI
Savitzky B.H., Zeltmann S.E., Hughes L.A., Brown H.G., Zhao S., Pelz P.M., Pekin T.C., Barnard E.S., Donohue J., Rangel DaCosta L., et al. py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis. Microsc. Microanal. 2021;27:712–743. doi: 10.1017/S1431927621000477. PubMed DOI
Song J., Allen C.S., Gao S., Huang C., Sawada H., Pan X., Warner J., Wang P., Kirkland A.I. Atomic Resolution Defocused Electron Ptychography at Low Dose with a Fast, Direct Electron Detector. Sci. Rep. 2019;9:3919. doi: 10.1038/s41598-019-40413-z. PubMed DOI PMC