Skip to main content
SpringerLink
Log in

Accounting for sample morphology in correlative X-ray microscopy via ray tracing

  • Original Paper
  • Published:
MRS Advances Aims and scope Submit manuscript

Abstract

The correlations in multi-modal microscopy data can be systematically reduced by the distinct probe-sample interactions and signal collection geometry for each modality. Extracting scientific insights from correlative datasets thus requires careful consideration of the mode-specific, and often non-overlapping, sampling volume used in the correlative microscopy. Here we describe a pencil beam, ray tracing method that accounts for the finite extent and roughness of thin-films and nanomaterials in synchrotron-based X-ray microscopy measurements, creating a first approximation of the probe-sample interaction for each modality that tightens correlations in multi-modal X-ray nanoprobe characterization. As a demonstrative example we analyze structure–function correlations in sequential microscopy data acquired for a Eu:CsPbBr3 halide perovskite thin-film crystal across three distinct measurement modes. Our ray-traced corrections account for local fluorescence matrix effects and sampling volume discrepancies and unveil structural, compositional, and optoelectronic relationships hidden in the raw data.

Graphic abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Data Availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Code Availability

The code described in this work is available at https://github.com/rekumar/XRayTracer.

References

  1. M. Kreuzer, S. Stamenković, S. Chen, P. Andjus, T. Dučić, Lipids status and copper in a single astrocyte of the rat model for amyotrophic lateral sclerosis: Correlative synchrotron-based X-ray and infrared imaging. J. Biophoton. 13(10), e202000069 (2020)

    Article  CAS  Google Scholar 

  2. B. De Samber, R. Evens, K. De Schamphelaere, G. Silversmit, B. Masschaele, T. Schoonjans, B. Vekemans, C.R. Janssen, L. Van Hoorebeke, I. Szalóki, F. Vanhaecke, G. Falkenberg, L. Vincze, A combination of synchrotron and laboratory X-ray techniques for studying tissue-specific trace level metal distributions in Daphnia magna. J. Anal. At. Spectrom. 23(6), 829 (2008)

    Article  CAS  Google Scholar 

  3. A. Conti, R. Sinibaldi, S. Capuani, T. Traini, G.L. Romani, S. Della Penna, Co-registration of Synchrotron Radiation-microCT and micro-MRI images: a new method for the complete characterization of newly-formed bone. Proc. Intl. Soc. Mag. Reson. Med 22, 1176 (2014)

    Google Scholar 

  4. N. Li, Y. Luo, Z. Chen, X. Niu, X. Zhang, J. Lu, R. Kumar, J. Jiang, H. Liu, X. Guo, B. Lai, G. Brocks, Q. Chen, S. Tao, D. P. Fenning, H. Zhou, Microscopic degradation in formamidinium-cesium lead iodide perovskite solar cells under operational stressors. Joule 4(8), 1743–1758 (2020)

  5. X.L. Quinn, R.E. Kumar, M. Kodur, D.N. Cakan, Z. Cai, T. Zhou, M.V. Holt, D. P. Fenning, Europium addition reduces local structural disorder and enhances photoluminescent yield in perovskite CsPbBr3. Adv. Optical Mater. (2021). https://doi.org/10.1002/adom.202002221

  6. M. Kodur, R.E. Kumar, Y. Luo, D.N. Cakan, X. Li, M. Stuckelberger, D.P. Fenning, X-Ray Microscopy of Halide Perovskites: Techniques, Applications, and Prospects. Adv. Energy Mater. 10(26), 1–25 (2020)

    Article  CAS  Google Scholar 

  7. Y. Luo, S. Aharon, M. Stuckelberger, E. Magaña, B. Lai, M.I. Bertoni, L. Etgar, D.P. Fenning, The relationship between chemical flexibility and nanoscale charge collection in hybrid halide perovskites. Adv. Func. Mater. 28(18), 1706995 (2018)

    Article  CAS  Google Scholar 

  8. B.M. West, M. Stuckelberger, H. Guthrey, L. Chen, B. Lai, J. Maser, V. Rose, W. Shafarman, M. Al-Jassim, M.I. Bertoni, Grain engineering: How nanoscale inhomogeneities can control charge collection in solar cells. Nano Energy 32, 488–493 (2017)

    Article  CAS  Google Scholar 

  9. M. Stuckelberger, B. West, T. Nietzold, B. Lai, J.M. Maser, V. Rose, M.I. Bertoni, Engineering solar cells based on correlative X-ray microscopy. J. Mater. Res. 32(10), 1825–1854 (2017)

    Article  CAS  Google Scholar 

  10. Y. Zhou, H. Zhou, J. Deng, W. Cha, Z. Cai, Decisive structural and functional characterization of halide perovskites with synchrotron. Matter 2, 360–377 (2020)

    Article  Google Scholar 

  11. B. Beckhoff, B. Kanngießer, N. Langhoff, R. Wedell, H. Wolff, Handbook of Practical X-Ray Fluorescence Analysis (Springer, New York, 2007)

    Google Scholar 

  12. P. Pfalzer, J.P. Urbach, M. Klemm, S. Horn, M.L. Den Boer, A.I. Frenkel, J.P. Kirkland, Elimination of self-absorption in fluorescence hard-x-ray absorption spectra. Phys. Rev. B 60(13), 9335–9339 (1999)

    Article  CAS  Google Scholar 

  13. B.M. West, M. Stuckelberger, A. Jeffries, S. Gangam, B. Lai, B. Stripe, J. Maser, V. Rose, S. Vogt, M.I. Bertoni, X-ray fluorescence at nanoscale resolution for multicomponent layered structures: a solar cell case study. J. Synchrotron Radiat. 24(1), 288–295 (2017)

  14. S.-M. Bak, Z. Shadike, R. Lin, X. Yu, X.-Q. Yang, In situ/operando synchrotron-based X-ray techniques for lithium-ion battery research. NPG Asia Mater. 10(7), 563–580 (2018)

    Article  Google Scholar 

  15. D.A. Shapiro, Y.-S.S. Yu, T. Tyliszczak, J. Cabana, R. Celestre, W. Chao, K. Kaznatcheev, A.L.D.D. Kilcoyne, F. Maia, S. Marchesini, Y.S. Meng, T. Warwick, L.L. Yang, H.A. Padmore, Chemical composition mapping with nanometre resolution by soft X-ray microscopy. Nat. Photon. 8(10), 765–769 (2014)

    Article  CAS  Google Scholar 

  16. F. Meirer, B.M. Weckhuysen, Spatial and temporal exploration of heterogeneous catalysts with synchrotron radiation. Nat. Rev. Mater. 3(9), 324–340 (2018)

    Article  Google Scholar 

  17. J. Becher, T.L. Sheppard, Y. Fam, S. Baier, W. Wang, D. Wang, S. Kulkarni, T.F. Keller, M. Lyubomirskiy, D. Brueckner, M. Kahnt, A. Schropp, C.G. Schroer, J.-D. Grunwaldt, Mapping the pore architecture of structured catalyst monoliths from nanometer to centimeter scale with electron and X-ray tomographies. J. Phys. Chem. C 123(41), 25197–25208 (2019)

    Article  CAS  Google Scholar 

  18. J. Deng, Y.H. Lo, M. Gallagher-Jones, S. Chen, A. Pryor, Q. Jin, Y.P. Hong, Y.S.G.G. Nashed, S. Vogt, J. Miao, C. Jacobsen, Correlative 3D x-ray fluorescence and ptychographic tomography of frozen-hydrated green algae. Sci. Adv. 4(11), 1–11 (2018)

    Article  CAS  Google Scholar 

  19. J. Bruley, M.J. Highland, S.O. Hruszkewycz, I. McNulty, C.E. Murray, M.V. Holt, A. Tripathi, P.H. Fuoss, O.G. Shpyrko, J. Holt, C.E. Murray, J. Bruley, J. Holt, A. Tripathi, O.G. Shpyrko, I. McNulty, M.J. Highland, P.H. Fuoss, S.O. Hruszkewycz, I. McNulty, C.E. Murray, M.V. Holt, A. Tripathi, P.H. Fuoss, O.G. Shpyrko, J. Holt, C.E. Murray, J. Bruley, J. Holt, A. Tripathi, O.G. Shpyrko, I. McNulty, M.J. Highland, P.H. Fuoss, Quantitative nanoscale imaging of lattice distortions in epitaxial semiconductor heterostructures using nanofocused X-ray Bragg projection ptychography. Nano Lett. 12(10), 5148–5154 (2012)

    Article  CAS  Google Scholar 

  20. M.S. del Rio, L. Rebuffi, OASYS: a software for beamline simulations and synchrotron virtual experiments. AIP Conference Proceedings 2054, 060081 (2019). https://doi.org/10.1063/1.5084712

  21. B. Lai, F. Cerrina, SHADOW: a synchrotron radiation ray tracing program. Nucl. Instrum. Methods Phys. Res. Sect. A 246(1–3), 337–341 (1986)

    Article  Google Scholar 

  22. M.S. del Rio, N. Canestrari, F. Jiang, F. Cerrina, SHADOW3: a new version of the synchrotron X-ray optics modelling package. J Synchrotron Radiat 18(Pt 5), 708–716 (2011)

    Google Scholar 

  23. P. Khoram, S. Brittman, W.I. Dzik, J.N.H. Reek, E.C. Garnett, Growth and Characterization of PDMS-Stamped Halide Perovskite Single Microcrystals. J. Phys. Chem. C 120(12), 6475–6481 (2016)

    Article  CAS  Google Scholar 

  24. B.L. Henke, E.M. Gullikson, J.C. Davis, X-ray interactions: photoabsorption, scattering, transmission, and reflection at E= 50–30,000 eV, Z= 1–92. At. Data Nucl. Data Tables 54(2), 181–342 (1993)

    Article  CAS  Google Scholar 

  25. D. Pettit, P. Fontana, Comparison of sodium chloride hopper cubes grown under microgravity and terrestrial conditions. NPJ Microgravity 5, 25 (2019)

    Article  CAS  Google Scholar 

  26. A. Kuczumow, Z. Rzaçzyńska, M. Szewczak, Matrix effects in the x-ray fluorescence method. X-Ray Spectrom. 11(3), 135–139 (1982)

    Article  CAS  Google Scholar 

  27. M. Franzini, L. Leoni, M. Saitta, A simple method to evaluate the matrix effects in X-ray fluorescence analysis. X-Ray Spectrom. 1(4), 151–154 (1972)

    Article  CAS  Google Scholar 

  28. J.G. Nagy, D.P. O’Leary, Restoring images degraded by spatially variant blur. SIAM J. Sci. Comput. 19(4), 1063–1082 (1998)

    Article  Google Scholar 

  29. K. Novak, A.T. Watnik, Imaging through deconvolution with a spatially variant point spread function. Comput. Imag. VI (2021)

  30. A. Shajkofci, M. Liebling, Semi-blind spatially-variant deconvolution in optical microscopy with local point spread function estimation by use of convolutional neural networks, vol. 2018. 25th IEEE International Conference on Image Processing, no. ICIP, pp. 3818–3822 (2018)

  31. É. Thiébaut, L. Denis, F. Soulez, R. Mourya, Spatially variant PSF modeling and image deblurring. Adapt. Opt. Syst. V (2016)

  32. T.R. Lauer, Deconvolution with a spatially-variant PSF. Astron. Data Anal. II 4847(520), 167 (2002)

    Google Scholar 

  33. X. Chen, C. Dejoie, T. Jiang, C.-S. Ku, N. Tamura, Quantitative microstructural imaging by scanning Laue x-ray micro- and nanodiffraction. MRS Bull. 41(6), 445–453 (2016)

    Article  CAS  Google Scholar 

  34. T.W. Cornelius, O. Thomas, Progress of in situ synchrotron X-ray diffraction studies on the mechanical behavior of materials at small scales. Prog. Mater Sci. 94, 384–434 (2018)

    Article  CAS  Google Scholar 

  35. F. Hofmann, R.J. Harder, W. Liu, Y. Liu, I.K. Robinson, Y. Zayachuk, Glancing-incidence focussed ion beam milling: a coherent X-ray diffraction study of 3D nano-scale lattice strains and crystal defects. Acta Mater. 154, 113–123 (2018)

    Article  CAS  Google Scholar 

  36. G.E. Ice, B.C. Larson, J.Z. Tischler, W. Liu, W. Yang, X-ray microbeam measurements of subgrain stress distributions in polycrystalline materials. Mater. Sci. Eng. A 399(1–2), 43–48 (2005)

    Article  CAS  Google Scholar 

  37. H.F. Poulsen, X. Fu, E. Knudsen, E.M. Lauridsen, L. Margulies, S. Schmidt, 3DXRD—mapping grains and their dynamics in 3 dimensions. Mater. Sci. Forum 467–470, 1363–1372 (2004)

    Article  Google Scholar 

  38. H. Simons, A.C. Jakobsen, S.R. Ahl, C. Detlefs, H.F. Poulsen, Multiscale 3D characterization with dark-field x-ray microscopy. MRS Bull. 41(6), 454–459 (2016)

    Article  CAS  Google Scholar 

  39. T. Tian, R. Morusupalli, H. Shin, H.-Y. Son, K.-Y. Byun, Y.-C. Joo, R. Caramto, L. Smith, Y.-L. Shen, M. Kunz, N. Tamura, A.S. Budiman, On the mechanical stresses of Cu through-silicon via (TSV) samples fabricated by SK Hynix vs. SEMATECH—enabling robust and reliable 3-D interconnect/integrated circuit (IC) technology. Procedia Eng. 139, 101–111 (2016)

    Article  CAS  Google Scholar 

  40. M. Holt, R. Harder, R. Winarski, V. Rose, Nanoscale hard X-ray microscopy methods for materials studies. Annu. Rev. Mater. Res. 43(1), 183–211 (2013)

    Article  CAS  Google Scholar 

  41. J. Deng, D.J. Vine, S. Chen, Q. Jin, Y.S.G. Nashed, T. Peterka, S. Vogt, C. Jacobsen, X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning. Sci. Rep. 7(1), 1–10 (2017)

    CAS  Google Scholar 

  42. W.S. Drisdell, L. Leppert, C.M. Sutter-Fella, Y. Liang, Y. Li, Q.P. Ngo, L.F. Wan, S. Gul, T. Kroll, D. Sokaras, A. Javey, J. Yano, J.B. Neaton, F.M. Toma, D. Prendergast, I.D. Sharp, Determining atomic-scale structure and composition of organo-lead halide perovskites by combining high-resolution X-ray absorption spectroscopy and first-principles calculations. ACS Energy Lett. 2(5), 1183–1189 (2017)

    Article  CAS  Google Scholar 

  43. F. Pfeiffer, R. Article, F. Pfeiffer, X-ray ptychography. Nat. Photonics 12(1), 9–17 (2018)

    Article  CAS  Google Scholar 

  44. T.W. Victor, L.M. Easthon, M. Ge, K.H. O’Toole, R.J. Smith, X. Huang, H. Yan, K.N. Allen, Y.S. Chu, L.M. Miller, X-ray fluorescence nanotomography of single bacteria with a sub-15 nm beam. Sci. Rep. 8(1), 1–8 (2018)

    Article  CAS  Google Scholar 

  45. D.J. Vine, D. Pelliccia, C. Holzner, S.B. Baines, A. Berry, I. McNulty, S. Vogt, A.G. Peele, K.A. Nugent, Simultaneous X-ray fluorescence and ptychographic microscopy of Cyclotella meneghiniana. Opt. Express 20(16), 18287 (2012)

    Article  CAS  Google Scholar 

  46. Y.S. Chu, W.-K. Lee, R. Tappero, M. Ge, X. Huang, X. Xiao, H. Yan, P. Northrup, J. Thieme, A.M. Kiss, G.J. Williams, Y. Yang, S.L. Nicholas, A. Pattammattel, R. Smith, P. Ilinski, Y. Du, Multimodal, multidimensional, and multiscale X-ray imaging at the national synchrotron light source II. Synchrotron Radiat. News 33(3), 29–36 (2020)

    Article  Google Scholar 

  47. T. Link, S. Zabler, A. Epishin, A. Haibel, M. Bansal, X. Thibault, Synchrotron tomography of porosity in single-crystal nickel-base superalloys. Mater. Sci. Eng. A 425(1–2), 47–54 (2006)

    Article  CAS  Google Scholar 

  48. L. Helfen, T. Baumbach, P. Mikulík, D. Kiel, P. Pernot, P. Cloetens, J. Baruchel, High-resolution three-dimensional imaging of flat objects by synchrotron-radiation computed laminography. Appl. Phys. Lett. 86(7), 071915 (2005)

    Article  CAS  Google Scholar 

  49. L. Helfen, A. Myagotin, A. Rack, P. Pernot, P. Mikulík, M. Di Michiel, T. Baumbach, Synchrotron-radiation computed laminography for high-resolution three-dimensional imaging of flat devices. Phys. Status Solidi A 204(8), 2760–2765 (2007)

    Article  CAS  Google Scholar 

  50. L.P. Hunter, Direct measurement of the angular dependence of the imaginary part of the atomic scattering factor of germanium. IBM J. Res. Dev. 3(2), 106–113 (1959)

    Article  CAS  Google Scholar 

  51. N.W.M. Ritchie, Efficient simulation of secondary fluorescence via NIST DTSA-II Monte Carlo. Microsc. Microanal. 23(3), 618–633 (2017)

    Article  CAS  Google Scholar 

  52. A.G. Karydas, Self-element secondary fluorescence enhancement in XRF analysis. X-Ray Spectrom. 34(5), 426–431 (2005)

    Article  CAS  Google Scholar 

  53. A. Shajkofci, M. Liebling, Spatially-variant CNN-based point spread function estimation for blind deconvolution and depth estimation in optical microscopy. IEEE Trans. Image Process. 29, 5848–5861 (2020)

    Article  Google Scholar 

  54. M. Weigert, U. Schmidt, T. Boothe, A. Müller, A. Dibrov, A. Jain, B. Wilhelm, D. Schmidt, C. Broaddus, S. Culley, M. Rocha-Martins, F. Segovia-Miranda, C. Norden, R. Henriques, M. Zerial, M. Solimena, J. Rink, P. Tomancak, L. Royer, F. Jug, E.W. Myers, Content-aware image restoration: pushing the limits of fluorescence microscopy. Nat Methods 15(12), 1090–1097 (2018)

    Article  CAS  Google Scholar 

  55. D. He, D. Cai, J. Zhou, J. Luo, S.-L. Chen, Restoration of out-of-focus fluorescence microscopy images using learning-based depth-variant deconvolution. IEEE Photon. J. 12(2), 1–13 (2020)

    Article  Google Scholar 

Download references

Acknowledgments

Thank you to Moses Kodur at UC San Diego for his help in taking the μPL data, and to Tao Zhou, Martin V. Holt, and Zhonghou Cai from the Center for Nanoscale Materials at Argonne National Laboratory for their assistance during and valuable discussion about our synchrotron measurements. This work was supported in part by the National Science Foundation under Grant No. DMR-1848371. Use of the Center for Nanoscale Materials and the Advanced Photon Source, both Office of Science user facilities, was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. This work was performed in part at the San Diego Nanotechnology Infrastructure (SDNI) of UCSD, a member of the National Nanotechnology Coordinated Infrastructure, which was supported by the National Science Foundation (Grant ECCS-1542148).

Author information

Authors and Affiliations

  1. Materials Science and Engineering, University of California, San Diego, La Jolla, USA

    Rishi E. Kumar, Xueying L. Quinn & David P. Fenning

  2. Department of Nanoengineering, University of California, San Diego, La Jolla, USA

    David P. Fenning

Authors
  1. Rishi E. Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xueying L. Quinn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David P. Fenning
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David P. Fenning.

Ethics declarations

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 1088 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kumar, R.E., Quinn, X.L. & Fenning, D.P. Accounting for sample morphology in correlative X-ray microscopy via ray tracing. MRS Advances 6, 547–553 (2021). https://doi.org/10.1557/s43580-021-00114-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1557/s43580-021-00114-0

Search

Navigation