Accurate 3D single-molecule localization via vectorial <italic toggle="yes">in situ</i> point spread function retrieval and aberration assessment

Xinxun Yang; Hongfei Zhu; Yile Sun; Hanmeng Wu; Yubing Han; Xiang Hao; Cuifang Kuang; Xu Liu

doi:10.1364/PRJ.520469

Photonics Research, Volume. 12, Issue 11, 2447(2024)

Accurate 3D single-molecule localization via vectorial in situ point spread function retrieval and aberration assessment

Xinxun Yang^1、†, Hongfei Zhu^2、†, Yile Sun¹, Hanmeng Wu¹, Yubing Han¹, Xiang Hao¹, Cuifang Kuang^1,3,4、*, and Xu Liu^1,3,4

Author Affiliations

¹State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China

²Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China

³ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China

⁴Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, China

show less

References(45)

[1] E. Betzig, G. H. Patterson, R. Sougrat. Imaging intracellular fluorescent proteins at nanometer resolution. Science, 313, 1642-1645(2006).

[2] S. T. Hess, T. P. Girirajan, M. D. Mason. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J., 91, 4258-4272(2006).

[3] M. J. Rust, M. Bates, X. Zhuang. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods, 3, 793-796(2006).

[4] F. Huang, G. Sirinakis, E. S. Allgeyer. Ultra-high resolution 3D imaging of whole cells. Cell, 166, 1028-1040(2016).

[5] T. Schlichthaerle, M. T. Strauss, F. Schueder. Direct visualization of single nuclear pore complex proteins using genetically-encoded probes for DNA-PAINT. Angew. Chem. Int. Ed., 58, 13004-13008(2019).

[6] M. Bates, J. Keller-Findeisen, A. Przybylski. Optimal precision and accuracy in 4Pi-STORM using dynamic spline PSF models. Nat. Methods, 19, 603-612(2022).

[7] M. F. Juette, T. J. Gould, M. D. Lessard. Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat. Methods, 5, 527-529(2008).

[8] B. Huang, W. Wang, M. Bates. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science, 319, 810-813(2008).

[9] S. R. Pavani, M. A. Thompson, J. S. Biteen. Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proc. Natl. Acad. Sci. USA, 106, 2995-2999(2009).

[10] D. Aquino, A. Schonle, C. Geisler. Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores. Nat. Methods, 8, 353-359(2011).

[11] P. Bon, J. Linarès-Loyez, M. Feyeux. Self-interference 3D super-resolution microscopy for deep tissue investigations. Nat. Methods, 15, 449-454(2018).

[12] D. Sage, T.-A. Pham, H. Babcock. Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software. Nat. Methods, 16, 387-395(2019).

[13] L. von Diezmann, Y. Shechtman, W. E. Moerner. Three-dimensional localization of single molecules for super-resolution imaging and single-particle tracking. Chem. Rev., 117, 7244-7275(2017).

[14] D. Burke, B. Patton, F. Huang. Adaptive optics correction of specimen-induced aberrations in single-molecule switching microscopy. Optica, 2, 177-185(2015).

[15] W. R. Legant, L. Shao, J. B. Grimm. High-density three-dimensional localization microscopy across large volumes. Nat. Methods, 13, 359-365(2016).

[16] K. F. Tehrani, Y. Zhang, P. Shen. Adaptive optics stochastic optical reconstruction microscopy (AO-STORM) by particle swarm optimization. Biomed. Opt. Express, 8, 5087-5097(2017).

[17] M. E. Siemons, N. A. K. Hanemaaijer, M. H. P. Kole. Robust adaptive optics for localization microscopy deep in complex tissue. Nat. Commun., 12, 3407(2021).

[18] M. J. Mlodzianoski, P. J. Cheng-Hathaway, S. M. Bemiller. Active PSF shaping and adaptive optics enable volumetric localization microscopy through brain sections. Nat. Methods, 15, 583-586(2018).

[19] T. Ku, J. Swaney, J.-Y. Park. Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues. Nat. Biotechnol., 34, 973-981(2016).

[20] Y. Zhao, O. Bucur, H. Irshad. Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. Nat. Biotechnol., 35, 757-764(2017).

[21] Y. Li, Y.-L. Wu, P. Hoess. Depth-dependent PSF calibration and aberration correction for 3D single-molecule localization. Biomed. Opt. Express, 10, 2708-2718(2019).

[22] P. Theer, C. Mongis, M. Knop. PSFj: know your fluorescence microscope. Nat. Methods, 11, 981-982(2014).

[23] O. Faklaris, L. Bancel-Vallée, A. Dauphin. Quality assessment in light microscopy for routine use through simple tools and robust metrics. J. Cell Biol., 221, e202107093(2022).

[24] D. Baddeley, M. Cannell, C. Soeller. Three-dimensional sub-100 nm super-resolution imaging of biological samples using a phase ramp in the objective pupil. Nano Res., 4, 589-598(2011).

[25] Y. Shechtman, S. J. Sahl, A. S. Backer. Optimal point spread function design for 3D imaging. Phys. Rev. Lett., 113, 133902(2014).

[26] M. Siemons, C. N. Hulleman, R. Ø. Thorsen. High precision wavefront control in point spread function engineering for single emitter localization. Opt. Express, 26, 8397-8416(2018).

[27] S. Liu, E. B. Kromann, W. D. Krueger. Three dimensional single molecule localization using a phase retrieved pupil function. Opt. Express, 21, 29462-29487(2013).

[28] P. N. Petrov, Y. Shechtman, W. E. Moerner. Measurement-based estimation of global pupil functions in 3D localization microscopy. Opt. Express, 25, 7945-7959(2017).

[29] Y. Li, M. Mund, P. Hoess. Real-time 3D single-molecule localization using experimental point spread functions. Nat. Methods, 15, 367-369(2018).

[30] E. Goi, S. Schoenhardt, M. Gu. Direct retrieval of Zernike-based pupil functions using integrated diffractive deep neural networks. Nat. Commun., 13, 7531(2022).

[31] A. Aristov, B. Lelandais, E. Rensen. ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range. Nat. Commun., 9, 2409(2018).

[32] F. Xu, D. Ma, K. P. MacPherson. Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval. Nat. Methods, 17, 531-540(2020).

[33] S. Liu, J. Chen, J. Hellgoth. Universal inverse modeling of point spread functions for SMLM localization and microscope characterization. Nat. Methods, 21, 1082-1093(2024).

[34] N. Hieu Thao, O. Soloviev, M. Verhaegen. Phase retrieval based on the vectorial model of point spread function. J. Opt. Soc. Am. A, 37, 16-26(2020).

[35] B. M. Hanser, M. G. Gustafsson, D. A. Agard. Phase-retrieved pupil functions in wide-field fluorescence microscopy. J. Microsc., 216, 32-48(2004).

[36] A. P. Dempster, N. M. Laird, D. B. Rubin. Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. B, 39, 1-22(1977).

[37] J. A. Hartigan, M. A. Wong. A K-means clustering algorithm. J. R. Stat. Soc. C, 28, 100-108(1979).

[38] J. J. M. Braat, P. Dirksen, A. J. E. M. Janssen. Extended Nijboer–Zernike approach to aberration and birefringence retrieval in a high-numerical-aperture optical system. J. Opt. Soc. Am. A, 22, 2635-2650(2005).

[39] M. Mansuripur. Classical Optics and its Applications(2009).

[40] E. P. Goodwin, J. C. Wyant. Field Guide to Interferometric Optical Testing(2006).

[41] http://bigwww.epfl.ch/smlm. http://bigwww.epfl.ch/smlm

[42] M. Lelek, M. T. Gyparaki, G. Beliu. Single-molecule localization microscopy. Nat. Rev. Methods Primers, 1, 39(2021).

[43] J. Antonello, J. Wang, C. He. Interferometric calibration of a deformable mirror(2020).

[44] https://github.com/ZJUOPTKuangLab/VISPR. https://github.com/ZJUOPTKuangLab/VISPR

[45] https://github.com/jries/SMAP. https://github.com/jries/SMAP

Tools

Get Citation

Copy Citation Text

Xinxun Yang, Hongfei Zhu, Yile Sun, Hanmeng Wu, Yubing Han, Xiang Hao, Cuifang Kuang, Xu Liu, "Accurate 3D single-molecule localization via vectorial in situ point spread function retrieval and aberration assessment," Photonics Res. 12, 2447 (2024)

Download Citation

EndNote(RIS)BibTex Plain Text

Set citation alerts for article

Save article for my favorites

Paper Information

Category: Imaging Systems, Microscopy, and Displays

Received: Jan. 31, 2024

Accepted: Aug. 12, 2024

Published Online: Oct. 10, 2024

The Author Email: Cuifang Kuang (cfkuang@zju.edu.cn)

DOI:10.1364/PRJ.520469

Topics

laser devices and laser physics

Lasers and Laser Optics

Laser physics

laser manufacturing

Instrumentation, Measurement and Metrology