Bibliography#

tBL-WSe2 dataset#

  • Nguyen KX, Jiang Y, Lee C-H, Kharel P, Zhang Y, van der Zande AM & Huang PY (2024). Achieving sub-0.5-angstrom–resolution ptychography in an uncorrected electron microscope. Science 383(6685), 865–870. 10.1126/science.adl2029

PSO dataset#

  • Chen Z, Jiang Y, Shao Y-T, Holtz ME, Odstr”il M, Guizar-Sicairos M, Hanke I, Ganschow S, Schlom DG & Muller DA (2021). Electron ptychography achieves atomic-resolution limits set by lattice vibrations. Science 372(6544), 826–831. 10.1126/science.abg2533

Multislice#

  • Maiden AM, Humphry MJ & Rodenburg JM (2012b). Ptychographic transmission microscopy in three dimensions using a multi-slice approach. J Opt Soc Am A Opt Image Sci Vis 29(8), 1606–1614. 10.1364/JOSAA.29.001606

  • Van den Broek W & Koch CT (2013). General framework for quantitative three-dimensional reconstruction from arbitrary detection geometries in tem. Phys Rev B Condens Matter Mater Phys 87(18), 184108. 10.1103/PhysRevB.87.184108

  • Godden TM, Suman R, Humphry MJ, Rodenburg JM & Maiden AM (2014). Ptychographic microscope for three-dimensional imaging. Opt Express 22(10), 12513–12523. 10.1364/OE.22.012513

  • Tsai EHR, Usov I, Diaz A, Menzel A & Guizar-Sicairos M (2016). X-ray ptychography with extended depth of field. Opt Express 24(25), 29089–29108. 10.1364/OE.24.029089

  • Chen Z, Jiang Y, Shao Y-T, Holtz ME, Odstr”il M, Guizar-Sicairos M, Hanke I, Ganschow S, Schlom DG & Muller DA (2021). Electron ptychography achieves atomic-resolution limits set by lattice vibrations. Science 372(6544), 826–831. 10.1126/science.abg2533

Mixed-state formalism#

  • Thibault P & Menzel A (2013). Reconstructing state mixtures from diffraction measurements. Nature 494(7435), 68–71. 10.1038/nature11806

Maximum-likelihood#

  • Odstr”il M, Menzel A & Guizar-Sicairos M (2018). Iterative least-squares solver for generalized maximum-likelihood ptychography. Opt Express 26(3), 3108–3123. 10.1364/OE.26.003108

  • Thibault P & Guizar-Sicairos M (2012). Maximum-likelihood refinement for coherent diffractive imaging. New J Phys 14(6), 063004. 10.1088/1367-2630/14/6/063004

Adpative tilt propagator#

  • Kirkland EJ (2020). Advanced Computing in Electron Microscopy, (3rd ed) . Boston, MA: Springer US. 10.1007/978-3-030-33260-0

  • Sha H, Cui J & Yu R (2022). Deep sub-angstrom resolution imaging by electron ptychography with misorientation correction. Sci Adv 8(19), eabn2275. 10.1126/sciadv.abn2275

Hyperparameter tuning#

PyTorch#

Adam optimizer#

  • Kingma DP & Ba J (2014). ‘Adam: A method for stochastic optimization.’ arXiv, arXiv:1412.6980, 10.48550/arXiv.1412.6980

L0 regularization (kr_thresh)#

  • Moshtaghpour A, Velazco-Torrejon A, Robinson AW, Browning ND & Kirkland AI (2025). Lorepie: L0 regularized extended ptychographical iterative engine for low-dose and fast electron ptychography. Opt Express 33(5), 9357–9368. 10.1364/OE.551986

“Missing Wedge” multislice regularizer (kz_filter)#

  • Wakonig K, Stadler H-C, Odstr”il M, Tsai EHR, Diaz A, Holler M, Usov I, Raabe J, Menzel A & Guizar-Sicairos M (2020). PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data. J Appl Crystallogr 53(2), 574–586. 10.1107/S1600576720001776

  • Chen Z, Jiang Y, Shao Y-T, Holtz ME, Odstr”il M, Guizar-Sicairos M, Hanke I, Ganschow S, Schlom DG & Muller DA (2021). Electron ptychography achieves atomic-resolution limits set by lattice vibrations. Science 372(6544), 826–831. 10.1126/science.abg2533

Complex relation (complex_ratio)#

  • Clark JN, Putkunz CT, Pfeifer MA, Peele AG, Williams GJ, Chen B, Nugent KA, Hall C, Fullagar W, Kim S & McNulty I (2010). Use of a complex constraint in coherent diffractive imaging. Opt Express 18(3), 1981–1993. 10.1364/OE.18.001981

  • Xu W, Ning S, Sheng P, Lin H, Kirkland AI, Peng Y & Zhang F (2024). A high-performance reconstruction method for partially coherent ptychography. Ultramicroscopy 267(1), 114068. 10.1016/j.ultramic.2024.114068