# 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](https://www.science.org/doi/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](https://www.science.org/doi/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://www.science.org/doi/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://doi.org/10.1126/sciadv.abn2275) ## Hyperparameter tuning - Akiba T, Sano S, Yanase T, Ohta T & Koyama M (2019). Optuna: A next-generation hyperparameter optimization framework. In The 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, pp. 2623–2631. New York: Association for Computing Machinery. [10.1145/3292500.3330701](https://doi.org/10.1145/3292500.3330701) - Bergstra J, Bardenet R, Bengio Y & Kégl B (2011). Algorithms for hyper- parameter optimization. In Advances in Neural Information Processing Systems 24. https://proceedings.neurips.cc/paper_files/paper/2011/file/86e8f7ab32cfd12577bc2619bc635690-Paper.pdf. - Cao MC, Chen Z, Jiang Y & Han Y (2022). Automatic parameter selection for electron ptychography via Bayesian optimization. Sci Rep 12(1), 12284. [10.1038/s41598-022-16041-5](https://doi.org/10.1038/s41598-022-16041-5) ## PyTorch - Paszke A, Gross S, Massa F, Lerer A, Bradbury J, Chanan G, Killeen T, Lin Z, Gimelshein N, Antiga L,et al. Desmaison A, Köpf A, Yang E, DeVito Z, Raison M, Tejani A, Chilamkurthy S, Steiner B, Fang L, Bai J, & Chintala S. (2019). Pytorch: An imperative style, high-performance deep learning library. In Advances in Neural Information Processing Systems 32. https://proceedings.neurips.cc/paper_files/paper/2019/file/bdbca288fee7f92f2bfa9f7012727740-Paper.pdf. ## Adam optimizer - Kingma DP & Ba J (2014). ‘Adam: A method for stochastic optimization.’ arXiv, arXiv:1412.6980, [10.48550/arXiv.1412.6980](https://doi.org/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](https://doi.org/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](https://doi.org/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](https://www.science.org/doi/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](https://doi.org/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](https://doi.org/10.1016/j.ultramic.2024.114068)