Supplementary-Data-Codes

Methods for accurate determination of the 3D atomic structure of amorphous materials Yuxuan Liao1, Haozhi Sha1, Colum M. O’Leary1, Hanfeng Zhong1, Yao Yang2, and Jianwei Miao1* 1Department of Physics and Astronomy and California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.2School of Engineering, Westlake University, Hangzhou, China.*Correspondence and requests for materials should be addressed to J.M. ([e-mail]) Contents Overview System Requirements Repositary Contents Overview This supplementary repository provides all data and MATLAB source codes associated with our paper, “Methods for accurate determination of the 3D atomic structure of amorphous materials.” It includes complete and reproducible workflows for robust image preprocessing, precise projection alignment, advanced tomographic reconstruction using the RESIRE algorithm, and systematic postprocessing for atomic tracing and elemental classification. These tools enable accurate 3D atomic structure determination across a range of disordered material systems. The repository supports both ADF-STEM-based atomic electron tomography (AET) and ptychographic AET (pAET), allowing researchers to reproduce key results, benchmark against published simulations, and apply the methodology to new experimental or simulated datasets. Code and data are modularly organized to facilitate adaptation to other atomic-scale imaging problems. System Requirements Hardware Requirements We recommend a computer with 32G DRAM, AMD Ryzen 7 6800H with Radeon Graphics 3.20 GHz CPU, and a NVIDIA GeForce RTX 3070 Ti GPU to run most data analysis source codes. But for the atomic tracing, we recommend a computer with 64G DRAM. Software Requirements OS Requirements This package has been tested on the following Operating System: Linux: CentOS 6 2.6.32 Windows: Windows 11 Version 24H2 Mac OSX: We have not tested it on a Mac yet, but it should in principle work. Matlab Version Requirements This package has been tested with Matlab R2022b. All the codes have to run in their own folders. We recommend the use of Matlab version R2021a or higher to test the data and source codes. Repository Contents Please download the all the data and code files. The contents includes the following folders: 1. NP1_aSi_208 Folder: Si Nanoparticle 208 atoms This folder contains the simulated data and source codes for the application of the AET workflow to a 208-atom amorphous Si nanoparticle. 1.1. NP1_aSi_208_From_Busch Folder: Si Nanoparticle 208 from Busch This folder contains the simulated data and source codes used for the reconstruction of a 208-atom amorphous Si nanoparticle by Busch et al. 2. NP2_aSi_19993 Folder: Si Nanoparticle 19993 This folder contains the simulated data and source codes for the application of the AET workflow to a 19993-atom amorphous Si nanoparticle. 3. NP3_aSiGeSn Folder: SiGeSn Nanoparticle This folder contains the simulated data and source codes for the application of the AET workflow to an amorphous SiGeSn nanoparticle, containing 4,610 Si, 4,709 Ge, and 4,663 Sn atoms. 3.1. NP3_aSiGeSn_Projection_from_Busch Folder: SiGeSn Nanoparticle from Busch This folder contains the simulated data and source codes used for the reconstruction of an amorphous SiGeSn nanoparticle by Busch et al. 4. NP4_aCoPdPt Folder: CoPdPt Nanoparticle This folder contains the simulated data and source codes for the application of the AET workflow to an amorphous CoPdPt nanoparticle, containing 8,322 Co, 6,896 Pd, and 3,138 Pt atoms. 4.1. NP4_aCoPdPt_Projection_from_Busch Folder: CoPdPt Nanoparticle from Busch This folder contains the simulated data and source codes used for the reconstruction of an amorphous CoPdPt nanoparticle by Busch et al. 5. NP5_aSiO2 Folder: SiO2 Nanoparticle This folder contains the simulated data and source codes for the application of the pAET workflow to an amorphous SiO2 nanoparticle, containing 2,603 Si and 5,101 O atoms. 6. BM3D_Codes Folder: BM3D This folder contains the BM3D source code used for image denoising. 7. SIRT_Code_From_Busch Folder: SIRT This folder contains the SIRT source code as used by Busch et al. in their reconstructions.