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Title: A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.
Authors:
 [1] ;  [2] ;  [1]
  1. Univ. of California, Los Angeles, CA (United States). Dept. of Physics and Astronomy and California NanoSystems Inst.
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Center for Electron Microscopy and Molecular Foundry
Publication Date:
Grant/Contract Number:
AC02-05CH11231; DMR 1548924; SC0010378; DMR-1437263
Type:
Published Article
Journal Name:
Advanced Structural and Chemical Imaging
Additional Journal Information:
Journal Volume: 3; Journal Issue: 1; Journal ID: ISSN 2198-0926
Publisher:
Springer
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
SC-22.3 USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Scientific User Facilities Division; National Science Foundation (NSF)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Scanning transmission electron microscopy; PRISM; Multislice; GPU; CUDA; Electron scattering; Imaging simulation; High performance computing; Atomic electron tomography
OSTI Identifier:
1404737
Alternate Identifier(s):
OSTI ID: 1440955