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

Year: 2017

Type: article

Abstract: 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. Here, 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 .

Source: Advanced Structural and Chemical Imaging

DOI: 10.1186/s40679-017-0048-z

Authors: Alan Pryor, Colin Ophus, Jianwei Miao

Institutions: California NanoSystems Institute, University of California, Los Angeles, Lawrence Berkeley National Laboratory, Molecular Foundry

Language: English

Topic: Advanced Electron Microscopy Techniques and Applications

Subfield: Structural Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $1,290

Funders: National Science Foundation, U.S. Department of Energy, National Institutes of Health, Office of Science, National Cancer Institute, Division of Materials Research, Basic Energy Sciences, Lawrence Berkeley National Laboratory

OpenAlex ID: W2734133642