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Title: GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

Abstract

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across differentmore » disciplines.« less

Authors:
 [1]; ORCiD logo [1];  [1];  [2];  [1];  [1];  [3];  [4];  [5];  [1]
  1. Univ. of California, Los Angeles, CA (United States)
  2. Univ. of California, Los Angeles, CA (United States); UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA (United States)
  3. Univ. of California, Los Angeles, CA (United States); CNRS-Univ. de Strasbourg, Strasbourg (France)
  4. Stanford Univ., Stanford, CA (United States)
  5. UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1394084
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; 97 MATHEMATICS AND COMPUTING; Applied physics; Imaging techniques; Nanoscale materials

Citation Formats

Pryor, Alan, Yang, Yongsoo, Rana, Arjun, Gallagher-Jones, Marcus, Zhou, Jihan, Lo, Yuan Hung, Melinte, Georgian, Chiu, Wah, Rodriguez, Jose A., and Miao, Jianwei. GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging. United States: N. p., 2017. Web. doi:10.1038/s41598-017-09847-1.
Pryor, Alan, Yang, Yongsoo, Rana, Arjun, Gallagher-Jones, Marcus, Zhou, Jihan, Lo, Yuan Hung, Melinte, Georgian, Chiu, Wah, Rodriguez, Jose A., & Miao, Jianwei. GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging. United States. doi:10.1038/s41598-017-09847-1.
Pryor, Alan, Yang, Yongsoo, Rana, Arjun, Gallagher-Jones, Marcus, Zhou, Jihan, Lo, Yuan Hung, Melinte, Georgian, Chiu, Wah, Rodriguez, Jose A., and Miao, Jianwei. Tue . "GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging". United States. doi:10.1038/s41598-017-09847-1. https://www.osti.gov/servlets/purl/1394084.
@article{osti_1394084,
title = {GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging},
author = {Pryor, Alan and Yang, Yongsoo and Rana, Arjun and Gallagher-Jones, Marcus and Zhou, Jihan and Lo, Yuan Hung and Melinte, Georgian and Chiu, Wah and Rodriguez, Jose A. and Miao, Jianwei},
abstractNote = {Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.},
doi = {10.1038/s41598-017-09847-1},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {2017},
month = {9}
}

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