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

Alan Pryor, Yongsoo Yang, Arjun Rana, Marcus Gallagher-Jones, Jihan Zhou, Yuan Hung Lo, Georgian Melinte, Wah Chiu, Jose A. Rodriguez, Jianwei Miao
2017 Scientific Reports  
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
more » ... RE), 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. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines. Tomography has found widespread applications in the physical, biological and medical sciences 1-7 . Electron tomography, for example, is experiencing a revolution in high-resolution 3D imaging of physical and biological samples. In the physical sciences, atomic electron tomography (AET) has been developed to determine the 3D atomic structure of crystal defects such as grain boundaries, anti-phase boundaries, stacking faults, dislocations, chemical order/disorder and point defects, and to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity 1, 8-12 . The atomic coordinates measured by AET have been used as direct input to density functional theory calculations to correlate crystal defects and chemical order/disorder with material properties at the single atomic level 13 . In the biological sciences, single-particle cryo-electron microscopy (EM) has been applied to achieve near atomic resolution of purified protein complexes 2, 7, 14-16 , and cryo-electron tomography allows for 3D imaging of pleomorphic samples such as viral infection mechanisms of cells with resolutions on the order of a few nanometers [17] [18] [19] . These advances are not limited to electron tomography. Tomographic implementation of synchrotron X-ray absorption and phase contrast imaging has also found interdisciplinary applications 5, 20-25 . Using the brilliance of advanced X-ray sources, coherent diffractive imaging (CDI) methods 26 have been combined with tomographic reconstruction for 3D quantitative imaging of thick samples with resolutions in the tens of nanometers 27-33 . Presently, a popular tomographic reconstruction method is filtered back projection (FBP) 2-4 . FBP works well when there are a large number of projections with no missing data. However, when the data is inadequately sampled due to the radiation dose and geometric constraints, it suffers from artifacts, potentially clouding Published: xx xx xxxx OPEN 2 Scientific RepoRts | 7: 10409 |
doi:10.1038/s41598-017-09847-1 pmid:28874736 pmcid:PMC5585178 fatcat:snfl2dxw7rda7nfs2av3tfh3ge