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Toward single particle reconstruction without particle picking: Breaking the detection limit

Tamir Bendory, Nicolas Boumal, William Leeb, Eitan Levin, Amit Singer
doi: https://doi.org/10.1101/431080
Tamir Bendory
aThe Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
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Nicolas Boumal
bDepartment of Mathematics, Princeton University, Princeton, NJ, USA
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William Leeb
cSchool of Mathematics, University of Minnesota, Minneapolis, MN, USA
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Eitan Levin
aThe Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
bDepartment of Mathematics, Princeton University, Princeton, NJ, USA
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Amit Singer
aThe Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
bDepartment of Mathematics, Princeton University, Princeton, NJ, USA
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Abstract

Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method for biological macromolecules. In a cryo-EM experiment, the microscope produces images called micrographs. Projections of the molecule of interest are embedded in the micrographs at unknown locations, and under unknown viewing directions. Standard imaging techniques first locate these projections (detection) and then reconstruct the 3-D structure from them. Unfortunately, high noise levels hinder detection. When reliable detection is rendered impossible, the standard techniques fail. This is a problem especially for small molecules, which can be particularly hard to detect. In this paper, we propose a radically different approach: we contend that the structure could, in principle, be reconstructed directly from the micrographs, without intermediate detection. As a result, even small molecules should be within reach for cryo-EM. To support this claim, we setup a simplified mathematical model and demonstrate how our autocorrelation analysis technique allows to go directly from the micrographs to the sought signals. This involves only one pass over the micrographs, which is desirable for large experiments. We show numerical results and discuss challenges that lay ahead to turn this proof-of-concept into a competitive alternative to state-of-the-art algorithms.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted October 02, 2018.
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Toward single particle reconstruction without particle picking: Breaking the detection limit
Tamir Bendory, Nicolas Boumal, William Leeb, Eitan Levin, Amit Singer
bioRxiv 431080; doi: https://doi.org/10.1101/431080
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Toward single particle reconstruction without particle picking: Breaking the detection limit
Tamir Bendory, Nicolas Boumal, William Leeb, Eitan Levin, Amit Singer
bioRxiv 431080; doi: https://doi.org/10.1101/431080

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