title: Compressed sensing electron tomography of needle-shaped biological specimens--Potential for improved reconstruction fidelity with reduced dose.
abstract: Electron tomography is an invaluable method for 3D cellular imaging. The technique is, however, limited by the specimen geometry, with a loss of resolution due to a restricted tilt range, an increase in specimen thickness with tilt, and a resultant need for subjective and time-consuming manual segmentation. Here we show that 3D reconstructions of needle-shaped biological samples exhibit isotropic resolution, facilitating improved automated segmentation and feature detection. By using scanning transmission electron tomography, with small probe convergence angles, high spatial resolution is maintained over large depths of field and across the tilt range. Moreover, the application of compressed sensing methods to the needle data demonstrates how high fidelity reconstructions may be achieved with far fewer images (and thus greatly reduced dose) than needed by conventional methods. These findings open the door to high fidelity electron tomography over critically relevant length-scales, filling an important gap between existing 3D cellular imaging techniques.
authors.affiliation: Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, UK. Electronic address: saghizineb@gmail.com.
authors.forename: Zineb
authors.initials: Z
authors.lastname: Saghi
authors.affiliation: Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, UK.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Divitini
authors.affiliation: Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 6, 91058 Erlangen, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Winter
authors.affiliation: Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, UK.
authors.forename: Rowan
authors.initials: R
authors.lastname: Leary
authors.affiliation: Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 6, 91058 Erlangen, Germany.
authors.forename: Erdmann
authors.initials: E
authors.lastname: Spiecker
authors.affiliation: Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, UK.
authors.forename: Caterina
authors.initials: C
authors.lastname: Ducati
authors.affiliation: Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, UK. Electronic address: pam33@cam.ac.uk.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Midgley
mesh_terms: D000465:Algorithms; D000818:Animals; D001921:Brain / Q000648:ultrastructure; D044962:Data Compression / Q000379:methods / Q000706:statistics & numerical data; D005583:Fourier Analysis; D016591:Histocytological Preparation Techniques; D007091:Image Processing, Computer-Assisted / Q000379:methods / Q000706:statistics & numerical data; D021621:Imaging, Three-Dimensional / Q000379:methods / Q000706:statistics & numerical data; D008297:Male; D017348:Microscopy, Electron, Scanning Transmission / Q000379:methods* / Q000706:statistics & numerical data; D051381:Rats; D017207:Rats, Sprague-Dawley
keywords: Compressed sensing; Electron tomography; Isotropic resolution; Life science