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Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy

Imaging ultrastructures in cells using Focused Ion Beam Scanning Electron Microscope (FIB-SEM) yields section-by-section images at nano-resolution. Unfortunately, we observe that FIB-SEM often introduces sub-pixel drifts between sections, in the order of 2.5 nm. The accumulation of these drifts sign...

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Autores principales: Stephensen, Hans Jacob Teglbjærg, Darkner, Sune, Sporring, Jon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035423/
https://www.ncbi.nlm.nih.gov/pubmed/32081999
http://dx.doi.org/10.1038/s42003-020-0809-4
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author Stephensen, Hans Jacob Teglbjærg
Darkner, Sune
Sporring, Jon
author_facet Stephensen, Hans Jacob Teglbjærg
Darkner, Sune
Sporring, Jon
author_sort Stephensen, Hans Jacob Teglbjærg
collection PubMed
description Imaging ultrastructures in cells using Focused Ion Beam Scanning Electron Microscope (FIB-SEM) yields section-by-section images at nano-resolution. Unfortunately, we observe that FIB-SEM often introduces sub-pixel drifts between sections, in the order of 2.5 nm. The accumulation of these drifts significantly skews distance measures and geometric structures, which standard image registration techniques fail to correct. We demonstrate that registration techniques based on mutual information and sum-of-squared-distances significantly underestimate the drift since they are agnostic to image content. For neuronal data at nano-resolution, we discovered that vesicles serve as a statistically simple geometric structure, making them well-suited for estimating the drift with sub-pixel accuracy. Here, we develop a statistical model of vesicle shapes for drift correction, demonstrate its superiority, and provide a self-contained freely available application for estimating and correcting drifted datasets with vesicles.
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spelling pubmed-70354232020-03-04 Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy Stephensen, Hans Jacob Teglbjærg Darkner, Sune Sporring, Jon Commun Biol Article Imaging ultrastructures in cells using Focused Ion Beam Scanning Electron Microscope (FIB-SEM) yields section-by-section images at nano-resolution. Unfortunately, we observe that FIB-SEM often introduces sub-pixel drifts between sections, in the order of 2.5 nm. The accumulation of these drifts significantly skews distance measures and geometric structures, which standard image registration techniques fail to correct. We demonstrate that registration techniques based on mutual information and sum-of-squared-distances significantly underestimate the drift since they are agnostic to image content. For neuronal data at nano-resolution, we discovered that vesicles serve as a statistically simple geometric structure, making them well-suited for estimating the drift with sub-pixel accuracy. Here, we develop a statistical model of vesicle shapes for drift correction, demonstrate its superiority, and provide a self-contained freely available application for estimating and correcting drifted datasets with vesicles. Nature Publishing Group UK 2020-02-21 /pmc/articles/PMC7035423/ /pubmed/32081999 http://dx.doi.org/10.1038/s42003-020-0809-4 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Stephensen, Hans Jacob Teglbjærg
Darkner, Sune
Sporring, Jon
Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy
title Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy
title_full Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy
title_fullStr Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy
title_full_unstemmed Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy
title_short Restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy
title_sort restoring drifted electron microscope volumes using synaptic vesicles at sub-pixel accuracy
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035423/
https://www.ncbi.nlm.nih.gov/pubmed/32081999
http://dx.doi.org/10.1038/s42003-020-0809-4
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