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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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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. |
format | Online Article Text |
id | pubmed-7035423 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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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