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Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology

Ultrastructural analysis of discrete neurobiological structures by volume scanning electron microscopy (SEM) often constitutes a “needle-in-the-haystack” problem and therefore relies on sophisticated search strategies. The appropriate SEM approach for a given relocation task not only depends on the...

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Autores principales: Schifferer, Martina, Snaidero, Nicolas, Djannatian, Minou, Kerschensteiner, Martin, Misgeld, Thomas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8548362/
https://www.ncbi.nlm.nih.gov/pubmed/34720890
http://dx.doi.org/10.3389/fnana.2021.732506
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author Schifferer, Martina
Snaidero, Nicolas
Djannatian, Minou
Kerschensteiner, Martin
Misgeld, Thomas
author_facet Schifferer, Martina
Snaidero, Nicolas
Djannatian, Minou
Kerschensteiner, Martin
Misgeld, Thomas
author_sort Schifferer, Martina
collection PubMed
description Ultrastructural analysis of discrete neurobiological structures by volume scanning electron microscopy (SEM) often constitutes a “needle-in-the-haystack” problem and therefore relies on sophisticated search strategies. The appropriate SEM approach for a given relocation task not only depends on the desired final image quality but also on the complexity and required accuracy of the screening process. Block-face SEM techniques like Focused Ion Beam or serial block-face SEM are “one-shot” imaging runs by nature and, thus, require precise relocation prior to acquisition. In contrast, “multi-shot” approaches conserve the sectioned tissue through the collection of serial sections onto solid support and allow reimaging. These tissue libraries generated by Array Tomography or Automated Tape Collecting Ultramicrotomy can be screened at low resolution to target high resolution SEM. This is particularly useful if a structure of interest is rare or has been predetermined by correlated light microscopy, which can assign molecular, dynamic and functional information to an ultrastructure. As such approaches require bridging mm to nm scales, they rely on tissue trimming at different stages of sample processing. Relocation is facilitated by endogenous or exogenous landmarks that are visible by several imaging modalities, combined with appropriate registration strategies that allow overlaying images of various sources. Here, we discuss the opportunities of using multi-shot serial sectioning SEM approaches, as well as suitable trimming and registration techniques, to slim down the high-resolution imaging volume to the actual structure of interest and hence facilitate ambitious targeted volume SEM projects.
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spelling pubmed-85483622021-10-28 Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology Schifferer, Martina Snaidero, Nicolas Djannatian, Minou Kerschensteiner, Martin Misgeld, Thomas Front Neuroanat Neuroanatomy Ultrastructural analysis of discrete neurobiological structures by volume scanning electron microscopy (SEM) often constitutes a “needle-in-the-haystack” problem and therefore relies on sophisticated search strategies. The appropriate SEM approach for a given relocation task not only depends on the desired final image quality but also on the complexity and required accuracy of the screening process. Block-face SEM techniques like Focused Ion Beam or serial block-face SEM are “one-shot” imaging runs by nature and, thus, require precise relocation prior to acquisition. In contrast, “multi-shot” approaches conserve the sectioned tissue through the collection of serial sections onto solid support and allow reimaging. These tissue libraries generated by Array Tomography or Automated Tape Collecting Ultramicrotomy can be screened at low resolution to target high resolution SEM. This is particularly useful if a structure of interest is rare or has been predetermined by correlated light microscopy, which can assign molecular, dynamic and functional information to an ultrastructure. As such approaches require bridging mm to nm scales, they rely on tissue trimming at different stages of sample processing. Relocation is facilitated by endogenous or exogenous landmarks that are visible by several imaging modalities, combined with appropriate registration strategies that allow overlaying images of various sources. Here, we discuss the opportunities of using multi-shot serial sectioning SEM approaches, as well as suitable trimming and registration techniques, to slim down the high-resolution imaging volume to the actual structure of interest and hence facilitate ambitious targeted volume SEM projects. Frontiers Media S.A. 2021-10-13 /pmc/articles/PMC8548362/ /pubmed/34720890 http://dx.doi.org/10.3389/fnana.2021.732506 Text en Copyright © 2021 Schifferer, Snaidero, Djannatian, Kerschensteiner and Misgeld. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Neuroanatomy
Schifferer, Martina
Snaidero, Nicolas
Djannatian, Minou
Kerschensteiner, Martin
Misgeld, Thomas
Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology
title Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology
title_full Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology
title_fullStr Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology
title_full_unstemmed Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology
title_short Niwaki Instead of Random Forests: Targeted Serial Sectioning Scanning Electron Microscopy With Reimaging Capabilities for Exploring Central Nervous System Cell Biology and Pathology
title_sort niwaki instead of random forests: targeted serial sectioning scanning electron microscopy with reimaging capabilities for exploring central nervous system cell biology and pathology
topic Neuroanatomy
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8548362/
https://www.ncbi.nlm.nih.gov/pubmed/34720890
http://dx.doi.org/10.3389/fnana.2021.732506
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