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Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit
Glial cells are the support cells of the nervous system. Glial cells typically have elaborate morphologies that facilitate close contacts with neighboring neurons, synapses, and the vasculature. In the retina, Müller glia (MG) are the principal glial cell type that supports neuronal function by prov...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108223/ https://www.ncbi.nlm.nih.gov/pubmed/36688682 http://dx.doi.org/10.1002/cpz1.654 |
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author | Kugler, Elisabeth Breitenbach, Eva‐Maria MacDonald, Ryan |
author_facet | Kugler, Elisabeth Breitenbach, Eva‐Maria MacDonald, Ryan |
author_sort | Kugler, Elisabeth |
collection | PubMed |
description | Glial cells are the support cells of the nervous system. Glial cells typically have elaborate morphologies that facilitate close contacts with neighboring neurons, synapses, and the vasculature. In the retina, Müller glia (MG) are the principal glial cell type that supports neuronal function by providing a myriad of supportive functions via intricate cell morphologies and precise contacts. Thus, complex glial morphology is critical for glial function, but remains challenging to resolve at a sub‐cellular level or reproducibly quantify in complex tissues. To address this issue, we developed GliaMorph as a Fiji‐based macro toolkit that allows 3D glial cell morphology analysis in the developing and mature retina. As GliaMorph is implemented in a modular fashion, here we present guides to (a) setup of GliaMorph, (b) data understanding in 3D, including z‐axis intensity decay and signal‐to‐noise ratio, (c) pre‐processing data to enhance image quality, (d) performing and examining image segmentation, and (e) 3D quantification of MG features, including apicobasal texture analysis. To allow easier application, GliaMorph tools are supported with graphical user interfaces where appropriate, and example data are publicly available to facilitate adoption. Further, GliaMorph can be modified to meet users’ morphological analysis needs for other glial or neuronal shapes. Finally, this article provides users with an in‐depth understanding of data requirements and the workflow of GliaMorph. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Download and installation of GliaMorph components including example data Basic Protocol 2: Understanding data properties and quality 3D—essential for subsequent analysis and capturing data property issues early Basic Protocol 3: Pre‐processing AiryScan microscopy data for analysis Alternate Protocol: Pre‐processing confocal microscopy data for analysis Basic Protocol 4: Segmentation of glial cells Basic Protocol 5: 3D quantification of glial cell morphology |
format | Online Article Text |
id | pubmed-10108223 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-101082232023-04-18 Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit Kugler, Elisabeth Breitenbach, Eva‐Maria MacDonald, Ryan Curr Protoc Protocol Glial cells are the support cells of the nervous system. Glial cells typically have elaborate morphologies that facilitate close contacts with neighboring neurons, synapses, and the vasculature. In the retina, Müller glia (MG) are the principal glial cell type that supports neuronal function by providing a myriad of supportive functions via intricate cell morphologies and precise contacts. Thus, complex glial morphology is critical for glial function, but remains challenging to resolve at a sub‐cellular level or reproducibly quantify in complex tissues. To address this issue, we developed GliaMorph as a Fiji‐based macro toolkit that allows 3D glial cell morphology analysis in the developing and mature retina. As GliaMorph is implemented in a modular fashion, here we present guides to (a) setup of GliaMorph, (b) data understanding in 3D, including z‐axis intensity decay and signal‐to‐noise ratio, (c) pre‐processing data to enhance image quality, (d) performing and examining image segmentation, and (e) 3D quantification of MG features, including apicobasal texture analysis. To allow easier application, GliaMorph tools are supported with graphical user interfaces where appropriate, and example data are publicly available to facilitate adoption. Further, GliaMorph can be modified to meet users’ morphological analysis needs for other glial or neuronal shapes. Finally, this article provides users with an in‐depth understanding of data requirements and the workflow of GliaMorph. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Download and installation of GliaMorph components including example data Basic Protocol 2: Understanding data properties and quality 3D—essential for subsequent analysis and capturing data property issues early Basic Protocol 3: Pre‐processing AiryScan microscopy data for analysis Alternate Protocol: Pre‐processing confocal microscopy data for analysis Basic Protocol 4: Segmentation of glial cells Basic Protocol 5: 3D quantification of glial cell morphology John Wiley and Sons Inc. 2023-01-23 2023-01 /pmc/articles/PMC10108223/ /pubmed/36688682 http://dx.doi.org/10.1002/cpz1.654 Text en © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Protocol Kugler, Elisabeth Breitenbach, Eva‐Maria MacDonald, Ryan Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit |
title | Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit |
title_full | Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit |
title_fullStr | Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit |
title_full_unstemmed | Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit |
title_short | Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit |
title_sort | glia cell morphology analysis using the fiji gliamorph toolkit |
topic | Protocol |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10108223/ https://www.ncbi.nlm.nih.gov/pubmed/36688682 http://dx.doi.org/10.1002/cpz1.654 |
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