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SynapsEM: Computer-Assisted Synapse Morphometry

The structural features of a synapse help determine its function. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified, a process called morphomet...

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Autores principales: Watanabe, Shigeki, Davis, M. Wayne, Kusick, Grant F., Iwasa, Janet, Jorgensen, Erik M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775558/
https://www.ncbi.nlm.nih.gov/pubmed/33390925
http://dx.doi.org/10.3389/fnsyn.2020.584549
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author Watanabe, Shigeki
Davis, M. Wayne
Kusick, Grant F.
Iwasa, Janet
Jorgensen, Erik M.
author_facet Watanabe, Shigeki
Davis, M. Wayne
Kusick, Grant F.
Iwasa, Janet
Jorgensen, Erik M.
author_sort Watanabe, Shigeki
collection PubMed
description The structural features of a synapse help determine its function. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified, a process called morphometry. Three parameters are typically assessed from each specimen: (1) the sizes of individual vesicles and organelles; (2) the absolute number and densities of organelles; and (3) distances between organelles and key features at synapses, such as active zone membranes and dense projections. For data to be meaningful, the analysis must be repeated from hundreds to thousands of images from several biological replicates, a daunting task. Here we report a custom computer program to analyze key structural features of synapses: SynapsEM. In short, we developed ImageJ/Fiji macros to record x,y-coordinates of segmented structures. The coordinates are then exported as text files. Independent investigators can reload the images and text files to reexamine the segmentation using ImageJ. The Matlab program then calculates and reports key synaptic parameters from the coordinates. Since the values are calculated from coordinates, rather than measured from each micrograph, other parameters such as locations of docked vesicles relative to the center of an active zone can be extracted in Matlab by additional scripting. Thus, this program can accelerate the morphometry of synapses and promote a more comprehensive analysis of synaptic ultrastructure.
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spelling pubmed-77755582021-01-02 SynapsEM: Computer-Assisted Synapse Morphometry Watanabe, Shigeki Davis, M. Wayne Kusick, Grant F. Iwasa, Janet Jorgensen, Erik M. Front Synaptic Neurosci Neuroscience The structural features of a synapse help determine its function. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified, a process called morphometry. Three parameters are typically assessed from each specimen: (1) the sizes of individual vesicles and organelles; (2) the absolute number and densities of organelles; and (3) distances between organelles and key features at synapses, such as active zone membranes and dense projections. For data to be meaningful, the analysis must be repeated from hundreds to thousands of images from several biological replicates, a daunting task. Here we report a custom computer program to analyze key structural features of synapses: SynapsEM. In short, we developed ImageJ/Fiji macros to record x,y-coordinates of segmented structures. The coordinates are then exported as text files. Independent investigators can reload the images and text files to reexamine the segmentation using ImageJ. The Matlab program then calculates and reports key synaptic parameters from the coordinates. Since the values are calculated from coordinates, rather than measured from each micrograph, other parameters such as locations of docked vesicles relative to the center of an active zone can be extracted in Matlab by additional scripting. Thus, this program can accelerate the morphometry of synapses and promote a more comprehensive analysis of synaptic ultrastructure. Frontiers Media S.A. 2020-12-18 /pmc/articles/PMC7775558/ /pubmed/33390925 http://dx.doi.org/10.3389/fnsyn.2020.584549 Text en Copyright © 2020 Watanabe, Davis, Kusick, Iwasa and Jorgensen. http://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 Neuroscience
Watanabe, Shigeki
Davis, M. Wayne
Kusick, Grant F.
Iwasa, Janet
Jorgensen, Erik M.
SynapsEM: Computer-Assisted Synapse Morphometry
title SynapsEM: Computer-Assisted Synapse Morphometry
title_full SynapsEM: Computer-Assisted Synapse Morphometry
title_fullStr SynapsEM: Computer-Assisted Synapse Morphometry
title_full_unstemmed SynapsEM: Computer-Assisted Synapse Morphometry
title_short SynapsEM: Computer-Assisted Synapse Morphometry
title_sort synapsem: computer-assisted synapse morphometry
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775558/
https://www.ncbi.nlm.nih.gov/pubmed/33390925
http://dx.doi.org/10.3389/fnsyn.2020.584549
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