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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-12-01
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| Series: | Frontiers in Synaptic Neuroscience |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fnsyn.2020.584549/full |
| _version_ | 1824032266345512960 |
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| author | Shigeki Watanabe Shigeki Watanabe M. Wayne Davis Grant F. Kusick Janet Iwasa Erik M. Jorgensen |
| author_facet | Shigeki Watanabe Shigeki Watanabe M. Wayne Davis Grant F. Kusick Janet Iwasa Erik M. Jorgensen |
| author_sort | Shigeki Watanabe |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-20T09:58:47Z |
| format | Article |
| id | doaj.art-8a1af260c2a24968814ea151815c57ed |
| institution | Directory Open Access Journal |
| issn | 1663-3563 |
| language | English |
| last_indexed | 2024-12-20T09:58:47Z |
| publishDate | 2020-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Synaptic Neuroscience |
| spelling | doaj.art-8a1af260c2a24968814ea151815c57ed2022-12-21T19:44:23ZengFrontiers Media S.A.Frontiers in Synaptic Neuroscience1663-35632020-12-011210.3389/fnsyn.2020.584549584549SynapsEM: Computer-Assisted Synapse MorphometryShigeki Watanabe0Shigeki Watanabe1M. Wayne Davis2Grant F. Kusick3Janet Iwasa4Erik M. Jorgensen5Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United StatesSolomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United StatesDepartment of Biology and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, United StatesDepartment of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United StatesDepartment of Biochemistry, University of Utah, Salt Lake City, UT, United StatesDepartment of Biology and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, United StatesThe 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.https://www.frontiersin.org/articles/10.3389/fnsyn.2020.584549/fullelectron microscopysynapsemorphometryultrastructural analysisSynapsEM |
| spellingShingle | Shigeki Watanabe Shigeki Watanabe M. Wayne Davis Grant F. Kusick Janet Iwasa Erik M. Jorgensen SynapsEM: Computer-Assisted Synapse Morphometry Frontiers in Synaptic Neuroscience electron microscopy synapse morphometry ultrastructural analysis SynapsEM |
| 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 | electron microscopy synapse morphometry ultrastructural analysis SynapsEM |
| url | https://www.frontiersin.org/articles/10.3389/fnsyn.2020.584549/full |
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