@article{98f4055093ab49f786da3a6e78898266,
title = "SynapsEM: Computer-Assisted Synapse Morphometry",
abstract = "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.",
keywords = "SynapsEM, electron microscopy, morphometry, synapse, ultrastructural analysis",
author = "Shigeki Watanabe and Davis, {M. Wayne} and Kusick, {Grant F.} and Janet Iwasa and Jorgensen, {Erik M.}",
note = "Funding Information: SW and this work were supported by start-up funds from the Johns Hopkins University School of Medicine, Johns Hopkins Discovery funds, Johns Hopkins Catalyst Award, the National Science Foundation (1727260), the National Institutes of Health (1DP2 NS111133-01 and 1R01 NS105810-01A1) awarded to SW. SW is an Alfred P. Sloan fellow, McKnight Foundation Scholar, and Klingenstein and Simons Foundation scholar. GK was supported by a grant from the National Institutes of Health to the Biochemistry, Cellular and Molecular Biology program of the Johns Hopkins University School of Medicine (T32 GM007445) and is a National Science Foundation Graduate Research Fellow (2016217537). MD{\textquoteright}s work was supported by the National Institutes of Health (R01 NS034307) awarded to EJ. EJ is an Investigator of the Howard Hughes Medical Institute. Funding Information: We thank H. James de St. Germain for training SW on Matlab coding and Marc Hammarlund for discussion. We are also indebted to Edward Hujber, Thien Vu, Morven Chien, and Stephen Alexander Lee for additional MatLab routines. Funding. SW and this work were supported by start-up funds from the Johns Hopkins University School of Medicine, Johns Hopkins Discovery funds, Johns Hopkins Catalyst Award, the National Science Foundation (1727260), the National Institutes of Health (1DP2 NS111133-01 and 1R01 NS105810-01A1) awarded to SW. SW is an Alfred P. Sloan fellow, McKnight Foundation Scholar, and Klingenstein and Simons Foundation scholar. GK was supported by a grant from the National Institutes of Health to the Biochemistry, Cellular and Molecular Biology program of the Johns Hopkins University School of Medicine (T32 GM007445) and is a National Science Foundation Graduate Research Fellow (2016217537). MD?s work was supported by the National Institutes of Health (R01 NS034307) awarded to EJ. EJ is an Investigator of the Howard Hughes Medical Institute. Publisher Copyright: {\textcopyright} Copyright {\textcopyright} 2020 Watanabe, Davis, Kusick, Iwasa and Jorgensen.",
year = "2020",
month = dec,
day = "18",
doi = "10.3389/fnsyn.2020.584549",
language = "English (US)",
volume = "12",
journal = "Frontiers in Synaptic Neuroscience",
issn = "1663-3563",
publisher = "Frontiers Research Foundation",
}