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SynPAnal: Software for Rapid Quantification of the Density and Intensity of Protein Puncta from Fluorescence Microscopy Images of Neurons

Continuous modification of the protein composition at synapses is a driving force for the plastic changes of synaptic strength, and provides the fundamental molecular mechanism of synaptic plasticity and information storage in the brain. Studying synaptic protein turnover is not only important for u...

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Detalles Bibliográficos
Autores principales: Danielson, Eric, Lee, Sang H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274056/
https://www.ncbi.nlm.nih.gov/pubmed/25531531
http://dx.doi.org/10.1371/journal.pone.0115298
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author Danielson, Eric
Lee, Sang H.
author_facet Danielson, Eric
Lee, Sang H.
author_sort Danielson, Eric
collection PubMed
description Continuous modification of the protein composition at synapses is a driving force for the plastic changes of synaptic strength, and provides the fundamental molecular mechanism of synaptic plasticity and information storage in the brain. Studying synaptic protein turnover is not only important for understanding learning and memory, but also has direct implication for understanding pathological conditions like aging, neurodegenerative diseases, and psychiatric disorders. Proteins involved in synaptic transmission and synaptic plasticity are typically concentrated at synapses of neurons and thus appear as puncta (clusters) in immunofluorescence microscopy images. Quantitative measurement of the changes in puncta density, intensity, and sizes of specific proteins provide valuable information on their function in synaptic transmission, circuit development, synaptic plasticity, and synaptopathy. Unfortunately, puncta quantification is very labor intensive and time consuming. In this article, we describe a software tool designed for the rapid semi-automatic detection and quantification of synaptic protein puncta from 2D immunofluorescence images generated by confocal laser scanning microscopy. The software, dubbed as SynPAnal (for Synaptic Puncta Analysis), streamlines data quantification for puncta density and average intensity, thereby increases data analysis throughput compared to a manual method. SynPAnal is stand-alone software written using the JAVA programming language, and thus is portable and platform-free.
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spelling pubmed-42740562014-12-31 SynPAnal: Software for Rapid Quantification of the Density and Intensity of Protein Puncta from Fluorescence Microscopy Images of Neurons Danielson, Eric Lee, Sang H. PLoS One Research Article Continuous modification of the protein composition at synapses is a driving force for the plastic changes of synaptic strength, and provides the fundamental molecular mechanism of synaptic plasticity and information storage in the brain. Studying synaptic protein turnover is not only important for understanding learning and memory, but also has direct implication for understanding pathological conditions like aging, neurodegenerative diseases, and psychiatric disorders. Proteins involved in synaptic transmission and synaptic plasticity are typically concentrated at synapses of neurons and thus appear as puncta (clusters) in immunofluorescence microscopy images. Quantitative measurement of the changes in puncta density, intensity, and sizes of specific proteins provide valuable information on their function in synaptic transmission, circuit development, synaptic plasticity, and synaptopathy. Unfortunately, puncta quantification is very labor intensive and time consuming. In this article, we describe a software tool designed for the rapid semi-automatic detection and quantification of synaptic protein puncta from 2D immunofluorescence images generated by confocal laser scanning microscopy. The software, dubbed as SynPAnal (for Synaptic Puncta Analysis), streamlines data quantification for puncta density and average intensity, thereby increases data analysis throughput compared to a manual method. SynPAnal is stand-alone software written using the JAVA programming language, and thus is portable and platform-free. Public Library of Science 2014-12-22 /pmc/articles/PMC4274056/ /pubmed/25531531 http://dx.doi.org/10.1371/journal.pone.0115298 Text en © 2014 Danielson, Lee http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Danielson, Eric
Lee, Sang H.
SynPAnal: Software for Rapid Quantification of the Density and Intensity of Protein Puncta from Fluorescence Microscopy Images of Neurons
title SynPAnal: Software for Rapid Quantification of the Density and Intensity of Protein Puncta from Fluorescence Microscopy Images of Neurons
title_full SynPAnal: Software for Rapid Quantification of the Density and Intensity of Protein Puncta from Fluorescence Microscopy Images of Neurons
title_fullStr SynPAnal: Software for Rapid Quantification of the Density and Intensity of Protein Puncta from Fluorescence Microscopy Images of Neurons
title_full_unstemmed SynPAnal: Software for Rapid Quantification of the Density and Intensity of Protein Puncta from Fluorescence Microscopy Images of Neurons
title_short SynPAnal: Software for Rapid Quantification of the Density and Intensity of Protein Puncta from Fluorescence Microscopy Images of Neurons
title_sort synpanal: software for rapid quantification of the density and intensity of protein puncta from fluorescence microscopy images of neurons
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274056/
https://www.ncbi.nlm.nih.gov/pubmed/25531531
http://dx.doi.org/10.1371/journal.pone.0115298
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