colocr: an R package for conducting co-localization analysis on fluorescence microscopy images
Background The co-localization analysis of fluorescence microscopy images is a widely used technique in biological research. It is often used to determine the co-distribution of two proteins inside the cell, suggesting that these two proteins could be functionally or physically associated. The limit...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2019-07-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/7255.pdf |
| _version_ | 1797424275624296448 |
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| author | Mahmoud Ahmed Trang Huyen Lai Deok Ryong Kim |
| author_facet | Mahmoud Ahmed Trang Huyen Lai Deok Ryong Kim |
| author_sort | Mahmoud Ahmed |
| collection | DOAJ |
| description | Background The co-localization analysis of fluorescence microscopy images is a widely used technique in biological research. It is often used to determine the co-distribution of two proteins inside the cell, suggesting that these two proteins could be functionally or physically associated. The limiting step in conducting microscopy image analysis in a graphical interface tool is the selection of the regions of interest for the co-localization of two proteins. Implementation This package provides a simple straightforward workflow for loading fluorescence images, choosing regions of interest and calculating co-localization measurements. Included in the package is a shiny app that can be invoked locally to interactively select the regions of interest where two proteins are co-localized. Availability colocr is available on the comprehensive R archive network, and the source code is available on GitHub under the GPL-3 license as part of the ROpenSci collection, https://github.com/ropensci/colocr. |
| first_indexed | 2024-03-09T07:59:58Z |
| format | Article |
| id | doaj.art-c7cbdce59a7a4a49811a99683ef63ad6 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:59:58Z |
| publishDate | 2019-07-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-c7cbdce59a7a4a49811a99683ef63ad62023-12-03T00:48:10ZengPeerJ Inc.PeerJ2167-83592019-07-017e725510.7717/peerj.7255colocr: an R package for conducting co-localization analysis on fluorescence microscopy imagesMahmoud Ahmed0Trang Huyen Lai1Deok Ryong Kim2Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, JinJu, Republic of KoreaDepartment of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, JinJu, Republic of KoreaDepartment of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, JinJu, Republic of KoreaBackground The co-localization analysis of fluorescence microscopy images is a widely used technique in biological research. It is often used to determine the co-distribution of two proteins inside the cell, suggesting that these two proteins could be functionally or physically associated. The limiting step in conducting microscopy image analysis in a graphical interface tool is the selection of the regions of interest for the co-localization of two proteins. Implementation This package provides a simple straightforward workflow for loading fluorescence images, choosing regions of interest and calculating co-localization measurements. Included in the package is a shiny app that can be invoked locally to interactively select the regions of interest where two proteins are co-localized. Availability colocr is available on the comprehensive R archive network, and the source code is available on GitHub under the GPL-3 license as part of the ROpenSci collection, https://github.com/ropensci/colocr.https://peerj.com/articles/7255.pdfR packageColocalizationImage analysisFluorescence microscopyStatistics |
| spellingShingle | Mahmoud Ahmed Trang Huyen Lai Deok Ryong Kim colocr: an R package for conducting co-localization analysis on fluorescence microscopy images PeerJ R package Colocalization Image analysis Fluorescence microscopy Statistics |
| title | colocr: an R package for conducting co-localization analysis on fluorescence microscopy images |
| title_full | colocr: an R package for conducting co-localization analysis on fluorescence microscopy images |
| title_fullStr | colocr: an R package for conducting co-localization analysis on fluorescence microscopy images |
| title_full_unstemmed | colocr: an R package for conducting co-localization analysis on fluorescence microscopy images |
| title_short | colocr: an R package for conducting co-localization analysis on fluorescence microscopy images |
| title_sort | colocr an r package for conducting co localization analysis on fluorescence microscopy images |
| topic | R package Colocalization Image analysis Fluorescence microscopy Statistics |
| url | https://peerj.com/articles/7255.pdf |
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