colocr: An R package for conducting co-localization analysis on fluorescence microscopy images
- Published
- Accepted
- Subject Areas
- Biochemistry, Bioinformatics, Cell Biology
- Keywords
- R package, colocalization, Image analysis, fluorescence microscopy, statistics
- Copyright
- © 2019 Ahmed et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. colocr: An R package for conducting co-localization analysis on fluorescence microscopy images. PeerJ Preprints 7:e27613v1 https://doi.org/10.7287/peerj.preprints.27613v1
Abstract
Background The co-localization analysis of fluorescence microscopy images is a widely used tech- nique 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 straight forward workflow for loading fluorescence images, choosing regions of interest and calculating co-localization statistics. Included in the package is a shiny app that can be invoked locally to select the regions of interest where two proteins are interactively co-localized.
Availability colocr is available on the comprehensive R archive network, and the source code is available on GitHub as part of the ROpenSci collection, https://github.com/ropensci/colocr. Keywords: R package, co-localization, image-analysis, fluorescence microscopy, statistics
Author Comment
This is a submission to PeerJ for review.