Abstract
BackgroundThe 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.ImplementationThis 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.Availabilitycolocr 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.
Highlights
Biologists use fluorescence microscopy imaging techniques in a variety of applications
Several methods are developed for quantifying the co-localization of the two intracelullar proteins using fluorescence microscopy images
The confocal fluorescence microscopy images presented in this article are from the DU145 prostate cancer cell line
Summary
Biologists use fluorescence microscopy imaging techniques in a variety of applications. Colocr: an R package for conducting co-localization analysis on fluorescence microscopy images. Scatter plot and density distribution of the pixel intensities from the selected regions in two channels. The function roi_select relies on different algorithms from the imager package.
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