colocr: an R package for conducting co-localization analysis on fluorescence microscopy images

PeerJ

article

Mahmoud Ahmed¹  Trang Huyen Lai¹  Deok Ryong Kim¹ 

[1] Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine

关键词: R package;    Colocalization;    Image analysis;    Fluorescence microscopy;    Statistics;   

DOI  :  10.7717/peerj.7255

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY