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

Mahmoud Ahmed; Trang Huyen Lai; Deok Ryong Kim

doi:10.7717/peerj.7255

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

PeerJ. 2019 Jul 4:7:e7255. doi: 10.7717/peerj.7255. eCollection 2019.

Authors

Mahmoud Ahmed¹, Trang Huyen Lai¹, Deok Ryong Kim¹

Affiliation

¹ Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, JinJu, Republic of Korea.

Abstract

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.

Keywords: Colocalization; Fluorescence microscopy; Image analysis; R package; Statistics.

Grants and funding

This study was supported by the Basic Research Program through the National Research Foundation of Korea (NRF) by the Ministry of Education Science and Technology (2018R1D1A1B07043715) and the Ministry of Science, ICT and Future Planning (NRF2015R1A5A2008833). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.