Package: colocr 0.1.1

Mahmoud Ahmed

colocr: Conduct Co-Localization Analysis of Fluorescence Microscopy Images

Automate the co-localization analysis of fluorescence microscopy images. Selecting regions of interest, extract pixel intensities from the image channels and calculate different co-localization statistics. The methods implemented in this package are based on Dunn et al. (2011) <doi:10.1152/ajpcell.00462.2010>.

Authors:Mahmoud Ahmed [aut, cre]

colocr_0.1.1.tar.gz
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colocr_0.1.1.tgz(r-4.5-emscripten)
colocr.pdf |colocr.html✨
colocr/json (API)
NEWS

# Install 'colocr' in R:

install.packages('colocr', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #243

Bug tracker:https://github.com/ropensci/colocr/issues

Pkgdown/docs site:https://docs.ropensci.org

On CRAN:

colocalization image-analysis

4.76 score 25 stars 23 scripts 56 downloads 2 mentions 11 exports 52 dependencies

Last updated from:9b7bd6ef54 (on master). Checks:5 NOTE, 5 OK. Indexed: yes.

Target	Result	Total time
linux-devel-x86_64	NOTE	180
pkgdown docs	OK	174
source / vignettes	OK	271
linux-release-x86_64	NOTE	188
macos-release-arm64	NOTE	122
macos-oldrel-arm64	OK	121
windows-devel	NOTE	140
windows-release	NOTE	140
windows-oldrel	OK	154
wasm-release	OK	147

Exports:.intensity_get .labels_add .manders .pearson %>%colocr_app image_load roi_check roi_select roi_show roi_test

Dependencies:base64enc bmp bslib cachem cli commonmark cpp11 curl digest downloader farver fastmap fontawesome fs glue htmltools httpuv igraph imager jpeg jquerylib jsonlite labeling later lattice lifecycle magick magrittr Matrix memoise mime pkgconfig png promises purrr R6 rappdirs RColorBrewer Rcpp readbitmap rlang sass scales shiny sourcetools stringi stringr tiff vctrs viridisLite withr xtable

Using colocr

Mahmoud Ahmed

Rendered fromusing_colocr.Rmdusingknitr::rmarkdownon Oct 07 2025.

Last update: 2019-05-28
Started: 2018-07-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get pixel intensities	.intensity_get
Label regions of interest	.labels_add
Calculate Marnders Overlap Coefficient	.manders
Calculate Pearson's Correlation Coefficient	.pearson
'colocr': Conduct Co-localization Analysis of Microscopy Images.	colocr-package colocr
Run the shiny App	colocr_app
Load images from files	image_load
Show pixel intensities	roi_check
Select regions of interest	roi_select
Show the selected regions of interest	roi_show
Test Co-localization	roi_test