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-4.4-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 site:https://docs.ropensci.org

On CRAN:

colocalization image-analysis

5.76 score 25 stars 23 scripts 157 downloads 2 mentions 11 exports 53 dependencies

Last updated 5 years agofrom:9b7bd6ef54 (on master). Checks:4 OK, 5 NOTE, 1 FAIL. Indexed: yes.

Target	Result	Total time
pkgdown docs	OK	274
source / vignettes	OK	593
linux-devel-x86_64	NOTE	509
linux-release-x86_64	NOTE	281
macos-release-arm64	NOTE	91
macos-oldrel-arm64	OK	126
windows-devel	NOTE	144
windows-release	NOTE	181
windows-oldrel	OK	164
wasm-release	FAIL	345

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 crayon 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 May 29 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