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nucim R package

nucim (Nucleome Imaging Toolbox) is an R package for quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

Installation

The stable version is available on CRAN:

setRepositories(ind=c(1,2))
install.packages(c("nucim"))

Installation will take about 5 to 10 seconds. Tested platforms can be found here.

The development version is available on github. The development version probably depends on the development version of bioimagetools:

setRepositories(ind=c(1,2))
install.packages(c("devtools","tiff","EBImage"))
devtools::install_github("bioimaginggroup/bioimagetools")
devtools::install_github("bioimaginggroup/nucim")

You may need to install additional libraries on your OS before you can install nucim. E.g. on Ubuntu/Debian systems, please execute:

sudo apt install libssl-dev libcurl4-openssl-dev libtiff5-dev libfftw3-dev

in the terminal before installing nucim.

More information

Description of the package and basic instructions can be found in:

• Volker J. Schmid, Marion Cremer, Thomas Cremer: Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy. Methods 123 (2017), p. 33–46. [DOI]

Contributors

This package is developed at the BioImaging group at the Department of Statistics, in cooperation with the Biocenter, Department of Biology II, both at LMU Munich.

• Main development and implementation: Volker J Schmid
• Developement of workflow: Marion and Thomas Cremer
• Input on specific parts: Barbara Hübner, Yolanda Markaki, Jens Popken, Lothar Schermelleh, Daniel Smeets

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.