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"))

The developement version is available on [github]. The developement version probably depends on the developement 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 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 (2017), available online first. [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