Nucleome Imaging Toolbox

Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.


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 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

News

NEWS

Version 1.0: Finalized for manuscript on Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy (Schmid, Cremer, Cremer)

Version 1.0.6: Add check for no observations in colors.in.classes(), small design fixes

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("nucim")

1.0.6 by Volker Schmid, a year ago


https://github.com/bioimaginggroup/nucim


Report a bug at https://github.com/bioimaginggroup/nucim/issues


Browse source code at https://github.com/cran/nucim


Authors: Volker Schmid [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports fields, parallel, stringr

Depends on EBImage, bioimagetools

Suggests knitr, rmarkdown, R.rsp


See at CRAN