bioimagetools

Synopsis

bioimagetools is an R package for working with images in 3D and 4D, mostly for biology/microscopy.

  • Read and write TIFF stacks.
  • Functions for filtering and segmentation.
  • Analysis of 3D point patterns.

Installation

The stable version is available on CRAN:

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

The development version is available on github:

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

You may need to install additional libraries on your OS before you can install bioimagetools. 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 bioimagetools.

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
  • Biological expertise: Marion and Thomas Cremer, Barbara Hübner, Yolanda Markaki, Jens Popken, Lothar Schermelleh, Daniel Smeets
  • Alpha testing: Priyanka Kukreja, Ramin Norousi and Marius Wagner
  • Contributions by Priyanka Kukreja and Fabian Scheipl