Tools for Microscopy Imaging

Tools for 3D imaging, mostly for biology/microscopy. Read and write TIFF stacks. Functions for segmentation, filtering and analyzing 3D point patterns.


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.


The stable version is available on CRAN:


The developement version is available on github:


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.


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



Version 1.1.1-3 Minor bug fixes

Version 1.1 Features:

  • Faster version of nearestClassDistances().
  • Use httr::GET for readTIF(). Fixes:
  • Example for readBMP().
  • Register dynamic symbols.

Version 1.0

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

Reference manual

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1.1.5 by Volker Schmid, a year ago

Report a bug at

Browse source code at

Authors: Volker Schmid [aut, cre] , Priyanka Kukreja [ctb] , Fabian Scheipl [ctb]

Documentation:   PDF Manual  

GPL-3 license

Imports parallel, tiff, stats, grDevices, utils, EBImage, httr

Suggests knitr, rmarkdown

System requirements: tiff fftw libcurl openssl

Depended on by nucim.

See at CRAN