Tools for Microscopy Imaging

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

bioimagetools is an R package for working with images in 3d and 4d.


This package is developed at the BioImaging group at the Department of Statistics, LMU Munich.

  • Volker Schmid [aut, cre],
  • Fabian Scheipl [ctb]



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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1.1.0 by Volker Schmid, 10 months ago

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

Depended on by nucim.

See at CRAN