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.


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

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

Contributors

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

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

News

NEWS

Version 1.1 Features:

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

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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install.packages("bioimagetools")

1.1.3 by Volker Schmid, a month ago


https://www.github.com/bioimaginggroup/bioimagetools


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


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