gitter: An R Package for Quantification of Pinned Microbial Cultures

gitter allows robust and quick quantification of pinned colony sizes in plate images. gitter works by first finding the grid of colonies from a preprocessed image and then locating the bounds of each colony separately. It includes several image pre-processing techniques, such as autorotation of plates, noise removal, contrast adjustment and image resizing.

Please refer to http://omarwagih.github.io/gitter/ for installation instructions, example code and documentation

For github installation:

devtools::install_github('omarwagih/gitter')

Note regarding depreciated dependency PET and autorotate feature

Update: Since PET is no longer being actively maintained, as of 1.1.4 I have removed it as a dependency. As a result, autorotate will no longer work in versions 1.1.4 and later. If you would like to use the autorotate feature, you'll have to manually install PET (see below) and an older version of gitter (<=1.1.3).

The package PET which is a dependency of gitter has been removed from CRAN so the auto-install may fail. To get around this, you can try manually installing PET from the CRAN Archives before trying to install gitter i.e.:

download PET_0.5.1.tar.gz from the Archives, then run the following in your command line:

R CMD INSTALL PET_0.5.1.tar.gz

If you use gitter, please cite the following work:
Wagih, O. and Parts L. (2014) gitter: a robust and accurate method for quantification of colony sizes from plate images. G3 (Bethesda) pii: g3.113.009431v1 pubmed