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
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