gitter: Quantification of Pinned Microbial Cultures

The goal of this package is to allow users to robustly and quickly grid and quantify sizes of pinned colonies 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.

Author
Omar Wagih, Leopold Parts
Date of publication
2015-10-11 18:45:24
Maintainer
Omar Wagih <wagih@ebi.ac.uk>
License
LGPL
Version
1.1.1

View on CRAN

Man pages

gitter
Process a single plate image
gitter.batch
Process a batch set of plate images
gitter.demo
Run a demo of gitter
gitter.read
Read in a data file as a 'gitter' data object.
plate.warnings
Show any plate-level warnings associated with a 'gitter' data...
plot.gitter
Plot a gitter dat file
summary.gitter
View the summary of a gitter data file

Files in this package

gitter
gitter/inst
gitter/inst/extdata
gitter/inst/extdata/sample.jpg.dat
gitter/inst/extdata/sample_dead.jpg
gitter/inst/extdata/sample.jpg
gitter/NAMESPACE
gitter/R
gitter/R/plot.r
gitter/R/Main.R
gitter/R/Help.R
gitter/R/Peaks.R
gitter/R/io.r
gitter/README.md
gitter/MD5
gitter/build
gitter/build/BUILD.R
gitter/DESCRIPTION
gitter/man
gitter/man/plot.gitter.Rd
gitter/man/gitter.demo.Rd
gitter/man/summary.gitter.Rd
gitter/man/plate.warnings.Rd
gitter/man/gitter.Rd
gitter/man/gitter.batch.Rd
gitter/man/gitter.read.Rd
gitter/CHANGES