Dataset Information

Gitter: a robust and accurate method for quantification of colony sizes from plate images.

ABSTRACT: Colony-based screens that quantify the fitness of clonal populations on solid agar plates are perhaps the most important source of genome-scale functional information in microorganisms. The images of ordered arrays of mutants produced by such experiments can be difficult to process because of laboratory-specific plate features, morphed colonies, plate edges, noise, and other artifacts. Most of the tools developed to address this problem are optimized to handle a single setup and do not work out of the box in other settings. We present gitter, an image analysis tool for robust and accurate processing of images from colony-based screens. gitter works by first finding the grid of colonies from a preprocessed image and then locating the bounds of each colony separately. We show that gitter produces comparable colony sizes to other tools in simple cases but outperforms them by being able to handle a wider variety of screens and more accurately quantify colony sizes from difficult images. gitter is freely available as an R package from http://cran.r-project.org/web/packages/gitter under the LGPL. Tutorials and demos can be found at http://omarwagih.github.io/gitter.

SUBMITTER: Wagih O

PROVIDER: S-EPMC3962492 | biostudies-other | 2014 Mar

REPOSITORIES: biostudies-other

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Publications

gitter: a robust and accurate method for quantification of colony sizes from plate images.

Wagih Omar O Parts Leopold L

G3 (Bethesda, Md.) 20140320 3

Colony-based screens that quantify the fitness of clonal populations on solid agar plates are perhaps the most important source of genome-scale functional information in microorganisms. The images of ordered arrays of mutants produced by such experiments can be difficult to process because of laboratory-specific plate features, morphed colonies, plate edges, noise, and other artifacts. Most of the tools developed to address this problem are optimized to handle a single setup and do not work out ...[more]

PMID: 24474170

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Project description:BackgroundQuantitative measurements of specific protein phosphorylation sites, as presented here, can be used to investigate signal transduction pathways, which is an important aspect of cell dynamics. The presented method quantitatively compares peptide abundances from experiments using 18O/16O labeling starting from elaborated MS spectra. It was originally developed to study signaling cascades activated by amyloid-beta treatment of neurons used as a cellular model system with relevance to Alzheimer's disease, but is generally applicable.ResultsThe presented method assesses, in complete cell lysates, the degree of phosphorylation of specific peptide residues from MS spectra using 18O/16O labeling. The abundance of each observed phospho-peptide from two cell states was estimated from three overlapping isotope contours. The influence of peptide-specific labeling efficiency was removed by performing a label swapped experiment and assuming that the labeling efficiency was unchanged upon label swapping. Different degrees of phosphorylation were reported using the fold change measure which was extended with a confidence interval found to reflect the quality of the underlying spectra. Furthermore a new way of method assessment using simulated data is presented. Using simulated data generated in a manner mimicking real data it was possible to show the method's robustness both with increasing noise levels and with decreasing labeling efficiency.ConclusionThe fold change error assessable on simulated data was on average 0.16 (median 0.10) with an error-to-signal ratio and labeling efficiency distributions similar to the ones found in the experimentally observed spectra. Applied to experimentally observed spectra a very good match was found to the model (<10% error for 85% of spectra) with a high degree of robustness, as assessed by data removal. This new method can thus be used for quantitative signal cascade analysis of total cell extracts in a high throughput mode.

Dataset Information

Gitter: a robust and accurate method for quantification of colony sizes from plate images.

Publications

gitter: a robust and accurate method for quantification of colony sizes from plate images.

Similar Datasets

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