ArticleG3 (Bethesda, Md.)2014
gitter: a robust and accurate method for quantification of colony sizes from plate images.
Article in G3 (Bethesda, Md.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
77 citing papers in PubMed.
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- Intergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses.Nature communications · 2026Article
- A time-resolved high-throughput screening of fission yeast deletion mutants for oxidative stress resistance.Microbial cell (Graz, Austria) · 2026Article
- Simple large-scale quantitative phenotyping and antimicrobial susceptibility testing with Q-PHAST.Nature protocols · 2026Review
- Protein structure shapes natural genetic variation andbioRxiv : the preprint server for biology · 2025Article
- High-throughput chemical genomic screening: a step-by-step workflow from plate to phenotype.mSystems · 2025Article
- Rapalink-1 reveals TOR-dependent genes and an agmatinergic axis-based metabolic feedback regulating TOR activity and lifespan in fission yeast.Communications biology · 2025Article
- Mitochondrial Translation Inhibition Triggers an Rst2-Controlled Transcriptional Reprogramming of Carbon Metabolism in Stationary-Phase Cells of Fission Yeast.Biomolecules · 2025Article
- Whole-genome sequencing of 1,060 Brettanomyces bruxellensis isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids.Nature communications · 2025Article
- The anti-cancer transition-state inhibitor MTDIA inhibits human MTAP, inducing autophagy in humanized yeast.Disease models & mechanisms · 2025Article
- Genome-wide conditional degron libraries for functional genomics.The Journal of cell biology · 2025Article
- Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis.RNA (New York, N.Y.) · 2024Article
- Ageing-associated long non-coding RNA extends lifespan and reduces translation in non-dividing cells.EMBO reports · 2024Article
- A Matlab-based application for quantification of yeast cell growth on solid media.Journal of the Royal Society, Interface · 2024Article
- Species-wide survey of the expressivity and complexity spectrum of traits in yeast.PLoS genetics · 2024Article
- Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.