ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data

Abstract

BackgroundMany high-throughput genomic experiments, such as Synthetic Genetic Array and yeast two-hybrid, use colony growth on solid media as a screen metric. These experiments routinely generate over 100,000 data points, making data analysis a time consuming and painstaking process. Here we describe ScreenMill, a new software suite that automates image analysis and simplifies data review and analysis for high-throughput biological experiments.ResultsThe ScreenMill, software suite includes three software tools or "engines": an open source Colony Measurement Engine (CM Engine) to quantitate colony growth data from plate images, a web-based Data Review Engine (DR Engine) to validate and analyze quantitative screen data, and a web-based Statistics Visualization Engine (SV Engine) to visualize screen data with statistical information overlaid. The methods and software described here can be applied to any screen in which growth is measured by colony size. In addition, the DR Engine and SV Engine can be used to visualize and analyze other types of quantitative high-throughput data.ConclusionsScreenMill automates quantification, analysis and visualization of high-throughput screen data. The algorithms implemented in ScreenMill are transparent allowing users to be confident about the results ScreenMill produces. Taken together, the tools of ScreenMill offer biologists a simple and flexible way of analyzing their data, without requiring programming skills.

Synthetic physical interactions map kinetochore regulators and regions sensitive to constitutive Cdc14 localization

“…S6A). We quantified the growth effects as previously described (33), comparing the wild-type GBP-Cdc14 with either Cdc14 or the catalytically inactive mutants. The two N-terminally tagged mutants (GBP-cdc14-CA and GBP-cdc14-CS) gave equivalent results ( Fig.…”

“…Yeast plasmids are listed in Table S2. Plasmids were transferred into the GFP strains using selective ploidy ablation (32) and the resulting colony growth assessed using ScreenMill software (33). Other methods are described in SI Text.…”

Selective ploidy ablation, a high-throughput plasmid transfer protocol, identifies new genes affecting topoisomerase I–induced DNA damage

“…However, since the SPA procedure can easily generate growth data for more than 100,000 colonies per experiment, visual inspection becomes impractical. We therefore developed an image-analysis software suite called ScreenMill to measure colony sizes and calculate descriptive statistics from plate images of all colonies in each data set (Dittmar et al 2010).…”

“…This observation is consistent with the finding that expression of the top1-T 722 A mutant results in a small amount of DNA damage, even in wild-type cells (Megonigal et al 1997). Importantly, platewide growth normalization performed by the ScreenMill software corrects for this systematic decrease in colony size (Dittmar et al 2010).…”

“…This transfer method can be used with any ura3 recipient strain. A genome-wide screen can be completed in ;1 wk using the SPA protocol combined with ScreenMill, our automated growth-analysis tool (Dittmar et al 2010).…”