Tools

Software and resources from the lab, free to use for everyone.

Assay Calculator

The Assay Calculator turns the raw output of a plate reader into the figures and numbers of a plant immunity experiment. It handles two assays: aequorin luminescence measurements of cytosolic calcium, normalized to the luminescence left in each well, and measurements of reactive oxygen species, blanked against the control wells of the same genotype.

Upload the measurement file and a plate layout specifying which genotype and which elicitor belongs to each well, and the app draws the curve of every single well, averages the replicates per genotype and elicitor, and reports peak heights and areas under the curve with their spread over the replicates. Wells can be excluded without editing the layout file, a reference curve can be drawn into every panel, and the whole analysis comes back as an Excel workbook, as a set of csv files or as a PDF of the plots. Every setting that influenced a number is written into the download, so a result stays reproducible.

The application was written by Alexander Kutschera at the Technical University of Munich as a community project of OpenPlantScience. We maintain this fork, which adds the areas under the curve, the reference curves, a configurable measurement interval, and a test suite of some 370 assertions that pins the numbers down. The code is under the GNU General Public License version 3.

Example data and empty templates are on the Instructions tab of the running application. The source is on GitHub.