Images of colony growth for 224 Arabidopsis thaliana bacterial strains on 46 carbon sources

This repository contains all data necessary to score colony growth on agar plates using the software tool 'platescan' (github.com/MicrobiologyETHZ/platescan) for the strains presented in Schäfer, Pacheco, et al.

The growth of the 224 strains was split into 3 screens. Rounds 1, 2, and half of 3 comprised the core of the screen for all strains, and the second half of 3 comprised the validation set for computing the false discovery rate. The directories containing the images, as well as their corresponding metadata files, are named accordingly:

    pictures_7dps_screen_*: folders contain pictures of screening plates to assess growth on tested garbon sources. Pictures were taken 7 days after spotting strains on the plates.

    *_d7_filenames.txt: files link the picture filename to the carbon source that was tested. In addition the screening round and the plate number within the screening round is indicated.

    strain_metadata_screen*.txt: files indicate the position of the strains on the test plates [row (alphabetical), row (numbered), column (numbered)] and additional comments relevant for analysis (swarmer). Screen_nr and plate_number allow to link data to the corresponding pictures.

This repository additionally includes a script to perform downstream processing of the platescan software output,

    plate_scan_analysis.R.

and a file reporting the latescan output values that were manually overwritten due to contamination or poor image quality

    manual_correction.txt.