Data from: Accelerated high-throughput imaging and phenotyping system for small organisms
Cite this dataset
Kose, Talha et al. (2023). Data from: Accelerated high-throughput imaging and phenotyping system for small organisms [Dataset]. Dryad. https://doi.org/10.5061/dryad.t4b8gtj6t
Abstract
Studying the complex web of interactions in biological communities requires large multifactorial experiments with sufficient statistical power. Automation tools reduce the time and labor associated with setup, data collection, and analysis in experiments that untangle these webs. We developed tools for high-throughput experimentation (HTE) in duckweeds, small aquatic plants that are amenable to autonomous experimental preparation and image-based phenotyping. We showcase the abilities of our HTE system in a study with 6,000 experimental units grown across 2,000 treatments. These automated tools facilitated the collection and analysis of time-resolved growth data, which revealed finer dynamics of plant-microbe interactions across environmental gradients. Altogether, our HTE system can run experiments with up to 11,520 experimental units and can be adapted for other small organisms.
README: Title of Dataset: Data from: Accelerated high-throughput imaging and phenotyping system for small organisms
This dataset contains the phenotypic data from an experiment in which the growth of one clonal genotype of the duckweed Lemna minor was measured across ten nitrogen concentrations for ten days, in both the presence and absence of microbes.
Description of the Data and file structure
The .csv file contains the following data:
block: temporal block (range 1-4)
daycol: day of the experiment (range 0-10)
nitr_N: nitrogen treatment level in mg/L (range 0-45)
inoc: inoculated (l+) or not inoculated (l-) with microbes isolated from field-collected duckweeds from the same site as the focal duckweed genotype
edge: whether the well is at the edge (TRUE) or in the interior (FALSE) of the well plate
well: The ID of the individual well in the 96-well plate
plate_number: A unique ID for each 96-well plate (range 1-16)
sqmm: The area in square millimeters of duckweed fronds in the well
green_per_arr: The greenness intensity of duckweed fronds in the well, calculated as G/(R+G+B), where R, G, B are the red, green, and blue values for each pixel, which each range from 0 to 255
Missing data is coded as NA.
Sharing/access Information
Data was derived from original images of experimental plates. The paper describes the MATLAB imaging processing tool that we developed to extract duckweed frond area and other phenotypes (e.g., greenness) from the original images.
Funding
Natural Sciences and Engineering Research Council
Gordon and Betty Moore Foundation, Award: GBMF9356
Gordon and Betty Moore Foundation, Award: GBMF10635