An automated, high-throughput method for standardizing image color profiles to improve image-based plant phenotyping

Journal Article · Thu Oct 04 00:00:00 EDT 2018 · PeerJ

DOI:https://doi.org/10.7717/peerj.5727· OSTI ID:1483477

Berry, Jeffrey C. ^[1]; Fahlgren, Noah ^[2]; Pokorny, Alexandria A. ^[2]; Bart, Rebecca S. ^[2]; Veley, Kira M. ^[2]

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1. Donald Danforth Plant Science Center, Saint Louis, MO (United States); Donald Danforth Plant Science Center
2. Donald Danforth Plant Science Center, Saint Louis, MO (United States)

High-throughput phenotyping has emerged as a powerful method for studying plant biology. Large image-based datasets are generated and analyzed with automated image analysis pipelines. A major challenge associated with these analyses is variation in image quality that can inadvertently bias results. Images are made up of tuples of data called pixels, which consist of R, G, and B values, arranged in a grid. Many factors, for example image brightness, can influence the quality of the image that is captured. These factors alter the values of the pixels within images and consequently can bias the data and downstream analyses. Here, we provide an automated method to adjust an image-based dataset so that brightness, contrast, and color profile is standardized. The correction method is a collection of linear models that adjusts pixel tuples based on a reference panel of colors. We apply this technique to a set of images taken in a high-throughput imaging facility and successfully detect variance within the image dataset. In this case, variation resulted from temperature-dependent light intensity throughout the experiment. Using this correction method, we were able to standardize images throughout the dataset, and we show that this correction enhanced our ability to accurately quantify morphological measurements within each image. We implement this technique in a high-throughput pipeline available with this paper, and it is also implemented in PlantCV.

• Research Organization: Donald Danforth Plant Science Center, Saint Louis, MO (United States); Donald Danforth Plant Science Center, St. Louis, MO (United States); University of Nebraska, Lincoln, NE (United States)
• Sponsoring Organization: USDOE Advanced Research Projects Agency - Energy (ARPA-E); USDOE Office of Science (SC); USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AR0000594; SC0014395; SC0018072
• OSTI ID: 1483477
• Alternate ID(s): OSTI ID: 2318638
• Journal Information: PeerJ, Journal Name: PeerJ Vol. 6; ISSN 2167-8359
• Publisher: PeerJ Inc.
• Country of Publication: United States
• Language: English

Related Subjects

47 OTHER INSTRUMENTATION
59 BASIC BIOLOGICAL SCIENCES
Image correction
Image analysis
Large-scale biology
Least-squares regression
Phenotyping