SeedExtractor: an open-source GUI for seed image analysis

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>Accurate measurement of seed size parameters is essential for both: breeding efforts□aimed at□enhancing yields and basic research□focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, <jats:italic>SeedExtractor</jats:italic> that□determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 seconds for analyzing an image, i.e. significantly less compared to the other tools. As this software is open-source, it can be modified by users□to serve more specific needs. The adaptability of <jats:italic>SeedExtractor</jats:italic> was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were subjected to genome-wide association analysis. We identified well-known loci for regulating seed length (<jats:italic>GS3</jats:italic>) and width (<jats:italic>qSW5/GW5</jats:italic>) in rice, which demonstrated the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops.</jats:p><jats:sec><jats:title>HIGHLIGHT</jats:title><jats:p><jats:italic>SeedExtractor</jats:italic> is an open-source application designed to accurately measure seed size and seed color in a time-efficient manner for a wide variety of plant species.</jats:p></jats:sec>

SeedExtractor: An Open-Source GUI for Seed Image Analysis

“…This manuscript has been released as a pre-print at bioRxiv ( Zhu et al, 2020 ). We would like to thank Manny Saluja and Scott Sattler for providing sorghum seeds, Carlos Urrea for common bean seeds, Yavuz Delen and Ismail Dweikat for sunflower seeds.…”

Allelic variation in rice Fertilization Independent Endosperm 1 contributes to grain width under high night temperature stress

“…The dehulled mature grains from primary panicles were scanned using an Epson Expression 12000 XL (Epson America Inc., Los Alamitos, CA, USA) scanner at 600 dpi resolution (Dhatt et al ., 2019). The scanned images were used to obtain morphometric measurements on mature grain size (length and width) using an inhouse developed Matlab application (Zhu et al ., 2020). The grain dimensions derived from the scanned grain images were checked for normality and outliers were removed.…”

Selection of Effective Software for the Analysis of the Fractional Composition of the Chaotic Seed Layer Using the Example of Oilseed Radish

“…The problem of determining the morphological variability of seeds for many crops is an urgent scientific task (Alomía et al, 2016;Silva et al, 2019;Zhu et al, 2020;Wu et al, 2020). In particular, it is reported that the rate of variation of individual linear seed sizes and their individual weight is quite high for cruciferous crops.…”

“…The first group involves the use of appropriate software based on Visual Studio C ++ (Python, Java) and the OpenCV library (Li & He, 2017;The OpenCV Reference Manual, 2019;Wu et al, 2020) which can analyse all images obtained from a camera or by scanning. As a result of the analysis, the seeds are automatically identified by taking consecutive points around their perimeters and maximising or minimising the values in the following sequence: image loading; conversion to a 1-bit image (black seed on a white background); morphology analysis to remove noise and gaps; contouring by marking all the seeds in the image and calculating the length L, width B, area S and length of the perimeter P of the seed (Dong et al, 2019;Zhu et al, 2020). In this method, it is possible to place the seeds with a uniform distribution over the scan area and the ability to more clearly separate along the contours of its location The use of this method with the chaotic mixing of single-layer seed thickness consists of the formation of appropriate image preparation, its chromatic transformation and corresponding binarisation (Zilbergleit & Temruk, 2017;Wu et al, 2020).…”

“…It is also possible to use other program versions to process scanned images. For instance, the software packages Digimizer, GrainScan, SmartGrain, SeedCount and others (Tanabata et al, 2012;Liu et al, 2017;Belin et al, 2018;Wu et al, 2018;Silva et al, 2019;Medeiros et al, 2020;Wu et al, 2020;Zhu et al, 2020) can be used.…”