Resources for image-based high-throughput phenotyping in crops and data sharing challenges.
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ABSTRACT:
SUBMITTER: Danilevicz MF
PROVIDER: S-EPMC8561249 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background Radiomic features may quantify characteristics present in medical imaging. However, the lack of standardized definitions and validated reference values have hampered clinical use. Purpose To standardize a set of 174 radiomic features. Materials and Methods Radiomic features were assessed in three phases. In phase I, 487 features were derived from the basic set of 174 features. Twenty-five research teams with unique radiomics software implementations computed feature values directly from a digital phantom, without any additional image processing. In phase II, 15 teams computed values for 1347 derived features using a CT image of a patient with lung cancer and predefined image processing configurations. In both phases, consensus among the teams on the validity of tentative reference values was measured through the frequency of the modal value and classified as follows: less than three matches, weak; three to five matches, moderate; six to nine matches, strong; 10 or more matches, very strong. In the final phase (phase III), a public data set of multimodality images (CT, fluorine 18 fluorodeoxyglucose PET, and T1-weighted MRI) from 51 patients with soft-tissue sarcoma was used to prospectively assess reproducibility of standardized features. Results Consensus on reference values was initially weak for 232 of 302 features (76.8%) at phase I and 703 of 1075 features (65.4%) at phase II. At the final iteration, weak consensus remained for only two of 487 features (0.4%) at phase I and 19 of 1347 features (1.4%) at phase II. Strong or better consensus was achieved for 463 of 487 features (95.1%) at phase I and 1220 of 1347 features (90.6%) at phase II. Overall, 169 of 174 features were standardized in the first two phases. In the final validation phase (phase III), most of the 169 standardized features could be excellently reproduced (166 with CT; 164 with PET; and 164 with MRI). Conclusion A set of 169 radiomics features was standardized, which enabled verification and calibration of different radiomics software. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Kuhl and Truhn in this issue.
| S-EPMC7193906 | biostudies-literature
Project description:The timing and duration of flowering are key agronomic traits that are often associated with the ability of a variety to escape abiotic stress such as heat and drought. Flowering information is valuable in both plant breeding and agricultural production management. Visual assessment, the standard protocol used for phenotyping flowering, is a low-throughput and subjective method. In this study, we evaluated multiple imaging sensors (RGB and multiple multispectral cameras), image resolution (proximal/remote sensing at 1.6 to 30 m above ground level/AGL), and image processing (standard and unsupervised learning) techniques in monitoring flowering intensity of four cool-season crops (canola, camelina, chickpea, and pea) to enhance the accuracy and efficiency in quantifying flowering traits. The features (flower area, percentage of flower area with respect to canopy area) extracted from proximal (1.6-2.2 m AGL) RGB and multispectral (with near infrared, green and blue band) image data were strongly correlated (r up to 0.89) with visual rating scores, especially in pea and canola. The features extracted from unmanned aerial vehicle integrated RGB image data (15-30 m AGL) could also accurately detect and quantify large flowers of winter canola (r up to 0.84), spring canola (r up to 0.72), and pea (r up to 0.72), but not camelina or chickpea flowers. When standard image processing using thresholds and unsupervised machine learning such as k-means clustering were utilized for flower detection and feature extraction, the results were comparable. In general, for applicability of imaging for flower detection, it is recommended that the image data resolution (i.e., ground sampling distance) is at least 2-3 times smaller than that of the flower size. Overall, this study demonstrates the feasibility of utilizing imaging for monitoring flowering intensity in multiple varieties of evaluated crops.
| S-EPMC7085647 | biostudies-literature
Project description: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.
| S-EPMC6174877 | biostudies-literature
Project description:Many biochemical and physiological properties of plants that are of interest to breeders and geneticists have extremely low throughput and/or can only be measured destructively. This has limited the use of information on natural variation in nutrient and metabolite abundance, as well as photosynthetic capacity in quantitative genetic contexts where it is necessary to collect data from hundreds or thousands of plants. A number of recent studies have demonstrated the potential to estimate many of these traits from hyperspectral reflectance data, primarily in ecophysiological contexts. Here, we summarize recent advances in the use of hyperspectral reflectance data for plant phenotyping, and discuss both the potential benefits and remaining challenges to its application in plant genetics contexts. The performances of previously published models in estimating six traits from hyperspectral reflectance data in maize were evaluated on new sample datasets, and the resulting predicted trait values shown to be heritable (e.g., explained by genetic factors) were estimated. The adoption of hyperspectral reflectance-based phenotyping beyond its current uses may accelerate the study of genes controlling natural variation in biochemical and physiological traits.
| S-EPMC8299078 | biostudies-literature
Project description:Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.
| S-EPMC5713628 | biostudies-literature
Project description:Canopy temperature (CT) has been related to water-use and yield formation in crops. However, constantly (e.g., sun illumination angle, ambient temperature) as well as rapidly (e.g., clouds) changing environmental conditions make it difficult to compare measurements taken even at short time intervals. This poses a great challenge for high-throughput field phenotyping (HTFP). The aim of this study was to i) set up a workflow for unmanned aerial vehicles (UAV) based HTFP of CT, ii) investigate different data processing procedures to combine information from multiple images into orthomosaics, iii) investigate the repeatability of the resulting CT by means of heritability, and iv) investigate the optimal timing for thermography measurements. Additionally, the approach was v) compared with other methods for HTFP of CT. The study was carried out in a winter wheat field trial with 354 genotypes planted in two replications in a temperate climate, where a UAV captured CT in a time series of 24 flights during 6 weeks of the grain-filling phase. Custom-made thermal ground control points enabled accurate georeferencing of the data. The generated thermal orthomosaics had a high spatial accuracy (mean ground sampling distance of 5.03 cm/pixel) and position accuracy [mean root-mean-square deviation (RMSE) = 4.79 cm] over all time points. An analysis on the impact of the measurement geometry revealed a gradient of apparent CT in parallel to the principle plane of the sun and a hotspot around nadir. Averaging information from all available images (and all measurement geometries) for an area of interest provided the best results by means of heritability. Correcting for spatial in-field heterogeneity as well as slight environmental changes during the measurements were performed with the R package SpATS. CT heritability ranged from 0.36 to 0.74. Highest heritability values were found in the early afternoon. Since senescence was found to influence the results, it is recommended to measure CT in wheat after flowering and before the onset of senescence. Overall, low-altitude and high-resolution remote sensing proved suitable to assess the CT of crop genotypes in a large number of small field plots as is required in crop breeding and variety testing experiments.
| S-EPMC7052280 | biostudies-literature
Project description:This study used high throughput, image-based phenotyping (HTP) to distinguish growth patterns, detect facilitation and interpret variations to nutrient uptake in a model mixed-pasture system in response to factorial low and high nitrogen (N) and phosphorus (P) application. HTP has not previously been used to examine pasture species in mixture. We used red-green-blue (RGB) imaging to obtain smoothed projected shoot area (sPSA) to predict absolute growth (AG) up to 70 days after planting (sPSA, DAP 70), to identify variation in relative growth rates (RGR, DAP 35-70) and detect overyielding (an increase in yield in mixture compared with monoculture, indicating facilitation) in a grass-legume model pasture. Finally, using principal components analysis we interpreted between species changes to HTP-derived temporal growth dynamics and nutrient uptake in mixtures and monocultures. Overyielding was detected in all treatments and was driven by both grass and legume. Our data supported expectations of more rapid grass growth and augmented nutrient uptake in the presence of a legume. Legumes grew more slowly in mixture and where growth became more reliant on soil P. Relative growth rate in grass was strongly associated with shoot N concentration, whereas legume RGR was not strongly associated with shoot nutrients. High throughput, image-based phenotyping was a useful tool to quantify growth trait variation between contrasting species and to this end is highly useful in understanding nutrient-yield relationships in mixed pasture cultivations.
| S-EPMC7540849 | biostudies-literature
Project description:Electronic Health Records aggregated in Clinical Data Warehouses (CDWs) promise to revolutionize Comparative Effectiveness Research and suggest new avenues of research. However, the effectiveness of CDWs is diminished by the lack of properly labeled data. We present a novel approach that integrates knowledge from the CDW, the biomedical literature, and the Unified Medical Language System (UMLS) to perform high-throughput phenotyping. In this paper, we automatically construct a graphical knowledge model and then use it to phenotype breast cancer patients. We compare the performance of this approach to using MetaMap when labeling records.MetaMap's overall accuracy at identifying breast cancer patients was 51.1% (n=428); recall=85.4%, precision=26.2%, and F1=40.1%. Our unsupervised graph-based high-throughput phenotyping had accuracy of 84.1%; recall=46.3%, precision=61.2%, and F1=52.8%.We conclude that our approach is a promising alternative for unsupervised high-throughput phenotyping.
| S-EPMC3426800 | biostudies-other
Project description:The accuracy of trait measurements greatly affects the quality of genetic analyses. During automated phenotyping, trait measurement errors, i.e. differences between automatically extracted trait values and ground truth, are often treated as random effects that can be controlled by increasing population sizes and/or replication number. In contrast, there is some evidence that trait measurement errors may be partially under genetic control. Consistent with this hypothesis, we observed substantial nonrandom, genetic contributions to trait measurement errors for five maize (Zea mays) tassel traits collected using an image-based phenotyping platform. The phenotyping accuracy varied according to whether a tassel exhibited "open" versus. "closed" branching architecture, which is itself under genetic control. Trait-associated SNPs (TASs) identified via genome-wide association studies (GWASs) conducted on five tassel traits that had been phenotyped both manually (i.e. ground truth) and via feature extraction from images exhibit little overlap. Furthermore, identification of TASs from GWASs conducted on the differences between the two values indicated that a fraction of measurement error is under genetic control. Similar results were obtained in a sorghum (Sorghum bicolor) plant height dataset, demonstrating that trait measurement error is genetically determined in multiple species and traits. Trait measurement bias cannot be controlled by increasing population size and/or replication number.
| S-EPMC8408462 | biostudies-literature
Project description:Data phenotyping traits on soybean seeds such as shape and color has been obscure because it is difficult to define them clearly. Further, it takes too much time and effort to have sufficient number of samplings especially length and width. These difficulties prevented seed morphology to be incorporated into efficient breeding program. Here, we propose methods for an image acquisition, a data processing, and analysis for the morphology and color of soybean seeds by high-throughput method using images analysis. As results, quantitative values for colors and various types of morphological traits could be screened to create a standard for subsequent evaluation of the genotype. Phenotyping method in the current study could define the morphology and color of soybean seeds in highly accurate and reliable manner. Further, this method enables the measurement and analysis of large amounts of plant seed phenotype data in a short time, which was not possible before. Fast and precise phenotype data obtained here may facilitate Genome Wide Association Study for the gene function analysis as well as for development of the elite varieties having desirable seed traits.
| S-EPMC6982885 | biostudies-literature