25978573beec9bdb37c25e5eea4297e1 pmc_34056620.pdf 04114ef633e90d74bf249aca81cad5b39c97e293 pmc_34056620.pdf 89996cdb69f7660baec3fb3eeaeea909dd94b0992a815b2d63b60f1c7cfa90a9 pmc_34056620.pdf Title: HDAAP_9812910 1..14 Creator: Aspose Ltd. Producer: Aspose.Pdf for .NET 10.1.0 PDF Creator http://www.pdf-tools.com; modified using iTextSharp™ 5.4.0 ©2000-2012 1T3XT BVBA (AGPL-version) CreationDate: Tue May 11 16:00:32 2021 CEST ModDate: Fri May 21 16:19:33 2021 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 14 Encrypted: no Page size: 599.98 x 799.99 pts Page rot: 0 File size: 1128347 bytes Optimized: no PDF version: 1.4 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- MinionPro-Regular CID Type 0C Identity-H yes no yes 30 0 MNGFLP+MinionProIt Type 1C WinAnsi yes yes no 31 0 MNGFMA+Minion-Black Type 1C WinAnsi yes yes no 32 0 MNGFPP+MinionProBold Type 1C WinAnsi yes yes no 33 0 MNGGFO+MinionProRegular Type 1C WinAnsi yes yes no 34 0 MNGGFP+MinionProRegular2 Type 1C Custom yes yes yes 35 0 MNGGHA+MinionMath-Regular Type 1C WinAnsi yes yes no 36 0 MNGGHB+TeXCMMathsItalic Type 1C WinAnsi yes yes no 37 0 MNGGIB+MinionProRegular3 Type 1C WinAnsi yes yes no 38 0 HFTMMW+MinionPro-Regular CID TrueType Identity-H yes yes yes 1 0 MNGGLB+MinionMath-Regular2 Type 1C Custom yes yes yes 141 0 MNGGLC+MinionMath Italic Type 1C WinAnsi yes yes no 142 0 MinionPro-Regular2 Type 1C Custom yes no yes 268 0 MNGLCJ+MinionScUnic Type 1C WinAnsi yes yes no 269 0 MNGPAC+MinionMath-Regular-Graphic Type 1C Custom yes yes yes 343 0 MNHCOL+TeXCMMathsSymbols Type 1C WinAnsi yes yes no 434 0 MNHCOM+MinionMath-Regular3 Type 1C Custom yes yes yes 435 0 MNHFKA+MinionMath-Bold2 Type 1C WinAnsi yes yes no 498 0 MNHFLA+MinionMath-Regular4 Type 1C Custom yes yes yes 499 0 MNHFLB+TeXCMMathsExtension Type 1C WinAnsi yes yes no 500 0 MNHFIN+MinionMath Italic2 Type 1C Custom yes yes yes 501 0 MNHFJO+MinionMath-BoldItalic Type 1C WinAnsi yes yes no 502 0 MNHFJP+MinionMath-Bold Type 1C Custom yes yes yes 503 0 MNHJIL+Minion-Black2 Type 1C WinAnsi yes yes no 831 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2022-03-10 02:56:20 CET RepresentationInformation: pmc_34056620.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2021-06-07 03:40:15 CEST Size: 1128347 Format: PDF Version: 1.4 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 1134 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Automatic Fruit Morphology Phenome and Genetic Analysis: An Application in the Octoploid Strawberry Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Item: Title: 1. Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@87f383f Item: Title: 2. Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4eb7f003 Children: Item: Title: 2.1. Plant Material and Imaging Acquisition Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@eafc191 Item: Title: 2.2. Preprocessing and Segmentation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612fc6eb Item: Title: 2.3. Automatic Fruit Phenotyping Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1060b431 Item: Title: 2.4. Autoencoder and k-Means to Infer Internal Color Patterns Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612679d6 Item: Title: 2.5. Superpixel Algorithm to Remove the Calyx Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@11758f2a Item: Title: 2.6. Univariate Phenotypes: Linear Descriptors Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@e720b71 Item: Title: 2.7. Generalized Procrustes Analysis (GPA) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1b26f7b2 Item: Title: 2.8. Elliptical Fourier Descriptors Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@491cc5c9 Item: Title: 2.9. Conditional Variational Autoencoders (VAE) to Cluster Shapes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@74ad1f1f Item: Title: 2.10. Genetic Parameter Inference Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6a1aab78 Item: Title: 3. Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@462d5aee Children: Item: Title: 3.1. Shape Descriptors Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@69b0fd6f Item: Title: 3.2. Color Descriptors Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@757942a1 Item: Title: 3.3. Genetic Parameter Estimation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4a87761d Item: Title: 4. Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@66d1af89 Item: Title: 5. Conclusion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@8646db9 Item: Title: Data Availability Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@37374a5e Item: Title: Conflicts of Interest Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4671e53b Item: Title: Authors’ Contributions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@2db7a79b Item: Title: Acknowledgments Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6950e31 Item: Title: Supplementary Materials Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@b7dd107 Info: Title: HDAAP_9812910 1..14 Creator: Aspose Ltd. 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Among phenotypes, morphological traits are relevant in many fruit breeding programs, as appearance influences consumer preference. Often, these traits are manually or semiautomatically obtained. Yet, fruit morphology evaluation can be enhanced using fully automatized procedures and digital images provide a cost-effective opportunity for this purpose. Here, we present an automatized pipeline for comprehensive phenomic and genetic analysis of morphology traits extracted from internal and external strawberry (Fragaria x ananassa) images. The pipeline segments, classifies, and labels the images and extracts conformation features, including linear (area, perimeter, height, width, circularity, shape descriptor, ratio between height and width) and multivariate (Fourier elliptical components and Generalized Procrustes) statistics. Internal color patterns are obtained using an autoencoder to smooth out the image. In addition, we develop a variational autoencoder to automatically detect the most likely number of underlying shapes. Bayesian modeling is employed to estimate both additive and dominance effects for all traits. As expected, conformational traits are clearly heritable. Interestingly, dominance variance is higher than the additive component for most of the traits. Overall, we show that fruit shape and color can be quickly and automatically evaluated and are moderately heritable. Although we study strawberry images, the algorithm can be applied to other fruits, as shown in the GitHub repository.Plant PhenomicsAAAS2021/05/12Research articledoi:10.34133/2021/9812910en Pages: Page: Label: 1 Annotations: Annotation: Subtype: Link Rect: 187, 557, 197, 567 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 296, 557, 307, 567 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 451, 557, 461, 567 Flags: Print AppearanceDictionary: true Annotation: Subtype: Link Rect: 160, 203, 165, 213 Flags: Print AppearanceDictionary: true Destination: 830 Annotation: Subtype: Link Rect: 258, 169, 263, 179 Flags: Print AppearanceDictionary: true Destination: 921 Annotation: Subtype: Link Rect: 268, 169, 272, 179 Flags: Print AppearanceDictionary: true Destination: 921 Annotation: Subtype: Link Rect: 244, 123, 249, 133 Flags: Print AppearanceDictionary: true Destination: 921 Annotation: Subtype: Link Rect: 254, 123, 259, 133 Flags: Print 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