A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scanners
Abstract Buried scanners are often used to study fine root dynamics by continuously observing them from the images taken at a fixed point. Accordingly, software have been developed to support operators to quantitatively analyse fine roots from scanned images. However, image processing is still time‐...
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| Format: | Article |
| Language: | English |
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Wiley
2022-11-01
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| Series: | Methods in Ecology and Evolution |
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| Online Access: | https://doi.org/10.1111/2041-210X.13972 |
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| author | Arata Yabuki Hidetoshi Ikeno Masako Dannoura |
| author_facet | Arata Yabuki Hidetoshi Ikeno Masako Dannoura |
| author_sort | Arata Yabuki |
| collection | DOAJ |
| description | Abstract Buried scanners are often used to study fine root dynamics by continuously observing them from the images taken at a fixed point. Accordingly, software have been developed to support operators to quantitatively analyse fine roots from scanned images. However, image processing is still time‐consuming work. Deep learning has achieved impressive results as a method for recognising objects in pixel units. In this study, we attempted to automate the image analysis of fine roots using convolutional neural network. Using a root auto tracing and analysis (ARATA), we succeeded in extracting fine roots from scanned images and calculated projected area of fine roots for long‐term dynamics. Our software enables the automatic processing of scanned images acquired at various study sites and accelerates the study of fine root dynamics over extended time periods. |
| format | Article |
| id | doaj-art-4b6ac21bf9f04338b976c1d4fa0393a6 |
| institution | DOAJ |
| issn | 2041-210X |
| language | English |
| publishDate | 2022-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Methods in Ecology and Evolution |
| spelling | doaj-art-4b6ac21bf9f04338b976c1d4fa0393a62025-08-20T03:23:30ZengWileyMethods in Ecology and Evolution2041-210X2022-11-0113112372237810.1111/2041-210X.13972A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scannersArata Yabuki0Hidetoshi Ikeno1Masako Dannoura2Laboratory of Forest Utilization Graduate School of Agriculture, Kyoto University Kyoto JapanFaculty of Informatics The University of Fukuchiyama Kyoto JapanLaboratory of Forest Utilization Graduate School of Agriculture, Kyoto University Kyoto JapanAbstract Buried scanners are often used to study fine root dynamics by continuously observing them from the images taken at a fixed point. Accordingly, software have been developed to support operators to quantitatively analyse fine roots from scanned images. However, image processing is still time‐consuming work. Deep learning has achieved impressive results as a method for recognising objects in pixel units. In this study, we attempted to automate the image analysis of fine roots using convolutional neural network. Using a root auto tracing and analysis (ARATA), we succeeded in extracting fine roots from scanned images and calculated projected area of fine roots for long‐term dynamics. Our software enables the automatic processing of scanned images acquired at various study sites and accelerates the study of fine root dynamics over extended time periods.https://doi.org/10.1111/2041-210X.13972convolutional neural networkdeep learningfine root dynamicsimage processingimage scanner |
| spellingShingle | Arata Yabuki Hidetoshi Ikeno Masako Dannoura A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scanners Methods in Ecology and Evolution convolutional neural network deep learning fine root dynamics image processing image scanner |
| title | A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scanners |
| title_full | A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scanners |
| title_fullStr | A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scanners |
| title_full_unstemmed | A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scanners |
| title_short | A root auto tracing and analysis (ARATA): An automatic analysis software for detecting fine roots in images from flatbed optical scanners |
| title_sort | root auto tracing and analysis arata an automatic analysis software for detecting fine roots in images from flatbed optical scanners |
| topic | convolutional neural network deep learning fine root dynamics image processing image scanner |
| url | https://doi.org/10.1111/2041-210X.13972 |
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