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MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings

Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT , a software...

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Autores principales: Betegón‐Putze, Isabel, González, Alejandro, Sevillano, Xavier, Blasco‐Escámez, David, Caño‐Delgado, Ana I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6618301/
https://www.ncbi.nlm.nih.gov/pubmed/30809923
http://dx.doi.org/10.1111/tpj.14297
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author Betegón‐Putze, Isabel
González, Alejandro
Sevillano, Xavier
Blasco‐Escámez, David
Caño‐Delgado, Ana I.
author_facet Betegón‐Putze, Isabel
González, Alejandro
Sevillano, Xavier
Blasco‐Escámez, David
Caño‐Delgado, Ana I.
author_sort Betegón‐Putze, Isabel
collection PubMed
description Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT , a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom‐up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R (2) = 0.997). When compared with previous developed software with similar features (BRAT and EZ‐Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high‐throughput root length measurements while saving both labor and time.
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spelling pubmed-66183012019-07-22 MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings Betegón‐Putze, Isabel González, Alejandro Sevillano, Xavier Blasco‐Escámez, David Caño‐Delgado, Ana I. Plant J Technical Advance Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT , a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom‐up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R (2) = 0.997). When compared with previous developed software with similar features (BRAT and EZ‐Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high‐throughput root length measurements while saving both labor and time. John Wiley and Sons Inc. 2019-04-06 2019-06 /pmc/articles/PMC6618301/ /pubmed/30809923 http://dx.doi.org/10.1111/tpj.14297 Text en © 2019 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology. This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Technical Advance
Betegón‐Putze, Isabel
González, Alejandro
Sevillano, Xavier
Blasco‐Escámez, David
Caño‐Delgado, Ana I.
MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_full MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_fullStr MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_full_unstemmed MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_short MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
title_sort myroot: a method and software for the semiautomatic measurement of primary root length in arabidopsis seedlings
topic Technical Advance
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6618301/
https://www.ncbi.nlm.nih.gov/pubmed/30809923
http://dx.doi.org/10.1111/tpj.14297
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