TY - JOUR
T1 - MyROOT
T2 - a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings
AU - Betegón-Putze, Isabel
AU - González, Alejandro
AU - Sevillano, Xavier
AU - Blasco-Escámez, David
AU - Caño-Delgado, Ana I.
N1 - Funding Information:
We would like to thank Caño-Delgado Laboratory members for helping with manual root length measurements and comments on the manuscript. AIC-D is a recipient of a BIO2016-78150-P grant funded by the Spanish Ministry of Economy and Competitiveness and Agencia Estatal de Investigación (MINECO/AEI) and Fondo Europeo de Desarrollo Regional (FEDER), and a European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163). IB-P is funded by the FPU15/02822 grant from the Spanish Ministry of Education, Culture and Sport. DB-E is funded by the ERC-2015-CoG – 683163 granted to the AIC-D laboratory. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme (Grant Agreement No. 683163). This work was supported by the CERCA Programme from the Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness (MINECO), through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV-2015-0533)’.
Funding Information:
We would like to thank Caño-Delgado Laboratory members for helping with manual root length measurements and comments on the manuscript. AIC-D is a recipient of a BIO2016-78150-P grant funded by the Spanish Ministry of Economy and Competitiveness and Agencia Estatal de Investigación (MINECO/AEI) and Fondo Europeo de Desarrollo Regional (FEDER), and a European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163). IB-P is funded by the FPU15/02822 grant from the Spanish Ministry of Education, Culture and Sport. DB-E is funded by the ERC-2015-CoG – 683163 granted to the AIC-D laboratory. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 683163). This work was supported by the CERCA Programme from the Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness (MINECO), through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV-2015-0533)’.
Publisher Copyright:
© 2019 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.
PY - 2019/6
Y1 - 2019/6
N2 - 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 (R2 = 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.
AB - 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 (R2 = 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.
KW - Arabidopsis thaliana
KW - high-throughput image analysis
KW - root length
KW - root phenotyping
KW - software
KW - technical advance
UR - https://www.scopus.com/pages/publications/85063992369
U2 - 10.1111/tpj.14297
DO - 10.1111/tpj.14297
M3 - Article
C2 - 30809923
AN - SCOPUS:85063992369
SN - 0960-7412
VL - 98
SP - 1145
EP - 1156
JO - Plant Journal
JF - Plant Journal
IS - 6
ER -