Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters
| العنوان: | Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters |
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| المؤلفون: | Jean-Marc Allain, Michele Wolfe Bianchi, Jean-Marie Frachisse, Marjorie Guichard |
| المساهمون: | Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Mathematical and Mechanical Modeling with Data Interaction in Simulations for Medicine (M3DISIM), Laboratoire de mécanique des solides (LMS), École polytechnique (X)-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Approches intégratives du Transport Ionique (MINION), Département Biologie Cellulaire (BioCell), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), École polytechnique (X)-Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Mines Paris - PSL (École nationale supérieure des mines de Paris) |
| المصدر: | Plant Methods Plant Methods, BioMed Central, 2019, 15 (1), ⟨10.1186/s13007-019-0483-z⟩ Plant Methods, 2019, 15 (1), ⟨10.1186/s13007-019-0483-z⟩ Plant Methods, Vol 15, Iss 1, Pp 1-13 (2019) |
| بيانات النشر: | HAL CCSD, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | 0106 biological sciences, 0301 basic medicine, Root (chord), Plant Science, Root hair, lcsh:Plant culture, Cell elongation, 01 natural sciences, Image analysis, 03 medical and health sciences, Length measurement, Medicago truncatula, Genetics, lcsh:SB1-1110, Growth rate, [PHYS.MECA.BIOM]Physics [physics]/Mechanics [physics]/Biomechanics [physics.med-ph], Throughput (business), lcsh:QH301-705.5, Mathematics, Spots, Methodology, Sigmoid function, 030104 developmental biology, lcsh:Biology (General), Root, Phenotyping, Short segment, Algorithm, 010606 plant biology & botany, Biotechnology |
| الوصف: | International audience; Background: The root is an important organ for water and nutrient uptake, and soil anchorage. It is equipped with root hairs (RHs) which are elongated structures increasing the exchange surface with the soil. RHs are also studied as a model for plant cellular development, as they represent a single cell with specific and highly regulated polarized elon-gation. For these reasons, it is useful to be able to accurately quantify RH length employing standardized procedures. Methods commonly employed rely on manual steps and are therefore time consuming and prone to errors, restricting analysis to a short segment of the root tip. Few partially automated methods have been reported to increase measurement efficiency. However, none of the reported methods allow an accurate and standardized definition of the position along the root for RH length measurement, making data comparison difficult. Results: We developed an image analysis algorithm that semi-automatically detects RHs and measures their length along the whole differentiation zone of roots. This method, implemented as a simple automated script in ImageJ/Fiji software that we termed Root Hair Sizer, slides a rectangular window along a binarized and straightened image of root tips to estimate the maximal RH length in a given measuring interval. This measure is not affected by heavily bent RHs and any bald spots. RH length data along the root are then modelled with a sigmoidal curve, generating several biologically significant parameters such as RH length, positioning of the root differentiation zone and, under certain conditions, RH growth rate. Conclusions: Image analysis with Root Hair Sizer and subsequent sigmoidal modelling of RH length data provide a simple and efficient way to characterize RH growth in different conditions, equally suitable to small and large scale phenotyping experiments. |
| اللغة: | English |
| تدمد: | 1746-4811 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::adbc29e3b95e28ca1a42d19861ee250cTest https://hal.archives-ouvertes.fr/hal-02293640/documentTest |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....adbc29e3b95e28ca1a42d19861ee250c |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 17464811 |
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