PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification
We developed the PHIV-RootCell software to quantify anatomical traits of rice roots transverse section images. Combined with an efficient root sample processing method for image acquisition, this program permits supervised measurements of areas (those of whole root section, stele, cortex and central...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-01-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00790/full |
| _version_ | 1819032908416942080 |
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| author | Marc eLartaud Christophe ePerin Brigitte eCourtois Emilie eThomas Sophia eHenry Mathilde eBettembourg Fanchon eDivol Nadege eLanau Florence eArtus Charlotte eBureau Jean-Luc eVerdeil Gautier eSarah Emmanuel eGuiderdoni Anne eDievart |
| author_facet | Marc eLartaud Christophe ePerin Brigitte eCourtois Emilie eThomas Sophia eHenry Mathilde eBettembourg Fanchon eDivol Nadege eLanau Florence eArtus Charlotte eBureau Jean-Luc eVerdeil Gautier eSarah Emmanuel eGuiderdoni Anne eDievart |
| author_sort | Marc eLartaud |
| collection | DOAJ |
| description | We developed the PHIV-RootCell software to quantify anatomical traits of rice roots transverse section images. Combined with an efficient root sample processing method for image acquisition, this program permits supervised measurements of areas (those of whole root section, stele, cortex and central metaxylem vessels), number of cell layers and number of cells per cell layer. The PHIV-RootCell toolset runs under ImageJ, an independent operating system that has a license-free status. To demonstrate the usefulness of PHIV-RootCell, we conducted a genetic diversity study and an analysis of salt-stress responses of root anatomical parameters in rice (Oryza sativa L.). Using 16 cultivars, we showed that we could discriminate between some of the varieties even at the 6 day-old stage, and that tropical japonica varieties had larger root sections due to an increase in cell number. We observed, as described previously, that root sections become enlarged under salt stress. However, our results show an increase in cell number in ground tissues (endodermis and cortex) but a decrease in external (peripheral) tissues (sclerenchyma, exodermis and epidermis). Thus, the PHIV-RootCell program is a user-friendly tool that will be helpful for future genetic and physiological studies that investigate root anatomical trait variations. |
| first_indexed | 2024-12-21T07:09:25Z |
| format | Article |
| id | doaj.art-17909914408644d096afbc033e05bc7d |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T07:09:25Z |
| publishDate | 2015-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-17909914408644d096afbc033e05bc7d2022-12-21T19:12:00ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-01-01510.3389/fpls.2014.00790125383PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantificationMarc eLartaud0Christophe ePerin1Brigitte eCourtois2Emilie eThomas3Sophia eHenry4Mathilde eBettembourg5Fanchon eDivol6Nadege eLanau7Florence eArtus8Charlotte eBureau9Jean-Luc eVerdeil10Gautier eSarah11Emmanuel eGuiderdoni12Anne eDievart13CIRADCIRADCIRADCIRADCIRADCIRADCIRADCIRADCIRADCIRADCIRADCIRADCIRADCIRADWe developed the PHIV-RootCell software to quantify anatomical traits of rice roots transverse section images. Combined with an efficient root sample processing method for image acquisition, this program permits supervised measurements of areas (those of whole root section, stele, cortex and central metaxylem vessels), number of cell layers and number of cells per cell layer. The PHIV-RootCell toolset runs under ImageJ, an independent operating system that has a license-free status. To demonstrate the usefulness of PHIV-RootCell, we conducted a genetic diversity study and an analysis of salt-stress responses of root anatomical parameters in rice (Oryza sativa L.). Using 16 cultivars, we showed that we could discriminate between some of the varieties even at the 6 day-old stage, and that tropical japonica varieties had larger root sections due to an increase in cell number. We observed, as described previously, that root sections become enlarged under salt stress. However, our results show an increase in cell number in ground tissues (endodermis and cortex) but a decrease in external (peripheral) tissues (sclerenchyma, exodermis and epidermis). Thus, the PHIV-RootCell program is a user-friendly tool that will be helpful for future genetic and physiological studies that investigate root anatomical trait variations.http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00790/fullrootricecell numberImage analysis softwaretissue areatransverse histological section |
| spellingShingle | Marc eLartaud Christophe ePerin Brigitte eCourtois Emilie eThomas Sophia eHenry Mathilde eBettembourg Fanchon eDivol Nadege eLanau Florence eArtus Charlotte eBureau Jean-Luc eVerdeil Gautier eSarah Emmanuel eGuiderdoni Anne eDievart PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification Frontiers in Plant Science root rice cell number Image analysis software tissue area transverse histological section |
| title | PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification |
| title_full | PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification |
| title_fullStr | PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification |
| title_full_unstemmed | PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification |
| title_short | PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification |
| title_sort | phiv rootcell a supervised image analysis tool for rice root anatomical parameter quantification |
| topic | root rice cell number Image analysis software tissue area transverse histological section |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2014.00790/full |
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