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Protocols

KineRoot specifications

Information


Unique identifier OMICS_12620
Name KineRoot
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Programming languages MATLAB
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Dr. Anupam Pal

Publication for KineRoot

KineRoot citations

 (6)
library_books

The build up of osmotic stress responses within the growing root apex using kinematics and RNA sequencing

2016
J Exp Bot
PMCID: 5100013
PMID: 27702994
DOI: 10.1093/jxb/erw350

[…] without any manipulation of the root or pause in the growth monitoring. Images were taken every 6min (Supplementary Fig. S2A). Raw velocity profiles were obtained by particle image velocimetry, using Kineroot (). The velocity profile along the root apex was interpolated with a cubic smoothing spline (smooth.spline, spar 0.5, ). The elemental elongation rate (EER) profile was calculated by spatiall […]

library_books

3D deformation field in growing plant roots reveals both mechanical and biological responses to axial mechanical forces

2016
J Exp Bot
PMCID: 5066484
PMID: 27664958
DOI: 10.1093/jxb/erw320

[…] ations within the mature zone.Analyses were performed using custom scripts and programs written in R and Matlab (Matlab R2011b, v7.13.0.564). Particle image velocimetry analysis was carried out using Kineroot software (). […]

library_books

Length and activity of the root apical meristem revealed in vivo by infrared imaging

2014
J Exp Bot
PMCID: 4339598
PMID: 25540436
DOI: 10.1093/jxb/eru488

[…] e (Nikon, v1.3). Shots were taken during at least 4–5h per root. Raw velocity profiles were obtained by particle image velocimetry, from the monitoring of mark displacement along the root apex, using Kineroot and the highest correlation coefficient search algorithm (, Matlab R2011b, v7.13.0.564). Depending on the root and on the time point, velocity profiles were either sigmoidal, bilinear, or a v […]

library_books

Very high resolution time lapse photography for plant and ecosystems research1

2013
Appl Plant Sci
PMCID: 4103149
PMID: 25202588
DOI: 10.3732/apps.1300033

[…] rest. Currently, extracting quantitative data from time-lapse sequences involves user interpretation and manipulation of individual frames using software such as ImageJ (http://rsbweb.nih.gov/ij/) or KineRoot (), and there is a distinct need for tools to automate quantitative data extraction from high-resolution images (). […]

library_books

High throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype

2011
Genome Biol
PMCID: 3129668
PMID: 21457493
DOI: 10.1186/gb-2011-12-3-219

[…] gital reconstruction of root systems and have potentially increased the levels of throughput for phenotyping in plants. Examples of software that allow higher-throughput phenotyping are RootTrace [], KineRoot [], SmartRoot [], RootLM [], Phytomorph [,], RootFlow [] and WinRhizo [].Many high-throughput methods have been developed for Arabidopsis, aided by its small size. For crop plants, an automat […]

call_split

Monitoring the regulation of gene expression in a growing organ using a fluid mechanics formalism

2010
BMC Biol
PMCID: 2845557
PMID: 20202192
DOI: 10.1186/1741-7007-8-18
call_split See protocol

[…] set close to the root for calibration. After a 1 h rest, a series of pictures was taken at 10 min intervals under a 'safe' green light (switched on for 1 min every 10 min). The MATLAB-based software Kineroot [] was used to track the displacement of graphite particles over space and time and determine the velocity (the local rate of longitudinal displacement due to growth of cells along the growth […]

Citations

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KineRoot institution(s)
Intercollege Program in Plant Biology, Pennsylvania State University, University Park, PA, USA; Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
KineRoot funding source(s)
This work was supported by U.S. Agency for International Development Bean/Cowpea Collaborative Research Support Program.

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