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RootTrace specifications

Information


Unique identifier OMICS_12621
Name RootTrace
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Programming languages C++
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Download


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Versioning


No version available

Maintainer


  • person_outline Andrew French

Publication for RootTrace

RootTrace citations

 (8)
library_books

The plant hormone ethylene restricts Arabidopsis growth via the epidermis

2018
Proc Natl Acad Sci U S A
PMCID: 5924893
PMID: 29643073
DOI: 10.1073/pnas.1717649115

[…] e assessed on 6-d-old seedlings grown on 1/2 MS medium containing 1% sucrose and supplemented with 100 nM IAA under a 16-h/8-h photoperiod.The plates were imaged, and the seedlings were analyzed with RootTrace () or/and ImageJ (NIH; https://imagej.nih.gov/ij/) software. At least 20 individuals per line and per treatment were analyzed in each experiment. […]

library_books

Phenotyping field state wheat root system architecture for root foraging traits in response to environment×management interactions

2018
Sci Rep
PMCID: 5805786
PMID: 29422488
DOI: 10.1038/s41598-018-20361-w

[…] advancement of RSA-related phenome research has promoted the provision of a number of modern tools, many of which were resorted to computer science or image processing, e.g. DART, SmartRoot, RootNav, RootTrace, RhizoScan, RootSystemAnalyser. As these platforms are largely varied from one to another, cross-platform protocols are needed, paving a way for inter-platform exchanges of information, e.g. […]

library_books

Deep machine learning provides state of the art performance in image based plant phenotyping

2017
GigaScience
PMCID: 5632296
PMID: 29020747
DOI: 10.1093/gigascience/gix083

[…] stem analysis [] and is often omitted from image analysis software due to the challenges localization presents. As another example, locating seed feature points must occur before automated tracing in RootTrace (RootTrace, RRID:SCR_015585) []. Localization of the different biological feature classes for a shoot is vital in capturing the architecture of the plant, essential for phenotyping. We also […]

call_split

Advancements in Root Growth Measurement Technologies and Observation Capabilities for Container Grown Plants

2015
PMCID: 4844396
PMID: 27135334
DOI: 10.3390/plants4030369
call_split See protocol

[…] ntified from whole root systems or specific roots of interest []. Several sophisticated image analysis programs have been developed to measure plant root system architecture and traits; these include RootTrace, REGR analysis, Kine-Root, and Root FlowRT. These programs focus on analyzing root growth and architecture from a time series of images and are extremely useful for measuring effects of temp […]

library_books

Characterizing root response phenotypes by neural network analysis

2015
J Exp Bot
PMCID: 4585416
PMID: 26019255
DOI: 10.1093/jxb/erv235

[…] her specific software for measuring global root characteristics. A number of such packages provide information on type-specific root number and length or growth dynamics, for example RootReader2D (), RootTrace (), or WinRhizo (). In fact Sholl analysis represents a potentially useful additional tool for commercial root analysis software, because it captures interactive and responsive properties of […]

library_books

Rhizoslides: paper based growth system for non destructive, high throughput phenotyping of root development by means of image analysis

2014
Plant Methods
PMCID: 4105838
PMID: 25093035
DOI: 10.1186/1746-4811-10-13

[…] pped working immediately after starting the analysis. We tested whether it would work with different image formats or resolution and requests assistance from the developer, which remained unanswered. RootTrace [] could not be successful installed in spite of intense support by the developer. The software DART [] could be installed, but not opened. Our help request was answered with the comment tha […]

Citations

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RootTrace institution(s)
Centre for Plant Integrative Biology, University of Nottingham, Nottingham, UK; School of Computer Science, Jubilee Campus, University of Nottingham, Nottingham, UK
RootTrace funding source(s)
This work was supported by the Biotechnology and Biological Sciences Research Council and the Engineering and Physical Sciences Research Council as part of their Systems Biology Initiative to establish a number of Centres for Integrative Systems Biology.

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