Re: Root

Available at
http://www.crop-roots.org/assets/SmartRoot-Setup.exe
http://www.crop-roots.org/assets/Simulator.zip
both are nice, I download both and am using them, regards Samuel India

On 3/30/06, Pedro Miguel César de Carvalho <pmccarvalho@xxxxxxxxxxxx> wrote:
>
> I saw a reference about SmartRoot plugin for ImageJ (http://www.crop-
> roots.org/assets/Epreuve%20de%20confirmation.doc), does anybody knows
> where can I get it.
>
> Thanks
>
> Pedro
>
> On 29 Mar 2006, at 21:51, Xavier Draye wrote:
>
> > Hallo Pedro,
> >
> > All depends on the kind of images that you have or are planning to
> > have. If you have been able to extract the intact root system from
> > the growing medium, have access to a transparency scanner to get
> > very well contrasted images and have enough time to prepare the
> > root material on the scanner to get rid of most of the ennoying
> > overlappings of your roots, then the solutions suggested by Michael
> > and Robert will work really well and will provide you with global
> > statistics on root system morphology. This is exactly what is
> > implemented in commercial software like WinRhizo, and you can get
> > similar data using ImageJ.
> >
> > If you are interested in length distribution among diameter
> > classes, I would suggest getting a mask of the root system
> > (Threshold), then get a skeleton and also get a distance map. You
> > can then AND the skeleton and the distance map to get the skeleton
> > with each pixel value being the radius of the root at that
> > location. I would then try to discretize the radius in radius
> > classes, successively select the sub-skeleton that belong to each
> > class and, for each class, calculate the cumulated perimeter of the
> > sub-skeleton.
> >
> > However, if you are more interested in quantifying specific
> > features on specific roots (which assumes that you have some a
> > priori knowledge on root morphology and you are therefore able to
> > sample your root system image and focus on a limited number of
> > roots) and especially if your images contains a lot of "parasit"
> > objects or have a structured background (like when you grow plants
> > on agar or you get pictures through a petry dish that get a lot of
> > scratches...) of if you have a lot of root overlapping, then one
> > solution is an interactive software that allows you to pick
> > specific roots, to fine tune the tracing of that root, to collect
> > information and to send them to some kind of database system
> > (because this way of working will supply you with a lot of
> > information). SmartRoot is an ImageJ plugin that does exactly that
> > (in addition to being a root annotation program). We have used
> > SmartRoot with scanner images of barley, lupin, maize, and
> > arabidopsis (if you have sufficient resolution - a root should be
> > minimum 5 pixels thick if you want to get the best results).
> >
> > I will probably be slow in answering your messages because I am
> > quite overloaded for the moment, but let me know if you are
> > interested. Probably what you could do is send me a typical of your
> > images and explain what measurements you would like to get and I
> > will tell you if SmartRoot would be helpfull or not.
> >
> > Cheers,
> >
> > Xavier.
> >
> > At 11:39 PM 3/28/2006 +0100, you wrote:
> >> Dear all,
> >>  Do you know if I can use ImageJ to analyse plant root systems
> >> morphology (Area, volume and diameter).
> >>
> >> Thanks
> >>
> >> Pedro
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________________ Yahoo!
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>
>
>
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