> 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
>>
>>
>>
>>
>>
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