Re: Root

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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