Sorry for polluting the list with this message which is to the attention of
Pedro, but I seem to be unable to send him any message directly.
SmartRoot is precisely the software I told you about in my previous
message. Based on the way you collect root samples, however, I am rather
sure that it will not be of any help, because it requires that you manually
specify which roots you want to measure. You really need something like
WinRhizo which can do a "brute-force" analysis and get global statistics.
The procedure I described in a previous message should really work as
WinRhizo uses a threshold routine to start its work.
Fell free to contact me if you would like to give a try to SmartRoot
anyway. The program is still beta and I am not willing to distribute it
right the way. But it is definitely my intention to make it freely
available as soon as it seems reasonable to do so.
Hope this helps,
Xavier.
At 11:56 AM 3/30/2006 +0100, you 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!
doce lar. Faça do Yahoo! sua homepage. http://br.yahoo.com/ homepageset.html
_______________________________________________________ Abra sua conta no
Yahoo! Mail: 1GB de espaço, alertas de e-mail no celular e anti-spam
realmente eficaz. http://br.info.mail.yahoo.com/
| 