Sorry for polluting the list with this message which is to the attention of
message. Based on the way you collect root samples, however, I am rather
specify which roots you want to measure. You really need something like
WinRhizo which can do a "brute-force" analysis and get global statistics.
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
>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
>>>
>>>
>>>
>>>
>>>
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>
>
>
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