Thanks Xavier, I want to give a try on SmartRoot. Can you send it?
> 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/Abra sua conta no Yahoo! Mail: 1GB de espaço, alertas de e-mail no celular e anti-spam realmente eficaz.