Root

[Pedro Miguel César de Carvalho]

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 

[Sullivan, Michael J (College of Med.)]

Pedro, ImageJ is useful in analyzing virtually any image -- the key word is image.  If you have the information about the root system in image form then you can apply ImageJ's tools to quantify it -- at least in a comparative way. --- Mike

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Pedro Miguel César de Carvalho
Sent: Tuesday, March 28, 2006 5:40 PM
To: [hidden email]
Subject: Root

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 

[Robert Baer]

>   Do you know if I can use ImageJ to analyse plant root systems
> morphology (Area, volume and diameter).

This should be entirely possible, but its complexity will depend on the
images you have for input, and the details of what you want to accomplish.
You may wish to open an image (or some images) and take a look at:

Image>Type>8-bit
Image>Threshold
Analyze>Set Scale
Analyze>Set Measure
Analyze>Measure

If and when you get the right kind of things look at:
Plugins>Macro>Record

To do volumes you will need some serial slices through the root system.  You
will likely build these into z-axis stack by opening them all and then doing
Images>Stacks>convert images to stacks.

As you can see there will be considerable complexity, and you may need to
extend ImageJ to take care of specific needs related to your project.  If
you are lucky you will find a plugin someone else has already written at
http://rsb.info.nih.gov/ij/plugins/index.html, but as likely as not, you
will end up writing a macro or plugin to make you task do-able, or at least
more seamless.

HTH,
Rob

[Pedro Miguel César de Carvalho]

Thanks Mike.

I tried to use imageJ on a simulated root system, but from the  
parameters I need to study, root area, volume, total length,  
diameter, I only found area! There is any "automatically" way to get  
this information (plug-in or something). There is another variable on  
the study of roots very useful, root length by diameter class, does  
anyone tried to do something similar? The study of roots is very  
similar to the study of other mathematical trees, like rivers, so  
maybe there is someone that knows how to do it. Sorry about this, but  
I am doing my PhD in roots, we usually use WinRhizo software for this  
kind of studies, but I am a Mac user and there is no application to  
do it on Mac Os X.

Thanks

Pedro

On 29 Mar 2006, at 13:56, Sullivan, Michael J (College of Med.) wrote:

> Pedro, ImageJ is useful in analyzing virtually any image -- the key  
> word is image.  If you have the information about the root system  
> in image form then you can apply ImageJ's tools to quantify it --  
> at least in a comparative way. --- Mike
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf  
> Of Pedro Miguel César de Carvalho
> Sent: Tuesday, March 28, 2006 5:40 PM
> To: [hidden email]
> Subject: Root
>
> 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

               
_______________________________________________________
Novo Yahoo! Messenger com voz: Instale agora e faça ligações de graça.
http://br.messenger.yahoo.com/

[Dong-Hyun Kim]

Hi guys,

I'm struggling in dealing with stack of images having little bit of drift.
My wish is to compensate this drift, to keep the position of pattern in
images at the same location.
Could you recommend any relevant plug-in or smart way of doing this ?
Thanks a lot in advance.

Dong-Hyun

[Xavier Draye-2]

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

[Sullivan, Michael J (College of Med.)]

Padro, are all the images done? Can you still take more? The measurements you are after such as volume could be done with images taken axially - slice after slice then added up. As far as plugins your best bet could be to spend some time exploring the plugin list at: http://rsb.info.nih.gov/ij/plugins/  --- Mike

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Pedro Miguel César de Carvalho
Sent: Wednesday, March 29, 2006 9:08 AM
To: [hidden email]
Subject: Re: Root

Thanks Mike.

I tried to use imageJ on a simulated root system, but from the parameters I need to study, root area, volume, total length, diameter, I only found area! There is any "automatically" way to get this information (plug-in or something). There is another variable on the study of roots very useful, root length by diameter class, does anyone tried to do something similar? The study of roots is very similar to the study of other mathematical trees, like rivers, so maybe there is someone that knows how to do it. Sorry about this, but I am doing my PhD in roots, we usually use WinRhizo software for this kind of studies, but I am a Mac user and there is no application to do it on Mac Os X.

Thanks

Pedro

On 29 Mar 2006, at 13:56, Sullivan, Michael J (College of Med.) wrote:

> Pedro, ImageJ is useful in analyzing virtually any image -- the key
> word is image.  If you have the information about the root system in
> image form then you can apply ImageJ's tools to quantify it -- at
> least in a comparative way. --- Mike
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Pedro Miguel César de Carvalho
> Sent: Tuesday, March 28, 2006 5:40 PM
> To: [hidden email]
> Subject: Root
>
> 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

               
_______________________________________________________
Novo Yahoo! Messenger com voz: Instale agora e faça ligações de graça.
http://br.messenger.yahoo.com/

[Pedro Miguel César de Carvalho]

Thank for your reply Xavier,
My roots are grown in 15 x 150 cm columns with sandy loam soil. The  
root extraction procedure is very simple, first I open the column in  
two halves, and then I take slices of soil (5 of 20 cm and 2 of 25  
cm), I first clean the roots with a Delta-t root washer (http://
www.delta-t.co.uk/products.html?product2005092818891) after that I do  
a manual fine clean. Than we have a A4 transparency root scanner. The  
images that we will get are in Tiff format, gray scale (256 grays) at  
300 dpi. The good thing of WinRhizo is that it does everything  
without knowing nothing about it, I think that I can get the  
algorithms of WinRhizo from the users manual, maybe then it maybe  
possible to develop a new plugin for ImageJ. Unfortunately the images  
I have know are in a Windows 98 PC without internet and CD-R, it just  
have Zip drive, that I do not have in my PowerBook. I have to install  
the driver of my USB disk on the PC then I can send you the images,  
but they are grayscale very clean root pictures. There is a clear  
distinction between the root (usually dark grey or black) and the  
background (usually white or very light grey), the problem is only  
the white tips that even the WinRhizo can't differentiate from the  
background  automatically, but adjusting the threshold or manually  
editing the image in photoshop we can make the software understand  
what is root and what is background.

Pedro

[Pedro Miguel César de Carvalho]

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/

[dksamuel]

Available at
http://www.crop-roots.org/assets/SmartRoot-Setup.exe
http://www.crop-roots.org/assets/Simulator.zip
both are nice, I download both and am using them, regards Samuel India

On 3/30/06, Pedro Miguel César de Carvalho <[hidden email]> 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/
>

[Xavier Draye-2]

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/

[Pedro Miguel César de Carvalho]

Thanks Xavier, I want to give a try on SmartRoot. Can you send it?

[hidden email]

Cheers

Pedro


On 31 Mar 2006, at 12:13, Xavier Draye wrote:

> 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.
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