Re: Root

>   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