Image J Measurements

[Justin Bloomfield]

Hi,

I have just begun using ImageJ and was hoping there is someone out there
that may be able to help. I am hoping to utilise ImageJ to analyse a
variety of measurements on plant leaves. Such measurements I am after are;
- Width of Leaf
- Length of Leaf
- Length of Petiole
- Area of Leaf (excluding Petiole)
- Length of Lobes

I am hoping to be able to write (or modify) a macro so as this can be done
automated as there are about 5000 samples that need to be analysed.

This is to be used by the University of Tasmania, Australia, and so the
final macro will be freely available to anyone.

Thanks,
Justin Bloomfield
[hidden email]

[Marcel]

Hello Justin,

there are several plugins available which can help you to do
this. But you have to give a little bit more information.
For example are the leaves in single images or not?
A sample of an image could also be helpful for others to give
you tips how to seperate the different parts of the leaf.

Macros can easily be recorded and created with ImageJ
and a lot of measurements options are available in
the Analyse->Set measurements dialog.
(see the ImageJ wiki and the documentation!)

To apply your created macro to multiple images this easy
to use plugin maybe does the trick.
http://ciar.rcm.upr.edu/projects/imageJ
But there are also other macros available.

To seperate the different part of the leaves if it is a rgb image
the Threshold colour plugin can be also very useful.
http://www.dentistry.bham.ac.uk/landinig/software/software.html

In addition for a preprocessing a very useful extraction tool can be found in Gimp >=2.4
to automatically select areas of leaves (siox).

But again a sample could be very useful to get
more suggestions from other people.