use of imageJ for herbivory assessment

[Jonathan Rosenthal]

Hello all,
    I'm attempting to use ImageJ to analyze scanned images of leaves in
order to assess percentage of leaf area lost to herbivory.  In so
doing, I've encountered two problems already (and I've just started):
1) The "wand" tool, selected from the toolbar, will, at most outline
only one hole per leaf, will not outline the leaf perimeter, and, more
generally, is often completely non-responsive; and 2) in trying to use
a mouse or trackpoint to control the "freehand" tool from the toolbar
to outline the leaf perimeter (or reconstruct an eaten leaf perimeter),
my hand clearly is not steady enough to closely follow the path that I
desire.     I would greatly appreciate it if anyone would suggest
either alternatives to these 2 tools, or ways that I can use them more
effectively.  Also, if you know of a standard protocol for herbivory
assessment that's compatible with the current version of ImageJ, that
would probably solve all of my problems.
          Thanks very much,
          Jonathan Rosenthal

[Justin McGrath]

Hi Jonathon,
Are you thresholding the images first?  The wand tool will only select
a group of pixels that have the same value.  If your pictures look
good and have even illumination and good contrast with the background,
convert them to greyscale then use Image->Adjust->Threshold.  If
they're already binary, try clicking slightly outside of the leaf
instead of in the interior.  I find that it works better.

If you're finding it hard to threshold the images because of uneven
illumination, I have a plugin that uses something like NDVI to create
an index of greeness that may make it easier.

You probably already know this, but just in case.  When you use the
measure command, it doesn't include interior holes, so you'll  have to
measure each hole and subtract from the total.  I don't know of a way
to make it not include interior holes (the analyze particles tool can
do it though), but it would be a nice addition to the measure command.

Justin

On 1/15/07, Jonathan Rosenthal <[hidden email]> wrote:

> Hello all,
>     I'm attempting to use ImageJ to analyze scanned images of leaves in
> order to assess percentage of leaf area lost to herbivory.  In so
> doing, I've encountered two problems already (and I've just started):
> 1) The "wand" tool, selected from the toolbar, will, at most outline
> only one hole per leaf, will not outline the leaf perimeter, and, more
> generally, is often completely non-responsive; and 2) in trying to use
> a mouse or trackpoint to control the "freehand" tool from the toolbar
> to outline the leaf perimeter (or reconstruct an eaten leaf perimeter),
> my hand clearly is not steady enough to closely follow the path that I
> desire.     I would greatly appreciate it if anyone would suggest
> either alternatives to these 2 tools, or ways that I can use them more
> effectively.  Also, if you know of a standard protocol for herbivory
> assessment that's compatible with the current version of ImageJ, that
> would probably solve all of my problems.
>           Thanks very much,
>           Jonathan Rosenthal
>

[Kenneth Sloan-2]

On Jan 15, 2007, at 12:49 AM, Jonathan Rosenthal wrote:

> Hello all,
>    I'm attempting to use ImageJ to analyze scanned images of leaves  
> in order to assess percentage of leaf area lost to herbivory.  In  
> so doing, I've encountered two problems already (and I've just  
> started): 1) The "wand" tool, selected from the toolbar, will, at  
> most outline only one hole per leaf, will not outline the leaf  
> perimeter, and, more generally, is often completely non-responsive;  
> and 2) in trying to use a mouse or trackpoint to control the  
> "freehand" tool from the toolbar to outline the leaf perimeter (or  
> reconstruct an eaten leaf perimeter), my hand clearly is not steady  
> enough to closely follow the path that I desire.     I would  
> greatly appreciate it if anyone would suggest either alternatives  
> to these 2 tools, or ways that I can use them more effectively.  
> Also, if you know of a standard protocol for herbivory assessment  
> that's compatible with the current version of ImageJ, that would  
> probably solve all of my problems.
>          Thanks very much,
>          Jonathan Rosenthal

Sometimes, the right solution requires moving sideways.  Let me ask  
what might be a silly question:

Are you using a mouse?

If so, consider getting a tablet.

That will not solve the software problems you are having - but it  
will definitely fix the "unsteady hand" problem.

--
Kenneth Sloan                                          
[hidden email]
Computer and Information Sciences                        [phone]
University of Alabama at Birmingham              FAX [phone]
Birmingham, AL 35294-1170                http://www.cis.uab.edu/sloan/

[Martin Wessendorf]

> On Jan 15, 2007, at 12:49 AM, Jonathan Rosenthal wrote:
>
>    I'm attempting to use ImageJ to analyze scanned images of leaves in
> order to assess percentage of leaf area lost to herbivory.  In so
> doing, I've encountered two problems already (and I've just started):
> 1) The "wand" tool, selected from the toolbar, will, at most outline
> only one hole per leaf, will not outline the leaf perimeter, and, more
> generally, is often completely non-responsive; and 2) in trying to use
> a mouse or trackpoint to control the "freehand" tool from the toolbar
> to outline the leaf perimeter (or reconstruct an eaten leaf
> perimeter), my hand clearly is not steady enough to closely follow the
> path that I desire.     I would greatly appreciate it if anyone would
> suggest either alternatives to these 2 tools, or ways that I can use
> them more effectively.  Also, if you know of a standard protocol for
> herbivory assessment that's compatible with the current version of
> ImageJ, that would probably solve all of my problems.

My guess is that the variability between leaves in your data will be
sufficient that making precise measurements of each leaf will be
unnecessary.  If that's the case, you can very quickly and easily
estimate the cross-sectional area of a leave by point-counting--just use
the "draw line or point grids" plug-in to cast a grid across the leaf.
Then count the number of grid intersections (or points) that fall within
the leaf.  That technique is referred to as "point counting"; the number
will provide a very quick and easy estimate of the area.  (You might
even be able to automate the point-counting by using the
"colocalization" plug-in to identify points that overlie the leaf, and
then "analyze" to count the overlaying points.)

For more on point-counting, on precision vs. variability, etc., see
Howard and Reed's "Unbiased Stereology".

Good luck!

Martin Wessendorf
--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455             E-mail: martinw[at]med.umn.edu

[Mario Guarracino]

Hello Jonathan,
Yawi (http://yawi3d.sourceforge.net) provides an enhanced magic wand for
ImageJ. It has been implemented to segment tumor masses (lymphoma) in CT
images or stacks. Current version, released last December, provides
functionalities that might handle your problem of easily outlining the leaf
parameter.

Mario Guarracino

> -----Messaggio originale-----
> Da: ImageJ Interest Group [mailto:[hidden email]] Per conto di
> Jonathan Rosenthal
> Inviato: Monday, January 15, 2007 7:49 AM
> A: [hidden email]
> Oggetto: use of imageJ for herbivory assessment
>
> Hello all,
>     I'm attempting to use ImageJ to analyze scanned images of leaves in
> order to assess percentage of leaf area lost to herbivory.  In so
> doing, I've encountered two problems already (and I've just started):
> 1) The "wand" tool, selected from the toolbar, will, at most outline
> only one hole per leaf, will not outline the leaf perimeter, and, more
> generally, is often completely non-responsive; and 2) in trying to use
> a mouse or trackpoint to control the "freehand" tool from the toolbar
> to outline the leaf perimeter (or reconstruct an eaten leaf perimeter),
> my hand clearly is not steady enough to closely follow the path that I
> desire.     I would greatly appreciate it if anyone would suggest
> either alternatives to these 2 tools, or ways that I can use them more
> effectively.  Also, if you know of a standard protocol for herbivory
> assessment that's compatible with the current version of ImageJ, that
> would probably solve all of my problems.
>           Thanks very much,
>           Jonathan Rosenthal