Posted by
Martin Wessendorf on
URL: http://imagej.273.s1.nabble.com/use-of-imageJ-for-herbivory-assessment-tp3700587p3700590.html
> 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: (612) 626-0145
Assoc Prof, Dept Neuroscience lab: (612) 624-2991
University of Minnesota Preferred FAX: (612) 624-8118
6-145 Jackson Hall, 321 Church St. SE Dept Fax: (612) 626-5009
Minneapolis, MN 55455 E-mail: martinw[at]med.umn.edu