Stack? Flatten? Overlay? How to superimpose mask

Posted by Sheryn Olson on
URL: http://imagej.273.s1.nabble.com/Stack-Flatten-Overlay-How-to-superimpose-mask-tp5001011.html

Hello all,

I need to quantify % coverage of vegetation, snow over an image of a
snowshoe hare.  I believe I need to mask the hare outline, but short of
drawing an outline on the photo, I can't determine how.   The
quantification part will be simple.  But I'm struggling with defining the
region of interest.   One person suggested convolution, another suggested
drawing the outline, but the problem is - I don't always have the whole
hare visible, so it needs to be outlined or masked with a predefined
outline.

Attached is one hare photo (of thousands).
[image: Inline image 2]


My roi file is a clean outline of the hare, but how to match it to the
photo(s)?.    I don't know how to manipulate the ROI to match the hare
outline in the photo;  I can move the ROI and resize it, but not "pull" it
out of proportion to match the photo.    (a click and drag would be great!)

Then how to incorporate it into the image to define the ROI.  ??

Thanks all

---
Sheryn Olson
Graduate Research Assistant
Department of Wildlife Ecology
The University of Maine
210 Nutting Hall
Orono, ME 04469

[phone]
[phone] cell

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