How to provide a segmented image to wndchrm

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What steps will reproduce the problem?
1. Create Signature on image with an object only part of it
2. Create Signature on same image but with more background area
3. Comparison of both shows many non-identical values

What version of the product are you using? On what operating system?
wndchrm 1.30-243 on Debian Linux Testing

In your publication you write:
"If segmentation of the subjects (e.g., cell segmentation,
bone segmentation, etc) is required, the user has to apply
a first step of segmentation using a designated utility. The
output of the utility (the segmented subjects) can be used
as input for wndchrm, rather than the original images."
How can it be done?

Original issue reported on code.google.com by erwin.ga...@gmail.com on 19 Aug 2011 at 9:19

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Original comment by christop...@nih.gov on 10 Jun 2012 at 6:18

• Changed state: Done

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I do not understand why this issue has been closed. I still have no idea how to 
provide the segmented part of an image unless it is a rectangle and can be 
cropped out.

Please tell me if irregular segmented shapes can be used or not?

Thanks

Original comment by erwin.ga...@gmail.com on 6 Aug 2012 at 2:53