Posted by
Michael Schmid on
Nov 29, 2015; 11:59am
URL: http://imagej.273.s1.nabble.com/Using-Find-Edge-Function-tp5015040p5015046.html
Hi Anonymous,
as I understand it, you can't get the object with Image>Adjust>Threshold,
but you see a closed outline with 'Find Edges'.
Withour 'Find Edges' there are several possibilities to preprocess before
Thresholding:
- Remove the background, e.g. Process>Subtract Background
- Apply an edge-preserving blur, e.g. the Thresholded Blur [1]
You can also run 'Find Edges', threshold the outline, and then use
'Analyze Particles' (on the areas including the inner holes). Or apply the
threshold and run 'Fill Holes' and then shrink it by half the width of the
outline (Process>Filters>Minimum), to get an area that is closer to the
original size.
Without 'Find Edges', you can also try the gradient threshold of the
Versatile Wand [2] (possibly after some [edge-preserving] smoothing).
If you are using Fiji, the Trainable Weka Segmentation might also help.
Without seeing the image, one can't say what is the best way...
Michael
[1]
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start[2]
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start_____________________________
On Fri, November 27, 2015 22:53, AMD123 wrote:
> Hello,
>
> How can I define ROI on boundaries of an object when it is not a composite
> ROI?
>
> I want the RIO to be the area inscribed in my object; so I used " find
> edge"
> and the edges were perfectly defined, but when I try to "create selection"
> I get this message " This command creates a composite selection from a
> mask
> ( 8-bit binary image with white background) or from an image that has been
> thresholded..."
>
> Thank you.
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