Less Filling

[Sullivan, Michael J (College of Med.)]

Please excuse the flippant subject line.  I've scoured the archives and
tried the Connected Threshold Growing plugin from the 3D-Toolkit and can't
find exactly what I want.  What I want is the function of starting a
plugin / macro that has a dialog, in which I set a upper and lower
threshold value.  I'm then able to click on a pixel in the current image
and have a connected growth of all the pixels that have values between
these thresholds.  The 3D-TK essentially does this; but what it also does
is it identifies them in a second "binary" image (i.e. I don't know what
the original values were) and a histogram only shows the counts of 0 and
255 valued pixels.  Never one to enjoy reinventing the wheel I'm wondering
if I'm not finding an already built plugin or if there is a adjustment to
the 3D-TK which I can make.  If not I guess I'll use as much of the 3D-TK
code that I can and develop my own.  --- Mike

[Gabriel Landini]

On Tue, 29 Nov 2005, Michael Sullivan wrote:

> What I want is the function of starting a
> plugin / macro that has a dialog, in which I set a upper and lower
> threshold value.  I'm then able to click on a pixel in the current image
> and have a connected growth of all the pixels that have values between
> these thresholds.

I wonder if this may help.
1. Open a greyscale image
2. bring up the Adjust Threshold dialog and move the boundary thresholds.
This will show in red the threshoded areas.
3. select the Wand tool and click on the image where you want to select
the area.
The wand selects the thresholded area (it appears with a yellow perimeter.

Now you have 2 options
4a. Fill the area (the connected area will be in the foreground colour)
4b. Go to Edit Selection Make Inverse and fill (this will leave the
connected area as original and fill the rest with the foreground colour.

Cheers

Gabriel

[Albert Cardona]

Gabriel, this is a very nice hack, but there is one problem: if there
are holes, they will be included as well in the Wand selection, since
the Wand doesn't out-ROI the holes in its selections.

Albert

[Gabriel Landini]

On Wednesday 30 November 2005 16:08, Albert Cardona wrote:
> Gabriel, this is a very nice hack, but there is one problem: if there
> are holes, they will be included as well in the Wand selection, since
> the Wand doesn't out-ROI the holes in its selections.

Not necessarily. Here is another hack.
I use black background and white foreground.

Duplicate the image.
Do as before: Adjust threshold, wand the blob, Make inverse, Fill, Invert.
Now the blob remains in the original grey levels but includes holes, the
background is black.
However the red threshold is still maintained, so do this:
Make Inverse (again, so the blob is selected) and apply the threshold making
sure that the 2 top checkboxes are checked, but the third one is not.
This will make a white blob that does not include the holes (they are black
now).
If you need the original grey levels, then AND this image with the duplicate
you already did.
This will work as far as the object does not include 0 grey level pixels, but
one can be 'creative' about this (for instance add 1 before processing or
similar).

Cheers,

Gabriel

[Wayne Rasband]

> Gabriel, this is a very nice hack, but there is one problem: if
> there are holes, they will be included as well in the Wand
> selection, since the Wand doesn't out-ROI the holes in its selections.

The Measure command excludes holes if "Limit to Threshold" is checked
in the the Set Measurements dialog box.

-wayne