Posted by
John Cahill on
Apr 26, 2013; 2:15pm
URL: http://imagej.273.s1.nabble.com/analyze-particles-exclude-holes-tp5002812p5002817.html
Hi Helmut,
The result also depends on whether you consider white as the object or the
background.
There are at least two places in ImageJ you have the opportunity to specify
which to want.
*Process>Binary>Options**
*This submenu contains commands that create or process binary (black and
white) images. They assume that objects are black and background is white
unless "Black Background" is checked in the dialog box.
*Image>Adjust>Threshold* tool,
a dialog pops up that lets you specify which pixels are set to the
background color and which to the foreground color, and whether the
background is black and the foreground is white.
As I understand, ImageJ was originally written with the convention of black
object and white background.
Then it was recognised some users required the inverse so these check boxes
were included.
Hope this helps
John
On Fri, Apr 26, 2013 at 9:15 AM, Michael Schmid <
[hidden email]>wrote:
> Hi Helmut,
>
> assuming you particles are not embedded in a frame, which would make it
> one big particle, the size of the frame (this is hard to see in your
> thumbnails):
>
> The measurements are done correctly:
> If I convert your image with thick outlines to 8-bit-grayscale, threshold
> it and run 'Analyze particles' with 'include holes' unchecked, I get the
> result for the thick outlines only. E.g. the 'Mean' brightness is about 10
> (very dark), maximum brightness is 127 or 129 (the threshold).
>
> If I select 'include holes', the maximum brightness is 255 (white in the
> interior) and the 'Mean' brightness is in the 66-104 range.
>
> You did not say it, but I guess that your second image is the result of
> 'show outlines'?
> Well, that's a question what you define as 'Outline'.
> Wikipedia says, "Outline drawing" is "a sketch depicting the outer edges
> of a person or object, without interior details or shading". So one would
> not expect interior edges, I guess?
>
> If you select 'Masks' as output, you will see the area that actually gets
> analyzed.
>
> Michael
> ________________________________________________________________
> On Apr 26, 2013, at 14:45, Helmut Bergen wrote:
>
> > Hello
> >
> > I try to do analyze particles and don't understand why ImageJ don't'
> exclude
> > holes, although I didn't check the "include holes" button.
> >
> > For example this picture.
> >
> > And the result is:
> >
> > Where is the mistake???
> >
> >
> >
> > Thanks for helping and best wishes
> >
> > Helmut
>
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