analyze particles exclude holes

[Helmut Bergen]

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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[Jean-Philippe Grossier]

Hi,

there is no mistake, imagej found 3 particles. If you ask imageJ to measure
area then you will find a difference between "include holes" ticked or not.

include holes just tell imageJ if it should consider the object filled
entirely or not.

if you want to exclude this kind of donut shape from your analysis,
unticked include holes And put a minimum criteria on the area (the best
would be a criteria based on a ratio area/perimeter, but you have to do it
after the particle analysis).


jean-philippe Grossier


2013/4/26 Helmut Bergen <[hidden email]>

> 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
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Michael Schmid]

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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[John Cahill]

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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[jool]

I think I have a similar issue. The thing is, I am interested in measuring the perimeter of the particles including any holes they might have. If I only have a single particle I can measure the perimeter of the particle, then treshold the image and measure the perimeter of the hole and add the two. The thing is, I have 10-50 particles pr image, som with holes and some without. Any suggestions?