Delaunay update

[dscho]

Dear ImageJ users,

I updated the Delaunay plugin (due to popular demand), to be able to
export the Delaunay lines into the results table.  Please find the plugin
here:

        http://pacific.mpi-cbg.de/wiki/index.php/Delaunay_Voronoi

Ciao,
Dscho

[karo03]

Hi, Image analysis and -J experts,

I have an example were I don't fully understand the routines "Analyze  
Particle ..." and "Wand (tracing) Tool"!

The image http://picasaweb.google.com/lh/photo/8Yo_5vJ1zLKZGwP22oDgsw 
delivers under "Analyze Particle ..." three particles (white is  
foreground). That is understandable, seemingly eight-connected  
neighborhood (of foreground) is assumed. Possibly four-connectedness  
could be helpful in such cases with thin lines dividing the particles.

But now, trying to overcome this problem by selecting the particles  
with "Wand (tracing) Tool", possibly in a macro, I run into  
difficulties. Clicking into particles on the left side of the image  
selection is okay, Wand is using 4-connectedness! Clicking into one of  
the two right-most particles seemingly wand is selecting background!

Is there any way to select one of these two right-most particles?

Help is appreciated
Regards
Karsten

[Gabriel Landini]

On Thursday 27 November 2008 16:57:39 Karsten Rodenacker wrote:

> Hi, Image analysis and -J experts,
>
> I have an example were I don't fully understand the routines "Analyze
> Particle ..." and "Wand (tracing) Tool"!
>
> The image http://picasaweb.google.com/lh/photo/8Yo_5vJ1zLKZGwP22oDgsw
> delivers under "Analyze Particle ..." three particles (white is
> foreground). That is understandable, seemingly eight-connected
> neighborhood (of foreground) is assumed. Possibly four-connectedness
> could be helpful in such cases with thin lines dividing the particles.

I think that your image has 4-conn particles. If you run Particles4 plugin with the label option you will get 20 particles.
If you created this with a watershed/skeletonisation, then to make it easier, you could use a 4-conneected watershed (which should give 8-connected particles).

If you analyse the image with the Particles8 plugin you get only 3 particles.

> But now, trying to overcome this problem by selecting the particles
> with "Wand (tracing) Tool", possibly in a macro, I run into
> difficulties. Clicking into particles on the left side of the image
> selection is okay, Wand is using 4-connectedness! Clicking into one of
> the two right-most particles seemingly wand is selecting background!
>
> Is there any way to select one of these two right-most particles?

That is a job for the BinaryReconstruct4 plugin in the Morphology collection. Now this is not compiled into a class, because I have not had time to test it thoroughly. If you test it, please send me some feedback.

You could get the XStart YStart points with Particles4, then create a new image with those pixels set for the particles you want to select and BinaryReconstruct4 with the original as mask and the new image as seed.

I hope it helps.

Gabriel

[Michael Schmid]

Hi Karsten,

funny enough, the wand behaves like "analyze particles" (8-connected)  
if I threshold the image.
Without thresholding, I can reproduce your observations concerning 4-
connected wand selection.

I could not reproduce selecting the background when clicking one of  
the particle at the right side, neither with nor without threshold.

Michael
________________________________________________________________

On 27 Nov 2008, at 17:57, Karsten Rodenacker wrote:

> Hi, Image analysis and -J experts,
>
> I have an example were I don't fully understand the routines  
> "Analyze Particle ..." and "Wand (tracing) Tool"!
>
> The image http://picasaweb.google.com/lh/photo/ 
> 8Yo_5vJ1zLKZGwP22oDgsw delivers under "Analyze Particle ..." three  
> particles (white is foreground). That is understandable, seemingly  
> eight-connected neighborhood (of foreground) is assumed. Possibly  
> four-connectedness could be helpful in such cases with thin lines  
> dividing the particles.
>
> But now, trying to overcome this problem by selecting the particles  
> with "Wand (tracing) Tool", possibly in a macro, I run into  
> difficulties. Clicking into particles on the left side of the image  
> selection is okay, Wand is using 4-connectedness! Clicking into one  
> of the two right-most particles seemingly wand is selecting  
> background!
>
> Is there any way to select one of these two right-most particles?
>
> Help is appreciated
> Regards
> Karsten

[karo03]

Gabriel, thank you for the hint. Very helpful! I will see to prepare a  
macro Wand 2 to test the BinaryReconstruction4/8.

Michael, In fact I did not threshold the image! It is a result of the  
Delaunay/Voronoi plugin from Johannes (Dscho?) after some broohaha  
with foreground and background color switches!. However, ImageJ1.42c  
(daily build) selects particels in the described way! I think I should  
preserve that example for tests!

Meanwhile I see and remind me to earlier findings that wand selects  
the next object to the right even if the selection point is not inside  
the object. This is perhaps an explaination for the queer selection on  
the right side!

Thanks again for the quick answers

Karsten

Am 27.11.2008 um 18:11 schrieb Gabriel Landini:

> On Thursday 27 November 2008 16:57:39 Karsten Rodenacker wrote:
>> Hi, Image analysis and -J experts,
>>
>> I have an example were I don't fully understand the routines "Analyze
>> Particle ..." and "Wand (tracing) Tool"!
>>
>> The image http://picasaweb.google.com/lh/photo/8Yo_5vJ1zLKZGwP22oDgsw
>> delivers under "Analyze Particle ..." three particles (white is
>> foreground). That is understandable, seemingly eight-connected
>> neighborhood (of foreground) is assumed. Possibly four-connectedness
>> could be helpful in such cases with thin lines dividing the  
>> particles.
>
> I think that your image has 4-conn particles. If you run Particles4  
> plugin with the label option you will get 20 particles.
> If you created this with a watershed/skeletonisation, then to make  
> it easier, you could use a 4-conneected watershed (which should give  
> 8-connected particles).
>
> If you analyse the image with the Particles8 plugin you get only 3  
> particles.
>
>> But now, trying to overcome this problem by selecting the particles
>> with "Wand (tracing) Tool", possibly in a macro, I run into
>> difficulties. Clicking into particles on the left side of the image
>> selection is okay, Wand is using 4-connectedness! Clicking into one  
>> of
>> the two right-most particles seemingly wand is selecting background!
>>
>> Is there any way to select one of these two right-most particles?
>
> That is a job for the BinaryReconstruct4 plugin in the Morphology  
> collection. Now this is not compiled into a class, because I have  
> not had time to test it thoroughly. If you test it, please send me  
> some feedback.
>
> You could get the XStart YStart points with Particles4, then create  
> a new image with those pixels set for the particles you want to  
> select and BinaryReconstruct4 with the original as mask and the new  
> image as seed.
>
> I hope it helps.
>
> Gabriel

[karo03]

Thanks for all the hints, a solution, hopefully not a coding error, is  
for the mentioned image example the application of Process->Binary-
 >Watershed . The thin skeleton lines (8-conn) of the background are  
extended by the operation to 4-connected ones.

After that (without Thresholding) the Wand selects each object nicely  
and Analyze Particle finds (after Thresholding) 19 objects (see http://picasaweb.google.com/lh/photo/3LPKPMUpPUe0iUoxSa7hsQ)
. Gabriel, the 20th under 4-conn. is a one pixel object at the right  
side which is 8-connected to another object.

Regards
Karsten

Am 27.11.2008 um 18:42 schrieb Karsten Rodenacker:

> Gabriel, thank you for the hint. Very helpful! I will see to prepare  
> a macro Wand 2 to test the BinaryReconstruction4/8.
>
> Michael, In fact I did not threshold the image! It is a result of  
> the Delaunay/Voronoi plugin from Johannes (Dscho?) after some  
> broohaha with foreground and background color switches!. However,  
> ImageJ1.42c (daily build) selects particels in the described way! I  
> think I should preserve that example for tests!
>
> Meanwhile I see and remind me to earlier findings that wand selects  
> the next object to the right even if the selection point is not  
> inside the object. This is perhaps an explaination for the queer  
> selection on the right side!
>
> Thanks again for the quick answers
>
> Karsten
>
> Am 27.11.2008 um 18:11 schrieb Gabriel Landini:
>
>> On Thursday 27 November 2008 16:57:39 Karsten Rodenacker wrote:
>>> Hi, Image analysis and -J experts,
>>>
>>> I have an example were I don't fully understand the routines  
>>> "Analyze
>>> Particle ..." and "Wand (tracing) Tool"!
>>>
>>> The image http://picasaweb.google.com/lh/photo/ 
>>> 8Yo_5vJ1zLKZGwP22oDgsw
>>> delivers under "Analyze Particle ..." three particles (white is
>>> foreground). That is understandable, seemingly eight-connected
>>> neighborhood (of foreground) is assumed. Possibly four-connectedness
>>> could be helpful in such cases with thin lines dividing the  
>>> particles.
>>
>> I think that your image has 4-conn particles. If you run Particles4  
>> plugin with the label option you will get 20 particles.
>> If you created this with a watershed/skeletonisation, then to make  
>> it easier, you could use a 4-conneected watershed (which should  
>> give 8-connected particles).
>>
>> If you analyse the image with the Particles8 plugin you get only 3  
>> particles.
>>
>>> But now, trying to overcome this problem by selecting the particles
>>> with "Wand (tracing) Tool", possibly in a macro, I run into
>>> difficulties. Clicking into particles on the left side of the image
>>> selection is okay, Wand is using 4-connectedness! Clicking into  
>>> one of
>>> the two right-most particles seemingly wand is selecting background!
>>>
>>> Is there any way to select one of these two right-most particles?
>>
>> That is a job for the BinaryReconstruct4 plugin in the Morphology  
>> collection. Now this is not compiled into a class, because I have  
>> not had time to test it thoroughly. If you test it, please send me  
>> some feedback.
>>
>> You could get the XStart YStart points with Particles4, then create  
>> a new image with those pixels set for the particles you want to  
>> select and BinaryReconstruct4 with the original as mask and the new  
>> image as seed.
>>
>> I hope it helps.
>>
>> Gabriel
>