question about tagged skeleton

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question about tagged skeleton

Aryeh Weiss
I have a tagged skeleton, but I do not understand the tagging. In
particular, the endpoints are not all the same.

I used Analyze>Skeleton>Analyze Skeleton 2D/3D

I attached one of the skeletons in my image. I expect four endpoints.
However, the two on the left have a value of 30, while the two on the
right have a value of 127, as does a segment in the middle , which are
not endpoints.

I also pasted the image here:

The two endpoints on the right are orange (127) and the two on the left
are blue (30). Notice the orange line in the middle, which is also a
value of 127.

Apparently, I do not know how the endpoints are defined.

Thanks in advance for clarifying this.
--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


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ppgnanohnkgjhimo.png (11K) Download Attachment
Tagged skeleton-1.png (1K) Download Attachment
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Re: question about tagged skeleton -- partially solved

Aryeh Weiss
I used skeleton3 (from the Morphology plugins) to generate the skeleton,
and this makes 4-connected skeletons. I think that is the problem.

skeleton1 seems to make 8-connected skeletons, and this produces the
result that I expected.

A 4-connected endpoint has 2 neighbors as far as the analyze skeleton
plugin is concerned, while an endpoint by definition must have only one
neighbor.

--aryeh

On 12/06/2018 19:08, Aryeh Weiss wrote:

>
> I have a tagged skeleton, but I do not understand the tagging. In
> particular, the endpoints are not all the same.
>
> I used Analyze>Skeleton>Analyze Skeleton 2D/3D
>
> I attached one of the skeletons in my image. I expect four endpoints.
> However, the two on the left have a value of 30, while the two on the
> right have a value of 127, as does a segment in the middle , which are
> not endpoints.
>
> I also pasted the image here:
>
> The two endpoints on the right are orange (127) and the two on the
> left are blue (30). Notice the orange line in the middle, which is
> also a value of 127.
>
> Apparently, I do not know how the endpoints are defined.
>
> Thanks in advance for clarifying this.
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: 972-3-7384051
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


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

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Re: question about tagged skeleton -- partially solved

Aryeh Weiss
Dear Richard,

Thank you for your reply.

On 13/06/2018 5:05, Domander, Richard wrote:
>
> Dear Aryeh,
>
> The voxels are colourized according to their 26-neighbourhood thusly:
>
> End-points (blue) have 0 or 1 neighbors.
> Junctions (purple)  have > 2 neighbors.
> Slabs (orange) have exactly 2 neighbors.
>
I should just add that there are different skeltonization routines. Some
of them create skeletons in which the end points will have more than one
neighbor (if the endpoint is on an "8-connected" pixel), while others
will not. For this kind of analysis , it is important to select the
appropriate skeletonization method.

Regards
--aryeh

> For further information, please refer to:
> https://imagej.net/AnalyzeSkeleton#General_Description
>
> Best regards,
> Richard Domander
>
>
> ------------------------------------------------------------------------
> *From:* ImageJ Interest Group <[hidden email]> on behalf of Aryeh
> Weiss <[hidden email]>
> *Sent:* 13 June 2018 03:39:17
> *To:* [hidden email]
> *Subject:* Re: question about tagged skeleton -- partially solved
> I used skeleton3 (from the Morphology plugins) to generate the skeleton,
> and this makes 4-connected skeletons. I think that is the problem.
>
> skeleton1 seems to make 8-connected skeletons, and this produces the
> result that I expected.
>
> A 4-connected endpoint has 2 neighbors as far as the analyze skeleton
> plugin is concerned, while an endpoint by definition must have only one
> neighbor.
>
> --aryeh
>
> On 12/06/2018 19:08, Aryeh Weiss wrote:
> >
> > I have a tagged skeleton, but I do not understand the tagging. In
> > particular, the endpoints are not all the same.
> >
> > I used Analyze>Skeleton>Analyze Skeleton 2D/3D
> >
> > I attached one of the skeletons in my image. I expect four endpoints.
> > However, the two on the left have a value of 30, while the two on the
> > right have a value of 127, as does a segment in the middle , which are
> > not endpoints.
> >
> > I also pasted the image here:
> >
> > The two endpoints on the right are orange (127) and the two on the
> > left are blue (30). Notice the orange line in the middle, which is
> > also a value of 127.
> >
> > Apparently, I do not know how the endpoints are defined.
> >
> > Thanks in advance for clarifying this.
> > --aryeh
> >

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: question about tagged skeleton -- partially solved

Gabriel Landini
Hi Aryeh,
If you are only dealing with 2D images and want to analyse 4-neighbour
connectivity, you only need to create a 3x3 summation convolution filter in
the shape of a cross. For example this does what you are after:

a=getTitle();
run("Duplicate...", "title=sum");
selectImage("sum");
run("Divide...", "value=255");
run("Convolve...", "text1=[0 1 0\n1 1 1\n0 1 0] ");
imageCalculator("AND create", a,"sum");
run("glasbey");
close("sum");

Hope this helps.

Gabriel

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Re: question about tagged skeleton -- partially solved

Gabriel Landini
Hi again,
I forgot to specify that the macro expects the blobs/skeleton to be binary,
with a value of 255 and the background to be 0.

Cheers

Gabriel


On Wednesday, 13 June 2018 13:43:03 BST you wrote:

> Hi Aryeh,
> If you are only dealing with 2D images and want to analyse 4-neighbour
> connectivity, you only need to create a 3x3 summation convolution filter in
> the shape of a cross. For example this does what you are after:
>
> a=getTitle();
> run("Duplicate...", "title=sum");
> selectImage("sum");
> run("Divide...", "value=255");
> run("Convolve...", "text1=[0 1 0\n1 1 1\n0 1 0] ");
> imageCalculator("AND create", a,"sum");
> run("glasbey");
> close("sum");
>
> Hope this helps.
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: question about tagged skeleton -- partially solved

Aryeh Weiss
In reply to this post by Gabriel Landini
Thank you Gabriel. That works as advertised.

--aryeh

On 13/06/2018 7:43, Gabriel Landini wrote:

> Hi Aryeh,
> If you are only dealing with 2D images and want to analyse 4-neighbour
> connectivity, you only need to create a 3x3 summation convolution filter in
> the shape of a cross. For example this does what you are after:
>
> a=getTitle();
> run("Duplicate...", "title=sum");
> selectImage("sum");
> run("Divide...", "value=255");
> run("Convolve...", "text1=[0 1 0\n1 1 1\n0 1 0] ");
> imageCalculator("AND create", a,"sum");
> run("glasbey");
> close("sum");
>
> Hope this helps.
>
> Gabriel
>
>
>
>
> .
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

--
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Re: question about tagged skeleton

Ignacio Arganda-Carreras-2
In reply to this post by Aryeh Weiss
Dear Aryeh,

That's not a valid skeleton for the Analyze Skeleton plugin because of its
connectivity. Please apply first Skeletonize 3D and then Analyze Skeleton
to obtain correct results.

Cheers!

ignacio

On Wed, Jun 13, 2018 at 2:08 AM, Aryeh Weiss <[hidden email]> wrote:

> I have a tagged skeleton, but I do not understand the tagging. In
> particular, the endpoints are not all the same.
>
> I used Analyze>Skeleton>Analyze Skeleton 2D/3D
>
> I attached one of the skeletons in my image. I expect four endpoints.
> However, the two on the left have a value of 30, while the two on the
> right have a value of 127, as does a segment in the middle , which are not
> endpoints.
>
> I also pasted the image here:
>
> The two endpoints on the right are orange (127) and the two on the left
> are blue (30). Notice the orange line in the middle, which is also a value
> of 127.
>
> Apparently, I do not know how the endpoints are defined.
>
> Thanks in advance for clarifying this.
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: 972-3-7384051
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/

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Re: question about tagged skeleton

Aryeh Weiss
Dear Ignacio

Thank you for your reply.
Indeed, making it an 8-connected skeleton solved the problem. This could
be done either by using a different
skeletonizer (I used skeleton1 from the Morphology collection), or by
converting a 4-conn3ected skeleton to an 8-connected one by convolving
with a cross, as suggested by Gabriel Landini.

Best regards
--aryeh

On 18/06/2018 16:24, Ignacio Arganda-Carreras wrote:

> Dear Aryeh,
>
> That's not a valid skeleton for the Analyze Skeleton plugin because of
> its connectivity. Please apply first Skeletonize 3D and then Analyze
> Skeleton to obtain correct results.
>
> Cheers!
>
> ignacio
>
> On Wed, Jun 13, 2018 at 2:08 AM, Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     I have a tagged skeleton, but I do not understand the tagging. In
>     particular, the endpoints are not all the same.
>
>     I used Analyze>Skeleton>Analyze Skeleton 2D/3D
>
>     I attached one of the skeletons in my image. I expect four endpoints.
>     However, the two on the left have a value of 30, while the two on
>     the right have a value of 127, as does a segment in the middle ,
>     which are not endpoints.
>
>     I also pasted the image here:
>
>     The two endpoints on the right are orange (127) and the two on the
>     left are blue (30). Notice the orange line in the middle, which is
>     also a value of 127.
>
>     Apparently, I do not know how the endpoints are defined.
>
>     Thanks in advance for clarifying this.
>     --aryeh
>
>     --
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


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