Selection tool of filament like structure

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Selection tool of filament like structure

anusuya pal
Dear all,

I have an image in which there are many filament like structures which is
attached. I want to select each of the filaments so that I can study in
detail. I can always do the free hand selection, but it is not perfect.

I am attaching one image from the stack. May I know whether there is any
tool for the selection of filament like structures?

Any suggestions?

Thanks
Anu

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Re: Selection tool of filament like structure

Volko Straub
You could try the Tubeness filter (Fiji/ImageJ: Analyze->Tubeness) to enhance tube/filament like structures, followed by thresholding the image. The image below shows the selection created after thresholding superimposed on your original image. The selection could be tidied up using some binary filter operations, before carrying out measurements on individual structures using the particle analyzer (depending on what you want to measure).


Hope this helps,

Volko


[cid:c4a453fc-3704-4dd9-8e77-66929a78e396]




________________________________
From: anusuya pal <[hidden email]>
Sent: 07 October 2017 19:56:02
To: [hidden email]
Subject: Selection tool of filament like structure

Dear all,

I have an image in which there are many filament like structures which is
attached. I want to select each of the filaments so that I can study in
detail. I can always do the free hand selection, but it is not perfect.

I am attaching one image from the stack. May I know whether there is any
tool for the selection of filament like structures?

Any suggestions?

Thanks
Anu

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

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

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pastedImage.png (59K) Download Attachment
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Re: Selection tool of filament like structure

ctrueden
Hi,

There is also the Frangi Vesselness Filter; see:

    https://imagej.net/Frangi

And we are currently in the process of adding an improved version of that
filter to ImageJ Ops, too [1].

Regards,
Curtis

[1] http://forum.imagej.net/t/frangi-vesselness-filter-feedback/6747

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Sun, Oct 8, 2017 at 11:59 PM, Straub, Volko A. (Dr.) <
[hidden email]> wrote:

> You could try the Tubeness filter (Fiji/ImageJ: Analyze->Tubeness) to
> enhance tube/filament like structures, followed by thresholding the image.
> The image below shows the selection created after thresholding superimposed
> on your original image. The selection could be tidied up using some binary
> filter operations, before carrying out measurements on individual
> structures using the particle analyzer (depending on what you want to
> measure).
>
>
> Hope this helps,
>
> Volko
>
>
> [cid:c4a453fc-3704-4dd9-8e77-66929a78e396]
>
>
>
>
> ________________________________
> From: anusuya pal <[hidden email]>
> Sent: 07 October 2017 19:56:02
> To: [hidden email]
> Subject: Selection tool of filament like structure
>
> Dear all,
>
> I have an image in which there are many filament like structures which is
> attached. I want to select each of the filaments so that I can study in
> detail. I can always do the free hand selection, but it is not perfect.
>
> I am attaching one image from the stack. May I know whether there is any
> tool for the selection of filament like structures?
>
> Any suggestions?
>
> Thanks
> Anu
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Selection tool of filament like structure

anusuya pal
Hello,

Thanks for the suggestions. I am successful in segmenting the only
filament-like structures.  But I have not really understood what Dr. Volko
suggested for the selection of the structures. May I request you to tell me
the details? The image which was attached by Dr. Volko is the exact one I
intend to do.

For the convenience, I have attached my image after filtering only
tube-like structures.

Thanks
Anu

On Mon, Oct 9, 2017 at 1:09 PM, Curtis Rueden <[hidden email]> wrote:

> Hi,
>
> There is also the Frangi Vesselness Filter; see:
>
>     https://imagej.net/Frangi
>
> And we are currently in the process of adding an improved version of that
> filter to ImageJ Ops, too [1].
>
> Regards,
> Curtis
>
> [1] http://forum.imagej.net/t/frangi-vesselness-filter-feedback/6747
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Sun, Oct 8, 2017 at 11:59 PM, Straub, Volko A. (Dr.) <
> [hidden email]> wrote:
>
> > You could try the Tubeness filter (Fiji/ImageJ: Analyze->Tubeness) to
> > enhance tube/filament like structures, followed by thresholding the
> image.
> > The image below shows the selection created after thresholding
> superimposed
> > on your original image. The selection could be tidied up using some
> binary
> > filter operations, before carrying out measurements on individual
> > structures using the particle analyzer (depending on what you want to
> > measure).
> >
> >
> > Hope this helps,
> >
> > Volko
> >
> >
> > [cid:c4a453fc-3704-4dd9-8e77-66929a78e396]
> >
> >
> >
> >
> > ________________________________
> > From: anusuya pal <[hidden email]>
> > Sent: 07 October 2017 19:56:02
> > To: [hidden email]
> > Subject: Selection tool of filament like structure
> >
> > Dear all,
> >
> > I have an image in which there are many filament like structures which is
> > attached. I want to select each of the filaments so that I can study in
> > detail. I can always do the free hand selection, but it is not perfect.
> >
> > I am attaching one image from the stack. May I know whether there is any
> > tool for the selection of filament like structures?
> >
> > Any suggestions?
> >
> > Thanks
> > Anu
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Selection tool of filament like structure

Volko Straub
Hi Anu,


Below is some macro code to illustrate what I meant. The code initially applies a threshold to your tubeness filtered image using Huang's method (you could also use another, more appropriate method or set it manually). It then uses a binary open operation to clean up a bit (smooth structures a bit and remove small isolated structures, may not be necessary). It then uses the Particle Analyser to measure all structures over a certain size limit (currently set to 10 pixels).

I don't quite know what you want to measure on your structures, so at the moment I included area and shape descriptors. This can easily be changed to your needs using the set measurements option/function. I also don't know whether you are just interested in single filament like structures without branches or want to include branched structures. If you want to exclude branched structures, it might be useful to skeletonize the structures and then identify branch pixels (i.e. more than 2 neighbors)  and remove those. Skeletonizing would also help with measuring the length of your filaments if that is something you are interested in (see Gabriel Landini's Morphology Toolbox, look for Lines8).


I hope this helps,

Volko


//Threshold image; Huang's autothreshold method appears to do a pretty good job on the sample image
setAutoThreshold("Huang dark");
//setThreshold(9, 255);
setOption("BlackBackground", true);
run("Convert to Mask");
//Run a binary open filter to remove small particles; not really necessary as they can be excluded by size using the Particle Analyzer (standard) or Extended Particle Analyzer (part of BioVoxxel toolbox)
run("Options...", "iterations=1 count=5 black do=Open");
//Set measurements to include shape descriptors, include any other measurements that may be of interest
run("Set Measurements...", "area shape redirect=None decimal=3");
//Run Particle Analyzer to measure all structures that are larger than 10 pixels in area, show measurement results and //add particles to ROI
run("Analyze Particles...", "size=10-Infinity display add");



________________________________
From: anusuya pal <[hidden email]>
Sent: 10 October 2017 21:40:38
To: [hidden email]
Subject: Re: Selection tool of filament like structure

Hello,

Thanks for the suggestions. I am successful in segmenting the only
filament-like structures.  But I have not really understood what Dr. Volko
suggested for the selection of the structures. May I request you to tell me
the details? The image which was attached by Dr. Volko is the exact one I
intend to do.

For the convenience, I have attached my image after filtering only
tube-like structures.

Thanks
Anu

On Mon, Oct 9, 2017 at 1:09 PM, Curtis Rueden <[hidden email]> wrote:

> Hi,
>
> There is also the Frangi Vesselness Filter; see:
>
>     https://imagej.net/Frangi
>
> And we are currently in the process of adding an improved version of that
> filter to ImageJ Ops, too [1].
>
> Regards,
> Curtis
>
> [1] http://forum.imagej.net/t/frangi-vesselness-filter-feedback/6747
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Sun, Oct 8, 2017 at 11:59 PM, Straub, Volko A. (Dr.) <
> [hidden email]> wrote:
>
> > You could try the Tubeness filter (Fiji/ImageJ: Analyze->Tubeness) to
> > enhance tube/filament like structures, followed by thresholding the
> image.
> > The image below shows the selection created after thresholding
> superimposed
> > on your original image. The selection could be tidied up using some
> binary
> > filter operations, before carrying out measurements on individual
> > structures using the particle analyzer (depending on what you want to
> > measure).
> >
> >
> > Hope this helps,
> >
> > Volko
> >
> >
> > [cid:c4a453fc-3704-4dd9-8e77-66929a78e396]
> >
> >
> >
> >
> > ________________________________
> > From: anusuya pal <[hidden email]>
> > Sent: 07 October 2017 19:56:02
> > To: [hidden email]
> > Subject: Selection tool of filament like structure
> >
> > Dear all,
> >
> > I have an image in which there are many filament like structures which is
> > attached. I want to select each of the filaments so that I can study in
> > detail. I can always do the free hand selection, but it is not perfect.
> >
> > I am attaching one image from the stack. May I know whether there is any
> > tool for the selection of filament like structures?
> >
> > Any suggestions?
> >
> > Thanks
> > Anu
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

--
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Re: Selection tool of filament like structure

anusuya pal
Hello,

Thank you so much for the help!

Thanks
Anu

On Thu, Oct 12, 2017 at 1:44 AM, Straub, Volko A. (Dr.) <
[hidden email]> wrote:

> Hi Anu,
>
>
> Below is some macro code to illustrate what I meant. The code initially
> applies a threshold to your tubeness filtered image using Huang's method
> (you could also use another, more appropriate method or set it manually).
> It then uses a binary open operation to clean up a bit (smooth structures a
> bit and remove small isolated structures, may not be necessary). It then
> uses the Particle Analyser to measure all structures over a certain size
> limit (currently set to 10 pixels).
>
> I don't quite know what you want to measure on your structures, so at the
> moment I included area and shape descriptors. This can easily be changed to
> your needs using the set measurements option/function. I also don't know
> whether you are just interested in single filament like structures without
> branches or want to include branched structures. If you want to exclude
> branched structures, it might be useful to skeletonize the structures and
> then identify branch pixels (i.e. more than 2 neighbors)  and remove those.
> Skeletonizing would also help with measuring the length of your filaments
> if that is something you are interested in (see Gabriel Landini's
> Morphology Toolbox, look for Lines8).
>
>
> I hope this helps,
>
> Volko
>
>
> //Threshold image; Huang's autothreshold method appears to do a pretty
> good job on the sample image
> setAutoThreshold("Huang dark");
> //setThreshold(9, 255);
> setOption("BlackBackground", true);
> run("Convert to Mask");
> //Run a binary open filter to remove small particles; not really necessary
> as they can be excluded by size using the Particle Analyzer (standard) or
> Extended Particle Analyzer (part of BioVoxxel toolbox)
> run("Options...", "iterations=1 count=5 black do=Open");
> //Set measurements to include shape descriptors, include any other
> measurements that may be of interest
> run("Set Measurements...", "area shape redirect=None decimal=3");
> //Run Particle Analyzer to measure all structures that are larger than 10
> pixels in area, show measurement results and //add particles to ROI
> run("Analyze Particles...", "size=10-Infinity display add");
>
>
>
> ________________________________
> From: anusuya pal <[hidden email]>
> Sent: 10 October 2017 21:40:38
> To: [hidden email]
> Subject: Re: Selection tool of filament like structure
>
> Hello,
>
> Thanks for the suggestions. I am successful in segmenting the only
> filament-like structures.  But I have not really understood what Dr. Volko
> suggested for the selection of the structures. May I request you to tell me
> the details? The image which was attached by Dr. Volko is the exact one I
> intend to do.
>
> For the convenience, I have attached my image after filtering only
> tube-like structures.
>
> Thanks
> Anu
>
> On Mon, Oct 9, 2017 at 1:09 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi,
> >
> > There is also the Frangi Vesselness Filter; see:
> >
> >     https://imagej.net/Frangi
> >
> > And we are currently in the process of adding an improved version of that
> > filter to ImageJ Ops, too [1].
> >
> > Regards,
> > Curtis
> >
> > [1] http://forum.imagej.net/t/frangi-vesselness-filter-feedback/6747
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Sun, Oct 8, 2017 at 11:59 PM, Straub, Volko A. (Dr.) <
> > [hidden email]> wrote:
> >
> > > You could try the Tubeness filter (Fiji/ImageJ: Analyze->Tubeness) to
> > > enhance tube/filament like structures, followed by thresholding the
> > image.
> > > The image below shows the selection created after thresholding
> > superimposed
> > > on your original image. The selection could be tidied up using some
> > binary
> > > filter operations, before carrying out measurements on individual
> > > structures using the particle analyzer (depending on what you want to
> > > measure).
> > >
> > >
> > > Hope this helps,
> > >
> > > Volko
> > >
> > >
> > > [cid:c4a453fc-3704-4dd9-8e77-66929a78e396]
> > >
> > >
> > >
> > >
> > > ________________________________
> > > From: anusuya pal <[hidden email]>
> > > Sent: 07 October 2017 19:56:02
> > > To: [hidden email]
> > > Subject: Selection tool of filament like structure
> > >
> > > Dear all,
> > >
> > > I have an image in which there are many filament like structures which
> is
> > > attached. I want to select each of the filaments so that I can study in
> > > detail. I can always do the free hand selection, but it is not perfect.
> > >
> > > I am attaching one image from the stack. May I know whether there is
> any
> > > tool for the selection of filament like structures?
> > >
> > > Any suggestions?
> > >
> > > Thanks
> > > Anu
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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