http://imagej.273.s1.nabble.com/Selection-tool-of-filament-like-structure-tp5019517p5019531.html
On Thu, Oct 12, 2017 at 1:44 AM, Straub, Volko A. (Dr.) <
> 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> >
>
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