3D skeleton and length measurement

[Paola Lepanto]

Hello
I´m using the "skeletonize (2D/3D)" and "analyze skeleton (2D/3D)" plugins to measure the length of cilia in confocal microscopy stacks.
Is it possible to assign each measurement given by the "analyze skeleton" plugin to the object being measured? I know that each branch comes with its spatial localization coordinates, but it is pretty difficult to find the object using this information, specially when there are many of them in the stack. What I have tried is to combine this plugin with the analysis of the skeletons using the "3D object counter" and "3D object manager" plugins, but I still can´t relate the object in the stack with the skeleton being measured using the "analyze skeleton" plugin.

Thanks in advance

Paola
PhD Student
Institut Pasteur Montevideo

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[Ignacio Arganda-Carreras]

Hello Paola,

You're not the first person on asking me about this lately. How would you
like to visualize the objects? In a new skeleton image where each skeleton
voxel has the value of its corresponding skeleton id?

ignacio

On Fri, Feb 27, 2015 at 8:31 PM, Paola Lepanto <[hidden email]>
wrote:

> Hello
> I´m using the "skeletonize (2D/3D)" and "analyze skeleton (2D/3D)" plugins
> to measure the length of cilia in confocal microscopy stacks.
> Is it possible to assign each measurement given by the "analyze skeleton"
> plugin to the object being measured? I know that each branch comes with its
> spatial localization coordinates, but it is pretty difficult to find the
> object using this information, specially when there are many of them in the
> stack. What I have tried is to combine this plugin with the analysis of the
> skeletons using the "3D object counter" and "3D object manager" plugins,
> but I still can´t relate the object in the stack with the skeleton being
> measured using the "analyze skeleton" plugin.
>
> Thanks in advance
>
> Paola
> PhD Student
> Institut Pasteur Montevideo
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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[Paola Lepanto]

Hi Ignacio

May be what you suggested (new skeleton image where each skeleton voxel has the value of its corresponding skeleton id) is too much. It would be great just to get a new stack where each skeleton has its corresponding id. In that way one would be able to select only the measurements of those skeletons that want to be measured.

Another alternative is to skeletonize, detect the skeletons using the 3D Object Counter plugin and incorporate the length measurement done by the analize skeleton plugin to the measurements options in the 3D Object Manager. May be this can already be done and I missed it...

Thanks for your time!

Paola



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[Olivier Burri]

Hi all,

Odd behavior here. If you run the following code, you will notice that after the median filter operation, the create selection outputs the inverse of the selection. I tried looking into the rankfilters code but could not find where this behavior could come from...

The problem is "Solved" if we invert the LUT, even though nothing was done to it.

So I thought that somehow the image was flagged as having an  inverted LUT, but checking for that gave no change...

I also looked into the ThresholdToSelection.java code to see if it was using some property or other, but to no avail...

If anyone has any thoughts, that would be great...

run("Blobs (25K)");
setAutoThreshold("Huang");
run("Convert to Mask");
run("Create Selection");
Roi.setName("Before Median");
roiManager("Add");
print("Inverting LUT: ", is("Inverting LUT"));
run("Select None");
run("Median...", "radius=4");
run("Create Selection");
Roi.setName("After Median");
roiManager("Add");
print("Inverting LUT: ", is("Inverting LUT"));

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[Ignacio Arganda-Carreras]

Hello Paola,


I´m sorry to bother again but I wanted to ask you something about the
> skeletonize 2D/3D plugin. Which algorithm does it use? If I understood
> correctly from the article from 2010, is it the thinning technique?
>

Yes exactly. The citation is in the website:
http://fiji.sc/Skeletonize3D#Related_work


> The structures I´m working in are like small, thin sticks, around 5um
> long. When I use the skeletonize plugin the skeletons doesn´t reach the end
> of the sticks.
>

That behavior is intended. Since it is a thinning algorithm, the extremes
of the objects are eroded.


> Do you know other algorithm that can make skeletons reach the end of the
> sticks? Do you think that could be the problem? may be I´m doing something
> wrong during the pre-processing of the images (deconvolution, gaussian
> blur, binarization)...
>

There's no problem. There are many skeletonization methods. You should find
the one that fits your requirements better. Have a look at this site about
different algorithms:

http://perso.esiee.fr/~info/ck/index.html

Cheers!

ignacio



--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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