Posted by
Ignacio Arganda-Carreras on
Mar 12, 2015; 3:31pm
URL: http://imagej.273.s1.nabble.com/3D-skeleton-and-length-measurement-tp5011810p5011954.html
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.htmlCheers!
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: (001) 617-324-3747
Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html--
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