Posted by
Ignacio Arganda-Carreras on
URL: http://imagej.273.s1.nabble.com/BoneJ-Analyze-Skeleton-on-Skeletons-with-32766-components-tp5009924p5009932.html
Hello Simon,
This limitation comes from the fact that I used a "short" image to store
the labeled skeletons in AnalzyeSkeleton. If you have some coding
experience you can easily create your own version of the plugin to use
Float instead of Short pixel values. That should make the trick.
In any case, I will talk to Michael Doube (BoneJ maintainer) to see if we
also add that change to our released version.
Best regards,
ignacio
On Mon, Oct 6, 2014 at 10:31 PM, Simon Carr <
[hidden email]> wrote:
> Dear All,
>
> I am using BoneJ to undertake pore analysis of soils and sediments, but
> keep coming up against the Java limit of a maximum of 32,766 components.
> Unfortunately, my samples have populations of pores to be measured in the
> order of ~120,000 components, some of which extend right through the CT
> volume that has been scanned. Whilst I appreciate that I can sub-sample
> each volume into smaller pieces that bring the component number below the
> magic number, I am aware that this is compromising the quality of the
> analysis, because numerous large pore networks that extend as a single
> network through the whole volume are being split into perhaps four (or
> more) skeletons for subsequent analysis.
>
> Can anyone advise whether there is a way to get around the Java-imposed
> limit on my volumes?
>
> Regards,
>
> Simon
> _________________________________
> Dr Simon Carr
> School of Geography,
> Queen Mary University of London,
> Mile End Road, London, E1 4NS, UK.
> t: 00 44 20 7882 2780
> f: 00 44 20 8981 6276
> e:
[hidden email]<mailto:
[hidden email]>
> twitter: @DrSimonCarr
>
>
>
>
>
>
>
>
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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: (001) 617-324-3747
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