[ITK Community] Isolating 3d touching regions

[Dan Mueller]

Hi Emiliano,

One possibility might be to use the mathematical watershed algorithm
to binary segment the fibres and separate touching labels.

See here:
http://www.insight-journal.org/browse/publication/92

and here:
http://www.vincent-net.com/luc/papers/96semstats_morpho_topics.pdf (pg 44)

This would essentially reduce your problem to find a good "marker" for
each fibre. In your case this should not be too difficult, as the
skeleton of each fibre should suffice (i.e. the skeletons will not
overlap).

Good luck.

Cheers, Dan

On 13 March 2014 23:16, Emiliano Pastorelli
<emiliano.pastorelli at gmail.com> wrote:
> Hi All,
>
> i'm quite new to ITK, and i'm trying to manipulate a 3d volume image
> representing some fibres floating in a block of concrete. Due to the
> scanning inaccuracies, some of them actually seem to "touch", also when they
> wouldn't be touching in the real dataset.
>
> I tried to separate them in every way, through the Frangi Vesselness
> filters, and another bunch of attempts, but i don't seem to find a way to do
> it reasonably quickly and smartly.
>
> http://www.kyb3.org/images/touchingFibres.png
>
> in the picture, exactly in the center you see an example of how the touching
> area usually looks like (the dataset is already divide in labeled regions as
> label map as well).
> I am pretty sure that some filter can do that, but for example i was taking
> a look at the connectedthresholdimagefilter and i couldn't really figure out
> if that's what i need, and in that case how i shall use the seeds (my
> software shall become flexible enough to deal with really similar in shapes
> but different in distribution, alignment and contact points datasets).
>
> Does anybody have any idea that might spare me another couple of endless
> days like the last ones?
>
> Thanks in advance,
> Emiliano
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