[ITK Community] Isolating 3d touching regions

[Bradley Lowekamp]

Hello,

You may also find this SimpleITK IPython Notebook which used the this suggested watershed approach to separate some coins:
http://simpleitk.github.io/SimpleITK-Notebooks/32_Watersheds_Segmentation.html

Also SimpleITK from Python may be a useful way to easily explore the many algorithms and infinite number of combinations available from ITK.

Brad

On Mar 13, 2014, at 5:37 PM, Dan Mueller <dan.muel at gmail.com> wrote:

> 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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