[ITK Community] Isolating 3d touching regions

[Emiliano Pastorelli]

Hi guys,

I started taking a look at the watershed and might indeed do the work. Due
to my inexperience though, finding the marker seems a less trivial problem
than what Dan mentions as not so difficult.

The problem is that somehow, i was trying to avoid skeletonization (i will
need later to compare my results to a similar dataset analyzed in a
different way that is centered on skeletonization). Do you happen to have
any idea on how to get those markers otherwise?

And should I go for the skeletonization (should it be the only solution, i
might have to) wouldn't the skeleton of the touching fibres be detected a
single skeleton? Also, what ITK algorithm would you best suggest should it
be needed to skeletonize a dataset like this one?

Thanks and sorry for the possible naivety of some of my questions!

Best,
Emiliano


2014-03-14 9:52 GMT+02:00 Emiliano Pastorelli <emiliano.pastorelli at gmail.com
>:

> Hi guys,
>
> thanks, there's quite some material to chew on there, i'll take a look at
> it today in the office. The whole process for me needs to be somehow
> automatized from the beginning to the end to achieve what i need, so the
> user will only have to specify the fibres size and length and no manual
> thresholding.
>
> Thanks, i'll get back to you if I have further problems!
>
> Best,
> Emiliano
>
> Il 14/03/14 03:13, Bradley Lowekamp ha scritto:
>
>  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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>>
>
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