[ITK Community] Isolating 3d touching regions

[Dan Mueller]

Hi,

You might try using markers computed from the regional maxima of a distance
map (where inside is positive)...

Sharing your dataset may also help community members suggest other options.

HTH

Cheers, Dan
On 14 Mar 2014 19:38, "Emiliano Pastorelli" <emiliano.pastorelli at gmail.com>
wrote:

> 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
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/community
>>>>>
>>>> _______________________________________________
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>>>>
>>>
>>
>
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