[Insight-users] ITK + VTK + 3D TIFFs

[Richard Beare]

Hi,
ConnectedComponentImageFilter is only the labelling step. Each
component comes out with a different ID, which you can then use to
index other measurements.

A filter that does the series of steps needed is
itkBinaryShapeOpeningImageFilter (available in the review section).

You need to confirm that the connectivity setting matches your
expectation - do you want diagonal connections to count, or not. This
is the FullyConnected option.

On Mon, Apr 25, 2011 at 4:40 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> Meantime I've been figuring out how to use itkConnectedComponentImageFilter,
> the idea being to find all the objects then remove those below a threshold
> size. I'm getting strange results with my small test image.
>
> The image is binary, 437x430.  Initially (using pixel type unsigned char) I
> got the error message about too many objects, so I changed the type to
> unsigned short.  The number of found objects is 838.  The image is basically
> white, with black spots, some of which enclose white regions (these are what
> I want to remove).  I'm finding that some of these enclosed "objects" are
> missed.  There are four with more than 100 pixels (excluding the white
> background), and only two are identified as objects.
>
> Do I have wrong expectations of itkConnectedComponentImageFilter?
>
> Thanks
> Gib
>
> On 25/04/2011 4:42 p.m., Bill Lorensen wrote:
>>
>> You could use one of itk's voting filters:
>> itkLabelVotingImageFIlter
>> itkVotingBinaryHoleFillingImageFilter
>> itkVotingBinaryIterativeHoleFillingImageFilter
>>
>>
>> On Sun, Apr 24, 2011 at 9:28 PM, Gib Bogle <g.bogle at auckland.ac.nz
>> <mailto:g.bogle at auckland.ac.nz>> wrote:
>>
>>    I'm not sure if this should be here or on the VTK message list, so I'm
>>    posting it to both lists.
>>
>>    I'm processing 3D TIFFs with ITK, but I want to use the island removal
>>    capability of VTK, to filter each 2D image in the 3D stack (as far as I
>> can
>>    see VTK doesn't know about 3D TIFFs).  I presume I need to open the 3D
>> image
>>    in ITK, select a 2D slice, convert it to VTK 2D image format, apply the
>>    island removal filter, convert it back to ITK image format, and write
>> it
>>    back into the 3D image.  It would be very nice if someone has done
>> something
>>    similar to this and could show me how to do it.
>>
>>    Thanks
>>    Gib
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