[Insight-users] Peel an image

[Gib Bogle]

I didn't think there would be a stock filter, but maybe somebody else has 
addressed this.

I have attached a typical frame.  I can't show the wanted result, but I think 
it's obvious when you know that the interior of this piece of tissue has the 
blood vessels stained, while the faint rim is clearly not blood vessel.  The 
problem is that there will in general be many vessels stained to a similar 
intensity as this rim.

Gib

On 23/05/2013 8:53 a.m., Dženan Zukić wrote:
> I don't think there is any stock filter which does what you want. And I still 
> don't understand your situation. Can you show us an example slice and wanted 
> result?
>
>
> On Wed, May 22, 2013 at 10:50 PM, Gib Bogle <g.bogle at auckland.ac.nz 
> <mailto:g.bogle at auckland.ac.nz>> wrote:
>
>     The reason why I don't think erode will work is that the part of the image
>     that contains the information of interest is made up of many disconnected
>     pieces, not very different from the boundary layer that I want to remove. 
>     The only thing that I can use to distinguish the pixels that need to be
>     removed is that they are near the outside of the region.  If I apply
>     erosion I will remove many small but important features (this is labelled
>     vasculature, and I do not want to lose fine capillaries).
>
>     Gib
>
>
>     On 22/05/2013 11:12 p.m., Dženan Zukić wrote:
>>     http://www.itk.org/Doxygen/html/group__MathematicalMorphologyImageFilters.html
>>
>>     What you probably want to do is BinaryErode and BinaryDilate.
>>
>>
>>     On Wed, May 22, 2013 at 7:04 AM, gib <g.bogle at auckland.ac.nz
>>     <mailto:g.bogle at auckland.ac.nz>> wrote:
>>
>>         It's hard to know what to call the processing I want to apply.  I
>>         have a set
>>         of biological images (actually a 3D image, but for now I'm happy to
>>         process
>>         the frames one-by-one) in which the region of interest has an
>>         irregular and
>>         incomplete labelled layer around the boundary.  The staining of the layer
>>         was unintended, and its presence interferes with the segmentation
>>         that I am
>>         doing.  The part of the image that I want to extract is made up of many
>>         disconnected objects, and there is not much difference in the intensity
>>         ranges of the objects of interest and the unwanted edge.  I am willing to
>>         trim a few pixels off the boundary all the way around - this will not
>>         cause
>>         much loss of information.  What I need is way to determine a sequence of
>>         pixels that in some sense defines the extent of the labelled region
>>         in the
>>         image, rather like a 2D shrink wrapping.  I could then use this to
>>         shave or
>>         peel off the outer layer of pixels.
>>
>>         Does this process have a name?  Are there any existing filters or
>>         code to do
>>         this?  Any clever suggestions (I have some ideas)?
>>
>>         Thanks
>>         Gib
>>
>>
>>
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>
>
>     -- 
>     Dr. Gib Bogle
>     Senior Research Fellow
>     Auckland Bioengineering Institute
>     University of Auckland
>     New Zealand
>
>     http://www.bioeng.auckland.ac.nz
>
>     g.bogle at auckland.ac.nz  <mailto:g.bogle at auckland.ac.nz>
>     (64-9) 373-7599 Ext. 87030
>
>


-- 
Dr. Gib Bogle
Senior Research Fellow
Auckland Bioengineering Institute
University of Auckland
New Zealand

http://www.bioeng.auckland.ac.nz

g.bogle at auckland.ac.nz
(64-9) 373-7599 Ext. 87030

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