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<div class="moz-cite-prefix">I didn't think there would be a stock
filter, but maybe somebody else has addressed this.<br>
<br>
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.<br>
<br>
Gib<br>
<br>
On 23/05/2013 8:53 a.m., Dženan Zukić wrote:<br>
</div>
<blockquote
cite="mid:CAPf2UMQ3r7ThTApqNQT7xSwWYyWpOkOnHRx8pF+-Qk9aWY4xRg@mail.gmail.com"
type="cite">
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<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small">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?</div>
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<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, May 22, 2013 at 10:50 PM, Gib
Bogle <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:g.bogle@auckland.ac.nz" target="_blank">g.bogle@auckland.ac.nz</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>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).<br>
<br>
Gib
<div>
<div class="h5"><br>
<br>
On 22/05/2013 11:12 p.m., Dženan Zukić wrote:<br>
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<div class="h5">
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small"><a
moz-do-not-send="true"
href="http://www.itk.org/Doxygen/html/group__MathematicalMorphologyImageFilters.html"
target="_blank">http://www.itk.org/Doxygen/html/group__MathematicalMorphologyImageFilters.html</a><br>
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<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small"><br>
</div>
<div class="gmail_default"
style="font-family:verdana,sans-serif;font-size:small">What
you probably want to do is BinaryErode and
BinaryDilate.</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, May 22, 2013 at
7:04 AM, gib <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:g.bogle@auckland.ac.nz"
target="_blank">g.bogle@auckland.ac.nz</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">It's hard to know what
to call the processing I want to apply. I
have a set<br>
of biological images (actually a 3D image, but
for now I'm happy to process<br>
the frames one-by-one) in which the region of
interest has an irregular and<br>
incomplete labelled layer around the boundary.
The staining of the layer<br>
was unintended, and its presence interferes
with the segmentation that I am<br>
doing. The part of the image that I want to
extract is made up of many<br>
disconnected objects, and there is not much
difference in the intensity<br>
ranges of the objects of interest and the
unwanted edge. I am willing to<br>
trim a few pixels off the boundary all the way
around - this will not cause<br>
much loss of information. What I need is way
to determine a sequence of<br>
pixels that in some sense defines the extent
of the labelled region in the<br>
image, rather like a 2D shrink wrapping. I
could then use this to shave or<br>
peel off the outer layer of pixels.<br>
<br>
Does this process have a name? Are there any
existing filters or code to do<br>
this? Any clever suggestions (I have some
ideas)?<br>
<br>
Thanks<br>
Gib<br>
<br>
<br>
<br>
--<br>
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<span class="HOEnZb"><font color="#888888">
<pre cols="80">--
Dr. Gib Bogle
Senior Research Fellow
Auckland Bioengineering Institute
University of Auckland
New Zealand
<a moz-do-not-send="true" href="http://www.bioeng.auckland.ac.nz" target="_blank">http://www.bioeng.auckland.ac.nz</a>
<a moz-do-not-send="true" href="mailto:g.bogle@auckland.ac.nz" target="_blank">g.bogle@auckland.ac.nz</a>
(64-9) 373-7599 Ext. 87030
</pre>
</font></span></div>
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<br>
<pre class="moz-signature" cols="80">--
Dr. Gib Bogle
Senior Research Fellow
Auckland Bioengineering Institute
University of Auckland
New Zealand
<a class="moz-txt-link-freetext" href="http://www.bioeng.auckland.ac.nz">http://www.bioeng.auckland.ac.nz</a>
<a class="moz-txt-link-abbreviated" href="mailto:g.bogle@auckland.ac.nz">g.bogle@auckland.ac.nz</a>
(64-9) 373-7599 Ext. 87030
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