<div dir="ltr"><div><div><div>Hi,<br></div>I'm not sure I understand completely, but here's my suggestion of an approach. It may turn out to be easier if you have other staining too. <br><br></div>1) Segment the entire tissue - i.e generate one large object that contains all your small vessels and a boundary on your layer that you need to peel. More on how this might be achieved later.<br>
<br></div>2) Erode this object and use the eroded version to mask out the accidental staining - i.e. do the peeling. Then apply your normal segmentation to what is left.<br><div><br> If you have another channel where all the tissue has contrast then segmenting the tissue will be relatively easy. Otherwise it will be a bit more of a challenge. My first guess if the latter is the case is to use 2 markers in a watershed. One marker will be the image border (definitely outside the tissue). Create the marker image as follows. <br>
</div><div> a) Apply a large closing, say about 15% of the tissue size. This will connect your interior objects together. Threshold the result, choose the largest connected component, then erode that component a little to make sure it stays inside the tissue and use the result as your foreground marker. Use rectangular structuring elements for the closing so you can take advantage of fast operations.<br>
</div><div> b) put the two markers together in an image such that they have different voxel values - i.e. image border has value 2, inside marker from step a has value 1.<br><br></div><div>Use the combined image as the marker image for the morphological markers filter, use the original as the control. You may need to smooth the original to close boundary gaps in faint areas. You shouldn't need to take a gradient because the staining forms a line which the watershed should find. <br>
<br></div><div>Select the foreground label from the watershed result. Erode it a bit (you'll need to look to confirm how much).<br><br></div><div>If there is a gap then the watershed will leak through, but this won't matter as you are going to erode the mask and areas with gaps don't need to be corrected anyway.<br>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, May 23, 2013 at 7:47 AM, Gib Bogle <span dir="ltr"><<a 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>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.<span class="HOEnZb"><font color="#888888"><br>
<br>
Gib</font></span><div><div class="h5"><br>
<br>
On 23/05/2013 8:53 a.m., Dženan Zukić wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">
<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>
</div>
<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 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><br>
<br>
On 22/05/2013 11:12 p.m., Dženan Zukić wrote:<br>
</div>
</div>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><a href="http://www.itk.org/Doxygen/html/group__MathematicalMorphologyImageFilters.html" target="_blank">http://www.itk.org/Doxygen/html/group__MathematicalMorphologyImageFilters.html</a><br>
</div>
<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 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><font color="#888888">
<pre cols="80">--
Dr. Gib Bogle
Senior Research Fellow
Auckland Bioengineering Institute
University of Auckland
New Zealand
<a href="http://www.bioeng.auckland.ac.nz" target="_blank">http://www.bioeng.auckland.ac.nz</a>
<a 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 cols="80">--
Dr. Gib Bogle
Senior Research Fellow
Auckland Bioengineering Institute
University of Auckland
New Zealand
<a href="http://www.bioeng.auckland.ac.nz" target="_blank">http://www.bioeng.auckland.ac.nz</a>
<a href="mailto:g.bogle@auckland.ac.nz" target="_blank">g.bogle@auckland.ac.nz</a>
(64-9) 373-7599 Ext. 87030
</pre>
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