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<div class="moz-cite-prefix">Hi Richard,<br>
<br>
I don't have other staining.<br>
<br>
Thanks for your suggestion of a procedure. I will have to study
it and understand it, before I can comment on it.<br>
<br>
Gib<br>
<br>
On 23/05/2013 12:25 p.m., Richard Beare wrote:<br>
</div>
<blockquote
cite="mid:CA+V7QS_9HkJTPF_rNmNgbq2fMm-zsUjiNpg018Xwt1_n2-m1xw@mail.gmail.com"
type="cite">
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<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 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>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
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><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
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>
</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
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>
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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 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
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<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
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<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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