[Insight-users] Peel an image

Thu May 23 06:04:39 EDT 2013

The steps I've given should also work in 3D if the slice thickness is low
enough to provide the connectivity between slices. Personally, I haven't
had much luck with the vesselness family. My rule of thumb is that if they
happen to work, then a simple morphological approach will probably work
too, more reliably and with fewer parameters to fiddle :-).

On Thu, May 23, 2013 at 5:36 PM, Dan Mueller <dan.muel at gmail.com> wrote:

> Hi Gib,
>
> Some more food for thought:
>
> (1) If you have a 3D image (as opposed to 2D slices) you may consider
> using Hessian-based vesselness enhancement:
>
> http://www.itk.org/Doxygen/html/classitk_1_1Hessian3DToVesselnessMeasureImageFilter.html
>
> http://www.itk.org/Doxygen/html/classitk_1_1MultiScaleHessianBasedMeasureImageFilter.html
> http://www.insight-journal.org/browse/publication/314
> http://www.insight-journal.org/browse/publication/175
> http://www.insight-journal.org/browse/publication/163
>
> This class of filters can enhance tube-like structures (e.g. vessels),
> while suppressing sheet like structures i.e. the outer border of your
> object.
>
> (2) You could consider using an active contour method to segment the
> outer structure (replacing step 1 in Richard's proposal above). You
> could achieve this by initializing the contour as the edge of your
> image, then shrink the contour until it attaches to the boundary of
> the tissue. Then continue to follow Richard's second step and remove
> the outer structure by erosion + masking.
>
> Good luck.
>
> Cheers, Dan
>
> On 23 May 2013 11:16, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> > Hi Richard,
> >
> > I don't have other staining.
> >
> > Thanks for your suggestion of a procedure.  I will have to study it and
> > understand it, before I can comment on it.
> >
> > Gib
> >
> >
> > On 23/05/2013 12:25 p.m., Richard Beare wrote:
> >
> > Hi,
> > 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.
> >
> > 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.
> >
> > 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.
> >
> >  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.
> >    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.
> >    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.
> >
> > 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.
> >
> > Select the foreground label from the watershed result. Erode it a bit
> > (you'll need to look to confirm how much).
> >
> > 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.
> >
> >
> > On Thu, May 23, 2013 at 7:47 AM, Gib Bogle <g.bogle at auckland.ac.nz>
> wrote:
> >>
> >> 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>
> >> 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> 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
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> View this message in context:
> >>>>
> http://itk-insight-users.2283740.n2.nabble.com/Peel-an-image-tp7583137.html
> >>>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
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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
> >>> (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
> >>
> >>
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
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> >> http://www.kitware.com/products/protraining.php
> >>
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> >>
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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
> > (64-9) 373-7599 Ext. 87030
> >
> >
> > _____________________________________
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> >
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