[Insight-users] Peel an image
Gib Bogle
g.bogle at auckland.ac.nz
Wed May 22 21:46:49 EDT 2013
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
> <mailto: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
>> <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
>>>
>>>
>>>
>>> --
>>> View this message in context:
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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 <mailto:g.bogle at auckland.ac.nz>
> (64-9) 373-7599 Ext. 87030
>
>
> _____________________________________
> Powered by www.kitware.com <http://www.kitware.com>
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
>
--
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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