[ITK] ITK Example ShapeOpeningLabelMapFilter

[Jeanna S.]

Thanks for letting me know. I've changed the output image type to float and
now it no longer shows up as just black. I've attached my output image (the
image on the left is the input image; the image on the right is the output
image). However, the filter seems not to detect blood vessels like I hoped,
even after testing various values of Alpha, Beta, and Gamma. I was
wondering if anybody has suggestions on how to improve the vessel detection?

Thanks,
Jeanna

On Tue, Aug 9, 2016 at 6:29 AM, Dženan Zukić <dzenanz at gmail.com> wrote:

> Hi Jeanna,
>
> output of this filter is in [0,1] range, and if your output image type is
> not float then you will get an all-black image. Here is an example
> invocation:
>
>     typedef itk::HessianToObjectnessMeasureImageFilter< HessianImageType,
> FloatImageType > ObjectnessFilterType;
>     ObjectnessFilterType::Pointer objectnessFilter =
> ObjectnessFilterType::New();
>     objectnessFilter->SetBrightObject(true);
>     objectnessFilter->SetScaleObjectnessMeasure(false);
>     objectnessFilter->SetObjectDimension(2.5);
>     objectnessFilter->SetAlpha(0.5);
>     objectnessFilter->SetBeta(1.0);
>     objectnessFilter->SetGamma(5.0);
>     objectnessFilter->SetInput(hc->GetOutput());
>     objectnessFilter->Update();
>     FloatImageType::Pointer objectness = objectnessFilter->GetOutput();
>
> On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. <jeannasheen at gmail.com> wrote:
>
>> Actually, I found a way to display the images to the screen. However, I
>> am still not quite sure how to detect the blood vessels in my image. When I
>> apply the itkHessianToObjectnessMeasureImageFilter on my image, it just
>> turns out black. I was wondering if this is because there is not enough
>> contrast between the vessels and the background. If so, is there any
>> setting or threshold on the filter I can change so that it can detect the
>> blood vessels?
>>
>> Thanks,
>> Jeanna
>>
>> On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. <jeannasheen at gmail.com> wrote:
>>
>>> Hi Timothee,
>>>
>>> I'm using the itk:HessianToObjectnessMeasureImageFilter that you
>>> suggested. I was wondering if there is any way for me to view the image on
>>> the screen after it has been run through the filter, and if you have any
>>> examples of the filter working on an image.
>>>
>>> Thanks,
>>> Jeanna
>>>
>>> On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. <jeannasheen at gmail.com> wrote:
>>>
>>>> Hi Timothee,
>>>>
>>>> Thank you for replying. I will look into these methods.
>>>>
>>>> Jeanna
>>>>
>>>> On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain <
>>>> tevain at telecom-paristech.fr> wrote:
>>>>
>>>>> Hello Jeanna,
>>>>>
>>>>> I think this will be difficult just with the LabelMap framework.
>>>>> Usually to filter vessels you rely on some measures based on their
>>>>> shape, but in the ShapeLabelObject, the elongation measure is "the ratio of
>>>>> the longest physical size of the region [i.e. the bounding box] on one
>>>>> dimension and its smallest physical size". This is a quite coarse measure,
>>>>> sensitive to rotation, and I doubt it will be useful in your case.
>>>>> Aside from the attribute problem, you also have to detect the vessels
>>>>> prior to filtering them (i.e. getting a binary or a label image of
>>>>> vessels), and the LabelMap framework doesn't do that.
>>>>>
>>>>> I would suggest taking a look at these other methods:
>>>>> -Frangi's vesselness (implemented in itk through these filter :
>>>>> itkHessianToObjectnessMeasureImageFilter or
>>>>> itkHessian3DToVesselnessMeasureImageFilter)
>>>>> -Ranking Orientation Responses of Path Openings, aka RORPO (
>>>>> http://path-openings.github.io/RORPO/)
>>>>> -Fast Marching (itkFastMarchingImageFilter)
>>>>>
>>>>> HTH,
>>>>>
>>>>> Tim
>>>>>
>>>>> ----- Mail original -----
>>>>> De: "Jeanna S." <jeannasheen at gmail.com>
>>>>> À: community at itk.org
>>>>> Envoyé: Mercredi 3 Août 2016 03:08:42
>>>>> Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter
>>>>>
>>>>> Hello,
>>>>>
>>>>> I am trying to process the attached image using the
>>>>> ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a
>>>>> retina, and I want to use the image filter to remove the blood vessels from
>>>>> the picture (the blood vessels are the long, skinny, branching lines). I
>>>>> was wondering if the example code for the ShapeOpeningLabelMapFilter ( here
>>>>> ) would be able to do this with a little modification, and if so, which
>>>>> attribute would be the most useful to identify and remove the blood vessels.
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/mailman/listinfo/community
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> when the rich wage war, it's the poor who die
>>>>
>>>
>>>
>>>
>>> --
>>> when the rich wage war, it's the poor who die
>>>
>>
>>
>>
>> --
>> when the rich wage war, it's the poor who die
>>
>> _______________________________________________
>> Community mailing list
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>> http://public.kitware.com/mailman/listinfo/community
>>
>>
>


-- 
when the rich wage war, it's the poor who die
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