[ITK] ITK Example ShapeOpeningLabelMapFilter

[Dženan Zukić]

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
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20160809/19c6914f/attachment-0001.html>