[ITK] ITK Example ShapeOpeningLabelMapFilter

Wed Aug 10 21:31:14 EDT 2016

Hi Dženan,

I actually found that I had to put
objectnessFilter->SetScaleObjectnessMeasure(false);. I already had
objectnessFilter->SetBrightObject(false); and
objectnessFilter->SetObjectDimension(1);. Now the output, which I've
attached, is much better, though it still shows some of the blobs. Thanks
for all your help.

Jeanna

On Wed, Aug 10, 2016 at 4:59 AM, Dženan Zukić <dzenanz at gmail.com> wrote:

> Hi Jeanna,
>
> by taking a look at the output, you need objectnessFilter->
> SetBrightObject(false); and a larger size of
> objectnessFilter->SetObjectDimension();
>
> HTH,
> Dženan
>
> On Wed, Aug 10, 2016 at 12:01 AM, Jeanna S. <jeannasheen at gmail.com> wrote:
>
>> 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
>>
>
>

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