[ITK] ITK Example ShapeOpeningLabelMapFilter
Dženan Zukić
dzenanz at gmail.com
Thu Aug 11 07:51:52 EDT 2016
Hi Jeanna,
since this is a 2D image, you may pay some extra computation to get better
results. Try using multi-scale
<https://itk.org/Doxygen/html/SphinxExamples_2src_2Nonunit_2Review_2SegmentBloodVesselsWithMultiScaleHessianBasedMeasure_2Code_8cxx-example.html#_a3>
approach, and then filter out smaller vessels.
Regards
On Wed, Aug 10, 2016 at 9:30 PM, Jeanna S. <jeannasheen at gmail.com> wrote:
> 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->SetBrightObj
>> ect(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.
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> when the rich wage war, it's the poor who die
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>>>>>
>>>>>
>>>>>
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>>>>> when the rich wage war, it's the poor who die
>>>>>
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>>>>> Community mailing list
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>>>>
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>
>
> --
> when the rich wage war, it's the poor who die
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