[Insight-users] [ITK Community] Automatically finding spheres in 3D images

Wed Dec 18 18:51:53 EST 2013

The ShapeLabelObject family that Bill has mentioned includes a "roundness"
attribute. This means that you can use AttributeOpeningLabelMapFilter to
filter connected components based on roundness. Roundness is a measure
based on surface area and volume. There are limitations to how well it can
separate some blobs, due to the discrete nature of the surfaces, but it is
a useful starting point for many applications.

Note that the wiki example does

BinaryImageToShapeLabelMapFilter then ShapeOpeningLabelMapFilter then
LabelMapToLabelImageFilter

The AttributeOpeningLabelMapFilter does that internally - it is a
helper class to avoid the need to deal with label maps directly

On Thu, Dec 19, 2013 at 7:51 AM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> But, I do think the label map tools might help find sphere... So if
> the blobs are spheres, then may the title is  OK. The ShapeAttributes
> example could be a start to detect spherical shapes.
>
> On Wed, Dec 18, 2013 at 3:50 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
> > I think the section title is a bit overzealous...
> >
> >
> > On Wed, Dec 18, 2013 at 12:01 PM, Bradley Lowekamp <brad at lowekamp.net>
> wrote:
> >> Bill,
> >>
> >> What is there (example/filter) that you would consider "Blob detection"?
> >>
> >> Brad
> >>
> >> On Dec 18, 2013, at 11:50 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
> >>
> >>> David,
> >>>
> >>> This section in the ITK Wiki Examples:
> >>>
> >>> Blob Detection, Labeling, and Properties
> >>>
> http://itk.org/Wiki/ITK/Examples#Blob_Detection.2C_Labeling.2C_and_Properties
> >>> may be useful. In particular: ShapeAttributes
> >>> http://itk.org/Wiki/ITK/Examples/ImageProcessing/ShapeAttributes
> >>> runs connected components on a binary image, converts it to a LabelMap
> >>> and prints lots of statistics. The Elongation parameter is the  ratio
> >>> of the largest principal moment to the second largest principal
> >>> moment. Its value is greater or equal to 1.
> >>>
> >>> On Wed, Dec 18, 2013 at 10:18 AM, Bill Lorensen <
> bill.lorensen at gmail.com> wrote:
> >>>> If you already have segmented the objects, look at Filtering/LabelMap.
> >>>> Look at the test: LabelMap/test/itkShapeLabelObjectAccessorsTest1.cxx
> >>>>
> >>>>
> >>>>
> >>>> On Wed, Dec 18, 2013 at 9:10 AM, Bradley Lowekamp <brad at lowekamp.net>
> wrote:
> >>>>> Ohh, yeah there are morphology techniques too.
> >>>>>
> >>>>> I believe the top-hat[1][2] filter can also be very useful for
> detecting dark/black spots smaller the the structuring element.
> >>>>>
> >>>>> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1BlackTopHatImageFilter.html
> >>>>> [2]
> http://www.itk.org/Doxygen/html/classitk_1_1WhiteTopHatImageFilter.html
> >>>>>
> >>>>> On Dec 18, 2013, at 9:05 AM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
> >>>>>
> >>>>>> Hi Dave,
> >>>>>>
> >>>>>> Binary morphological opening [1] may work well.  See, for example
> [2].
> >>>>>>
> >>>>>> Hope this helps,
> >>>>>> Matt
> >>>>>>
> >>>>>> [1]
> http://itk.org/Doxygen/html/classitk_1_1BinaryMorphologicalOpeningImageFilter.html
> >>>>>> [2] http://homepages.inf.ed.ac.uk/rbf/HIPR2/open.htm
> >>>>>>
> >>>>>> On Wed, Dec 18, 2013 at 8:57 AM, David Cole <dlrdave at aol.com>
> wrote:
> >>>>>>>> Have you tried Hough transforms?
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> http://www.itk.org/Doxygen/html/classitk_1_1HoughTransform2DCirclesImageFilter.html
> >>>>>>>
> >>>>>>>
> >>>>>>> Not yet, but I will now, thanks very much!
> >>>>>>>
> >>>>>>>
> >>>>>>> D
> >>>>>>>
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