[Insight-users] Image filtering and feature detection-

[Dan Mueller]

Hi Ryan,

It looks like you have a problem with pixel type. Consider using a
real pixel type (eg. float or double).

HTH

Cheers, Dan

On 20 August 2010 22:06, Ryan Smith <ryanleesmith at gmail.com> wrote:
> Thanks again for all the help Dan.  I tried your suggestion for using
> the itkSignedMaurerDistanceMapImageFilter and got different results.  I sent
> in my BinaryThresholdImageFilter output and got the following from
> my itkSignedMaurerDistanceMapImageFilter
> http://i.imgur.com/jZ1AN.png
>
> Are there any other inputs I need to set for my Mauerer Distance Map?  This
> one is new to me and I didn't find much in the documentation.  Thanks-
> -Ryan
> p.s. You were right about my previous lossy compression woes
> On Thu, Aug 19, 2010 at 2:51 PM, Dan Mueller <dan.muel at gmail.com> wrote:
>>
>> Hi Ryan,
>>
>> 1. The output of the connected component filter you provided does not
>> seem right. Are you doubly sure you are passing the binary image to
>> the connected component filter? I have attached the output you should
>> get.
>>
>> 2. That said, if you just need to extract seeds for further
>> processing, I don't think you need to use the connected component
>> filter. This filter simply assigns a unique identifier (Eg. 1, 2, 3,
>> 4, etc) to each component or "blob" in the image. One way of obtaining
>> seeds is to take the binary image, compute the distance transform (try
>> Code/BasicFilters/itkSignedMaurerDistanceMapImageFilter.h), and the
>> apply the regional maxima filter
>> (Code/Review/itkRegionalMaximaImageFilter.h). I have attached the
>> output from this chain.
>>
>> HTH
>>
>> Cheers, Dan
>>
>> On 19 August 2010 21:20, Ryan Smith <ryanleesmith at gmail.com> wrote:
>> > Hi Dan-
>> > The white top hat worked great at removing my extra features, and the
>> > binary
>> > thresholding cleaned everything else up, however I am still having some
>> > trouble using the ConnectedComponentFilter.  I found this article which
>> > is
>> > trying to do exactly what I am attempting:
>> > http://www.itk.org/pipermail/insight-users/2007-January/020532.html
>> > I want the position and full width half max (FWHM) of each intensity
>> > maxima
>> > in the image.  I tried using the connected component filter and got the
>> > output found at the following URL: http://i.imgur.com/TCqL8.png
>> > It appears each feature is being tagged as several different features.
>> >  Just
>> > to confirm I am sending the binary thresholded image, not the
>> > original Gaussian spot image into the ConnectedComponentFilter.
>> > I feel like I am going down the wrong path here.  I don't necessarily
>> > need
>> > to segment my points, I just need to clean up the image (done) and
>> > potentially use techniques such as those in other ITK problems I have
>> > read
>> > to find 'seed points' for some region growing algorithms based on the
>> > intensity maxima of my image.  Any thoughts? Thanks in advance-
>> > -Ryan
>> >
>> >
>> > On Sun, Aug 15, 2010 at 11:22 PM, Dan Mueller <dan.muel at gmail.com>
>> > wrote:
>> >>
>> >> Hi Ryan,
>> >>
>> >> You might consider using the "white top hat" operation to remove the
>> >> background:
>> >>    WhiteTopHat = I - Dilate( Erode(I) )
>> >> where I is the image, Erode is morphological erosion, and Dilate is
>> >> morphological dilation.
>> >>
>> >> You can find an implementation of this operation in:
>> >>    Code/BasicFilters/itkWhiteTopHatImageFilter.h
>> >>
>> >> Once the background is removed, a simple global intensity threshold
>> >> should suffice to segment the spots. The following filters may be
>> >> helpful for that task:
>> >>    Code/BasicFilters/itkBinaryThresholdImageFilter.h
>> >>    Code/Algorithms/itkOtsuThresholdImageFilter.h
>> >>    Code/Review/itkKappaSigmaThresholdImageFilter.h
>> >>
>> >> HTH
>> >>
>> >> Cheers, Dan
>> >>
>> >> On 15 August 2010 23:04, Ryan Smith <ryanleesmith at gmail.com> wrote:
>> >> > Hi-
>> >> > I am attempting to remove the background and detect features in the
>> >> > following image:
>> >> > http://i.imgur.com/wd3Yt.jpg
>> >> >
>> >> > I have a series of images in which the white circular spots travel
>> >> > and
>> >> > the
>> >> > white vertical stripes remain stationary.  I would like to apply some
>> >> > simple
>> >> > background subtraction to remove the white stripes then autodetect
>> >> > the
>> >> > intensity maxima associated with the circular features.
>> >> >
>> >> > A brief search provided the following results which address similar
>> >> > problems
>> >> > using itkConnectedComponentFilter.  Is this what I want after my
>> >> > background
>> >> > is subtracted?  Any example code on how to get the location and sizes
>> >> > of
>> >> > the
>> >> > components? Thanks in advance-
>> >> >
>> >> > -Ryan
>> >> >
>> >> >
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