Hi Dan-<div>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:</div>
<div><a href="http://www.itk.org/pipermail/insight-users/2007-January/020532.html" target="_blank">http://www.itk.org/pipermail/insight-users/2007-January/020532.html</a></div><div><br></div><div><a href="http://www.itk.org/pipermail/insight-users/2007-January/020532.html" target="_blank"></a>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: <span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><a href="http://i.imgur.com/TCqL8.png" target="_blank" style="color: rgb(28, 81, 168); ">http://i.imgur.com/TCqL8.png</a></span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><a href="http://i.imgur.com/TCqL8.png" target="_blank" style="color: rgb(28, 81, 168); "></a><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">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. </span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; "><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">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-</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">-Ryan</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font>
<br><div class="gmail_quote">On Sun, Aug 15, 2010 at 11:22 PM, Dan Mueller <span dir="ltr"><<a href="mailto:dan.muel@gmail.com" target="_blank">dan.muel@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Ryan,<br>
<br>
You might consider using the "white top hat" operation to remove the background:<br>
WhiteTopHat = I - Dilate( Erode(I) )<br>
where I is the image, Erode is morphological erosion, and Dilate is<br>
morphological dilation.<br>
<br>
You can find an implementation of this operation in:<br>
Code/BasicFilters/itkWhiteTopHatImageFilter.h<br>
<br>
Once the background is removed, a simple global intensity threshold<br>
should suffice to segment the spots. The following filters may be<br>
helpful for that task:<br>
Code/BasicFilters/itkBinaryThresholdImageFilter.h<br>
Code/Algorithms/itkOtsuThresholdImageFilter.h<br>
Code/Review/itkKappaSigmaThresholdImageFilter.h<br>
<br>
HTH<br>
<br>
Cheers, Dan<br>
<div><div></div><div><br>
On 15 August 2010 23:04, Ryan Smith <<a href="mailto:ryanleesmith@gmail.com" target="_blank">ryanleesmith@gmail.com</a>> wrote:<br>
> Hi-<br>
> I am attempting to remove the background and detect features in the<br>
> following image:<br>
> <a href="http://i.imgur.com/wd3Yt.jpg" target="_blank">http://i.imgur.com/wd3Yt.jpg</a><br>
><br>
> I have a series of images in which the white circular spots travel and the<br>
> white vertical stripes remain stationary. I would like to apply some simple<br>
> background subtraction to remove the white stripes then autodetect the<br>
> intensity maxima associated with the circular features.<br>
><br>
> A brief search provided the following results which address similar problems<br>
> using itkConnectedComponentFilter. Is this what I want after my background<br>
> is subtracted? Any example code on how to get the location and sizes of the<br>
> components? Thanks in advance-<br>
><br>
> -Ryan<br>
><br>
><br>
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