<font><font face="verdana,sans-serif"><div>Have you considered this approach: <a href="http://www.ncbi.nlm.nih.gov/pubmed/14643218">Fernandez: An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms</a></div>
<div>or is this tensor approach equivalent to Hessian?</div><div><br></div><div>I have implemented this one using ITK, and I can provide the code if you want to compare it with the other approaches.</div></font></font><br>
<div class="gmail_quote">On Wed, Sep 5, 2012 at 6:08 PM, Dr. Roman Grothausmann <span dir="ltr"><<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.roman@mh-hannover.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Michel, dear Matt,<br>
<br>
<br>
Thanks for Your hints. I'll try Your implementations. So far I had limited my search to plateness and had not considered the word sheetness.<br>
<br>
Many Thanks<span class="HOEnZb"><font color="#888888"><br>
Roman</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
<br>
<br>
On 05/09/12 17:47, Matt McCormick wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Roman,<br>
<br>
We (Andinet Enquobarhrie) are working on a SheetnessImageFilter in TubeTK:<br>
<br>
<a href="http://tubetk.org/" target="_blank">http://tubetk.org/</a><br>
<a href="http://tubetk.org/gitweb?p=TubeTK.git;a=blob;f=Base/Filtering/itkSheetnessMeasureImageFilter.h;h=38b501eb9f5bc77e0b1d2b88c2b6c8ebc9fdc036;hb=635b5521a82dd3e333fa6febb01a5eabc1b3c7ba" target="_blank">http://tubetk.org/gitweb?p=<u></u>TubeTK.git;a=blob;f=Base/<u></u>Filtering/<u></u>itkSheetnessMeasureImageFilter<u></u>.h;h=<u></u>38b501eb9f5bc77e0b1d2b88c2b6c8<u></u>ebc9fdc036;hb=<u></u>635b5521a82dd3e333fa6febb01a5e<u></u>abc1b3c7ba</a><br>
<br>
Hope this helps,<br>
Matt<br>
<br>
On Wed, Sep 5, 2012 at 11:10 AM, Audette, Michel A.<<a href="mailto:maudette@odu.edu" target="_blank">maudette@odu.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Do a google on sheetness. Maxime Descôteaux and I had modified this type of operator a few years back to improve the detection of curviplanar bones (MICCAI paper, republished in J. Computer Assisted Surgery), which was a tweak of his and Frangi's work on vesselness operators.<br>
<br>
Michel<br>
<br>
Michel Audette, Ph.D.<br>
Assistant Professor,<br>
Department of Modeling, Simulation and Visualization Engineering,<br>
Old Dominion University,<br>
Norfolk, VA.<br>
______________________________<u></u>__________<br>
From: <a href="mailto:insight-users-bounces@itk.org" target="_blank">insight-users-bounces@itk.org</a> [<a href="mailto:insight-users-bounces@itk.org" target="_blank">insight-users-bounces@itk.org</a><u></u>] on behalf of Ho Cheung [<a href="mailto:hocheung20@gmail.com" target="_blank">hocheung20@gmail.com</a>]<br>
Sent: Wednesday, September 05, 2012 8:41 AM<br>
To: Dr. Roman Grothausmann<br>
Cc: <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a>; <a href="mailto:vmtk-users@lists.sourceforge.net" target="_blank">vmtk-users@lists.sourceforge.<u></u>net</a>; Luca Antiga<br>
Subject: Re: [Insight-users] enhancing plate like structures (by modifying itkHessianSmoothed3DToVesselne<u></u>ssMeasureImageFilter)<br>
<br>
Hi Dr. Grothausmann,<br>
<br>
The measure in ITK appears to be based on Sato (<a href="http://www.spl.harvard.edu/archive/spl-pre2007/pages/papers/yoshi/node3.html#SECTION00021000000000000000" target="_blank">http://www.spl.harvard.edu/<u></u>archive/spl-pre2007/pages/<u></u>papers/yoshi/node3.html#<u></u>SECTION00021000000000000000</a>) and I don't see an easy way to modify it so that it detects plate like structures instead of line like structures.<br>
<br>
If speed is not a major concern for you, may I suggest you implement a similar measure? Frangi's original vesselness enhancement formula (<a href="http://www.dtic.upf.edu/~afrangi/articles/miccai1998.pdf" target="_blank">http://www.dtic.upf.edu/~<u></u>afrangi/articles/miccai1998.<u></u>pdf</a>) can be easily modified for what you need and is based on Eigenvalues like Sato.<br>
<br>
According to equations 10, 11, 12, 13 in Frangi's paper and my interpretation of what the measures do, what you need is high Ra, Rb, and S values, so the formula becomes:<br>
<br>
V = [1 - exp(-Ra^2/2a^2)][1 - exp(-Rb^2/2b^2)][1 - exp(-S^2/2c62)]<br>
<br>
Hope, this helps,<br>
<br>
Ho Cheung<br>
Research Assistant<br>
Bio-Image Analytics Laboratory - University of Houston<br>
(832) 215-6347<br>
<br>
<br>
<br>
On Sep 5, 2012, at 3:36 AM, Dr. Roman Grothausmann<<a href="mailto:grothausmann.roman@mh-hannover.de" target="_blank">grothausmann.<u></u>roman@mh-hannover.de</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear mailing list members, dear Luca,<br>
<br>
<br>
Recently I was trying to enhance vascular structures from airways with the vessel enhancement filters from ITK (objectness and vessel enhancement). The problem is that these vessels are not filled in the tomograms our imaging technique yields. Only the airway walls are imaged, which corresponds to an uneven 2D surface. Since it is only a 3D not an ND problem, I tried to modify itkHessianSmoothed3DToVesselne<u></u>ssMeasureImageFilter to enhance not vessels (1D) structures but plates/walls. Therefore I exchanged lambda 1 and 3 in the weighting function. Sadly, I could not get the filter to enhance the airway walls.<br>
Have I missed anything or would enhancing plateness this way only work for not-curved planes?<br>
<br>
<br>
Here the important part of the diff of my changes:<br>
<br>
diff -au itk/IJ-Vessel_Enhancement_<u></u>Diffusion.1/<u></u>itkHessianSmoothed3DToVesselne<u></u>ssMeasureImageFilter.txx itk/plateness3D_01/<u></u>itkHessianSmoothed3DToPlatenes<u></u>sMeasureImageFilter.txx<br>
<br>
<br>
<br>
+ ////swap Lambda1 and Lambda3 to enhance "plateness"<br>
+ double swap_tmp= Lambda1;<br>
+ Lambda3= Lambda1;<br>
+ Lambda1= swap_tmp;<br>
+ ///swapping done<br>
+<br>
double Lambda1Abs = vnl_math_abs( Lambda1 );<br>
double Lambda2Abs = vnl_math_abs( Lambda2 );<br>
double Lambda3Abs = vnl_math_abs( Lambda3 );<br>
@@ -162,14 +168,13 @@<br>
double vesMeasure_3 =<br>
( 1 - vcl_exp( -1.0 * (( vnl_math_sqr( S )) / ( 2.0 * ( GammaSqr)))));<br>
<br>
- double vesMeasure_4 =<br>
- vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C )) /<br>
- ( Lambda2Abs * (Lambda3Sqr)));<br>
+ double vesMeasure_4 = 1; ////plateness for now not smoothed<br>
+ //double vesMeasure_4 = vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C )) / ( Lambda2Abs * (Lambda3Sqr))); ////check if this makes sense for plateness<br>
<br>
<br>
Many thanks for any help or hints.<br>
Roman<br>
<br>
--<br>
Dr. Roman Grothausmann<br>
<br>
Tomographie und Digitale Bildverarbeitung<br>
Tomography and Digital Image Analysis<br>
<br>
Institut für Funktionelle und Angewandte Anatomie, OE 4120<br>
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<br>
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<br>
-- <br>
Dr. Roman Grothausmann<br>
<br>
Tomographie und Digitale Bildverarbeitung<br>
Tomography and Digital Image Analysis<br>
<br>
Institut für Funktionelle und Angewandte Anatomie, OE 4120<br>
Medizinische Hochschule Hannover<br>
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