[Insight-users] enhancing plate like structures (by modifying itkHessianSmoothed3DToVesselnessMeasureImageFilter)

Thu Sep 6 04:49:03 EDT 2012

Have you considered this approach: Fernandez: An improved algorithm for
anisotropic nonlinear diﬀusion for denoising
cryo-tomograms<http://www.ncbi.nlm.nih.gov/pubmed/14643218>
or is this tensor approach equivalent to Hessian?

I have implemented this one using ITK, and I can provide the code if you
want to compare it with the other approaches.

On Wed, Sep 5, 2012 at 6:08 PM, Dr. Roman Grothausmann <
grothausmann.roman at mh-hannover.de> wrote:

> Dear Michel, dear Matt,
>
>
> 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.
>
> Many Thanks
> Roman
>
>
>
>
> On 05/09/12 17:47, Matt McCormick wrote:
>
>> Hi Roman,
>>
>> We (Andinet Enquobarhrie) are working on a SheetnessImageFilter in TubeTK:
>>
>>    http://tubetk.org/
>>    http://tubetk.org/gitweb?p=**TubeTK.git;a=blob;f=Base/**Filtering/**
>> itkSheetnessMeasureImageFilter**.h;h=**38b501eb9f5bc77e0b1d2b88c2b6c8**
>> ebc9fdc036;hb=**635b5521a82dd3e333fa6febb01a5e**abc1b3c7ba<http://tubetk.org/gitweb?p=TubeTK.git;a=blob;f=Base/Filtering/itkSheetnessMeasureImageFilter.h;h=38b501eb9f5bc77e0b1d2b88c2b6c8ebc9fdc036;hb=635b5521a82dd3e333fa6febb01a5eabc1b3c7ba>
>>
>> Hope this helps,
>> Matt
>>
>> On Wed, Sep 5, 2012 at 11:10 AM, Audette, Michel A.<maudette at odu.edu>
>>  wrote:
>>
>>> 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.
>>>
>>> Michel
>>>
>>> Michel Audette, Ph.D.
>>> Assistant Professor,
>>> Department of Modeling, Simulation and Visualization Engineering,
>>> Old Dominion University,
>>> Norfolk, VA.
>>> ______________________________**__________
>>> From: insight-users-bounces at itk.org [insight-users-bounces at itk.org**]
>>> on behalf of Ho Cheung [hocheung20 at gmail.com]
>>> Sent: Wednesday, September 05, 2012 8:41 AM
>>> To: Dr. Roman Grothausmann
>>> Cc: insight-users at itk.org; vmtk-users at lists.sourceforge.**net<vmtk-users at lists.sourceforge.net>;
>>> Luca Antiga
>>> Subject: Re: [Insight-users] enhancing plate like structures (by
>>> modifying      itkHessianSmoothed3DToVesselne**ssMeasureImageFilter)
>>>
>>> Hi Dr. Grothausmann,
>>>
>>> The measure in ITK appears to be based on Sato (
>>> http://www.spl.harvard.edu/**archive/spl-pre2007/pages/**
>>> papers/yoshi/node3.html#**SECTION00021000000000000000<http://www.spl.harvard.edu/archive/spl-pre2007/pages/papers/yoshi/node3.html#SECTION00021000000000000000>)
>>> and I don't see an easy way to modify it so that it detects plate like
>>> structures instead of line like structures.
>>>
>>> If speed is not a major concern for you, may I suggest you implement a
>>> similar measure? Frangi's original vesselness enhancement formula (
>>> http://www.dtic.upf.edu/~**afrangi/articles/miccai1998.**pdf<http://www.dtic.upf.edu/~afrangi/articles/miccai1998.pdf>)
>>> can be easily modified for what you need and is based on Eigenvalues like
>>> Sato.
>>>
>>> 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:
>>>
>>> V = [1 - exp(-Ra^2/2a^2)][1 - exp(-Rb^2/2b^2)][1 - exp(-S^2/2c62)]
>>>
>>> Hope, this helps,
>>>
>>> Ho Cheung
>>> Research Assistant
>>> Bio-Image Analytics Laboratory - University of Houston
>>> (832) 215-6347
>>>
>>>
>>>
>>> On Sep 5, 2012, at 3:36 AM, Dr. Roman Grothausmann<grothausmann.**
>>> roman at mh-hannover.de <grothausmann.roman at mh-hannover.de>>  wrote:
>>>
>>>  Dear mailing list members, dear Luca,
>>>>
>>>>
>>>> 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**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.
>>>> Have I missed anything or would enhancing plateness this way only work
>>>> for not-curved planes?
>>>>
>>>>
>>>> Here the important part of the diff of my changes:
>>>>
>>>> diff -au itk/IJ-Vessel_Enhancement_**Diffusion.1/**
>>>> itkHessianSmoothed3DToVesselne**ssMeasureImageFilter.txx
>>>> itk/plateness3D_01/**itkHessianSmoothed3DToPlatenes**
>>>> sMeasureImageFilter.txx
>>>>
>>>>
>>>>
>>>> +      ////swap Lambda1 and Lambda3 to enhance "plateness"
>>>> +      double swap_tmp= Lambda1;
>>>> +      Lambda3= Lambda1;
>>>> +      Lambda1= swap_tmp;
>>>> +      ///swapping done
>>>> +
>>>>        double Lambda1Abs = vnl_math_abs( Lambda1 );
>>>>        double Lambda2Abs = vnl_math_abs( Lambda2 );
>>>>        double Lambda3Abs = vnl_math_abs( Lambda3 );
>>>> @@ -162,14 +168,13 @@
>>>>        double vesMeasure_3  =
>>>>           ( 1 - vcl_exp( -1.0 * (( vnl_math_sqr( S )) / ( 2.0 * (
>>>> GammaSqr)))));
>>>>
>>>> -      double vesMeasure_4  =
>>>> -         vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C )) /
>>>> -                                   ( Lambda2Abs * (Lambda3Sqr)));
>>>> +      double vesMeasure_4  = 1; ////plateness for now not smoothed
>>>> +      //double vesMeasure_4  = vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr(
>>>> m_C )) / ( Lambda2Abs * (Lambda3Sqr))); ////check if this makes sense for
>>>> plateness
>>>>
>>>>
>>>> Many thanks for any help or hints.
>>>> Roman
>>>>
>>>> --
>>>> Dr. Roman Grothausmann
>>>>
>>>> Tomographie und Digitale Bildverarbeitung
>>>> Tomography and Digital Image Analysis
>>>>
>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>> Medizinische Hochschule Hannover
>>>> Carl-Neuberg-Str. 1
>>>> 30625 Hannover
>>>>
>>>> Tel. +49 511 532-9574
>>>> ______________________________**_______
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/**opensource/opensource.html<http://www.kitware.com/opensource/opensource.html>
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/**products/protraining.php<http://www.kitware.com/products/protraining.php>
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_**FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://www.itk.org/mailman/**listinfo/insight-users<http://www.itk.org/mailman/listinfo/insight-users>
>>>>
>>>
>>> ______________________________**_______
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/**opensource/opensource.html<http://www.kitware.com/opensource/opensource.html>
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/**products/protraining.php<http://www.kitware.com/products/protraining.php>
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_**FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://www.itk.org/mailman/**listinfo/insight-users<http://www.itk.org/mailman/listinfo/insight-users>
>>>
>>>
>>> --
>>> BEGIN-ANTISPAM-VOTING-LINKS
>>> ------------------------------**------------------------
>>>
>>> Teach CanIt if this mail (ID 699566122) is spam:
>>> Spam:        https://www.spamtrap.odu.edu/**b.php?i=699566122&m=**
>>> 6758d860fb26&t=20120905&c=s<https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=s>
>>> Not spam:    https://www.spamtrap.odu.edu/**b.php?i=699566122&m=**
>>> 6758d860fb26&t=20120905&c=n<https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=n>
>>> Forget vote: https://www.spamtrap.odu.edu/**b.php?i=699566122&m=**
>>> 6758d860fb26&t=20120905&c=f<https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=f>
>>> ------------------------------**------------------------
>>> END-ANTISPAM-VOTING-LINKS
>>>
>>> ______________________________**_______
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/**opensource/opensource.html<http://www.kitware.com/opensource/opensource.html>
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/**products/protraining.php<http://www.kitware.com/products/protraining.php>
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_**FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://www.itk.org/mailman/**listinfo/insight-users<http://www.itk.org/mailman/listinfo/insight-users>
>>>
>>
> --
> Dr. Roman Grothausmann
>
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
>
> Institut für Funktionelle und Angewandte Anatomie, OE 4120
> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> 30625 Hannover
>
> Tel. +49 511 532-9574
> ______________________________**_______
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/**opensource/opensource.html<http://www.kitware.com/opensource/opensource.html>
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/**products/protraining.php<http://www.kitware.com/products/protraining.php>
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_**FAQ <http://www.itk.org/Wiki/ITK_FAQ>
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/**listinfo/insight-users<http://www.itk.org/mailman/listinfo/insight-users>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20120906/d20be50f/attachment.htm>