[Insight-users] suggestions for ITK-based projects for a graduate image analysis class?

Thu Sep 27 09:14:49 EDT 2012

Hi Arnaud, 

actually, you got me there :-D. I'm familiar with his work from his papers at ICCV 2005, in which I took part, namely at the Variational, Geometric, and Level Set Methods in Computer Vision workshop, but I have not followed his work closely since then. 

Essentially, I would like the students to be able to do a relatively simple statistical training, which as far as I know, is basically limited to 2D contours (correct me if I'm wrong...). There seems to be a survey paper out there in IJCV: A review of statistical approaches to level set segmentation: Integrating color, texture, motion and shape, so I would like my students to implement the simplest one. 

I anticipate that they will interact with you quite a bit if they opt for this project. 

Warm wishes,

Michel

Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
________________________________________
From: Arnaud Gelas [arnaudgelas at gmail.com]
Sent: Thursday, September 27, 2012 2:30 AM
To: Audette, Michel A.
Cc: Leila Baghdadi; insight-users at itk.org; wanlinzhu at gmail.com
Subject: Re: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?

Hi Michel,

In the current state of the v4 implementation, there is no shape prior
terms / formulations available; but that should not be too complicated
to implement.

Daniel Cremers has been quite prolific on that matters... Could you be
more specific and in which paper you would be interested?

Thanks!

Cheers,
Arnaud

On 09/26/2012 08:29 PM, Audette, Michel A. wrote:
> Hi Arnaud,
>
> I'm glad to hear back from you. Thanks for the intro to Dr Zhu's implementation; it reminds me of some of Dr Gilles topological operators.
>
> Getting back to the original discussion... can you comment on how much of the Level Sets implementation integrates statistical shape priors in the manner presented by Daniel Cremers?
>
> Cheers,
>
> Michel
>
> Michel Audette, Ph.D.
> Assistant Professor,
> Department of Modeling, Simulation and Visualization Engineering,
> Old Dominion University,
> Norfolk, VA.
> ________________________________________
> From: Arnaud Gelas [arnaudgelas at gmail.com]
> Sent: Wednesday, September 26, 2012 11:43 AM
> To: Leila Baghdadi
> Cc: Audette, Michel A.; insight-users at itk.org; wanlinzhu at gmail.com
> Subject: Re: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?
>
> Note that the sqrt 3 subdivision has already been implemented and
> submitted to an insight journal by wanlin zhu. He has also extended his
> work to deal with adaptive subdivision.
>
> The code is in really good shape and could be integrated in ITK quite
> quickly.
>
> my 2cts,
> Arnaud
>
> On 09/26/2012 05:40 PM, Leila Baghdadi wrote:
>> regarding number 2, to my knowledge most of the simplex deformable code in ITK is related to the work of Herve Delingette (also from INRIA), so my code just uses that concept and elaborates on it for multi object segmentation,
>>
>> one other note regarding subdivision of mesh for segmentation of high curvature areas, the paper I published uses vtk linear subdivision method which I do not think its the right thing but later I heard about
>> root 3 subdivision by Leif Kobbelt, I think its a great addition to the ITK deformable model segmentation which I hope to implement and submit it to ITK, so I will wait and see what changes you guys do to the original models,
>>
>> anyhow, I am all in for it, I can provide you with my code or help develop some of it, i.e the above
>>
>>
>> Leila
>>
>> ----- Original Message -----
>> From: "Audette, Michel A." <maudette at odu.edu>
>> Sent: Wed, 9/26/2012 11:17am
>> To: Leila Baghdadi <baghdadi at phenogenomics.ca> ; insight-users at itk.org
>> Subject: RE: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?
>>
>> Hi Leila,
>>
>> I'm familiar with both topics.
>>
>> I became interested in FSL through my interest in FIRST, for deep brain stimulation applications.
>>
>> The kind of multi-surface simplex modeling that you describe is related to the work of Benjamin Gilles of INRIA, and Dr Gilles is helping my group with our applications of multi-surface simplex. I can tell you that I have an on-going collaboration that is looking at reimplementing the ITK Simplex implementation, and it may be of interest to use code that does multi-surface, in the manner suggested by Dr Gilles.
>>
>> If you have code that relates to either area  that is ITK-friendly, I think that we could use it, and it would be great to make a contribution via Insight Journal.
>>
>> Cheers,
>>
>> Michel
>>
>> Michel Audette, Ph.D.
>> Assistant Professor,
>> Department of Modeling, Simulation and Visualization Engineering,
>> Old Dominion University,
>> Norfolk, VA.
>> ________________________________________
>> From: Leila Baghdadi [baghdadi at phenogenomics.ca]
>> Sent: Wednesday, September 26, 2012 10:58 AM
>> To: Audette, Michel A.; insight-users at itk.org
>> Subject: RE: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?
>>
>> Hi Michel,
>>
>> I was actually looking at a few of the ITK projects I have done in the past and wondering if I could find some free time to rewrite some of them for ITK4 and submit them to the journal,
>> so not sure if this is exactly the right thing for your students but I am gonna give it a shot anyways,
>>
>> 1. BET (brain segmentation algorithm) http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
>> I wrote the code for ITK 3.2 sometime ago and found it very useful, infact I think it was used to segment preterm baby brains. not sure if this is in ITK yet
>>
>> 2. simplex deformable model segmentation (multi-object) --> I added extra code for multi-object and collision detection of multi-mouse embryo segmentation, also in ITK3.2
>> published last year http://www.ncbi.nlm.nih.gov/pubmed/21679425
>>
>> Leila
>>
>> ----- Original Message -----
>> From: "Audette, Michel A." <maudette at odu.edu>
>> Sent: Wed, 9/26/2012 10:42am
>> To: insight-users at itk.org
>> Subject: [Insight-users] suggestions for ITK-based projects for a graduate image analysis class?
>>
>> Dear ITK users,
>>
>> I am teaching a graduate class in medical image analysis, and I would like to provide my students with a list of possible projects based on ITK that could implement recent algorithms, which possibly could then be submitted to Insight Journal and meet some needs of the ITK community. This class is based on the Toennies textbook from 2012, and will feature a number of registration and segmentation techniques, including graph cuts and level sets, as well as meshing methods not in the textbook. These projects will be for two students on which to collaborate, typically.
>>
>> If the community has any suggestions on how ITKv4 might be extended, based on recent papers in MICCAI, MedIA, or IEEE TMI, please let me know as soon as possible. Thanks for your kind consideration.
>>
>> Cheers,
>>
>> Michel
>>
>> Michel Audette, Ph.D.
>> Assistant Professor,
>> Department of Modeling, Simulation and Visualization Engineering,
>> Old Dominion University,
>> Norfolk, VA.
>> _____________________________________
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>> Visit other Kitware open-source projects at
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>>
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>>
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