[Paraview] Re: biomedical data and VTK

[Jordi Campos i Miralles]

El dt 16 de 01 del 2007 a les 19:35 +0200, en/na Dan White va escriure:
> Hi,

Hi! Thank you for your answer ;) I took a lot of time to answer
because we were preparing a ParaView introduction workshop to high
school students (I've just sent a message to the list about it, that is
placed here [1]). So, sorry for the delay.

> 
> paraview isnt really designed for biomedical image data visualisation.
> 
> however several other free open source projects using VTK,
> ARE designed for biomedical data.
> 
> on OS X there is the brilliant Osirix,
> and on all  platforms there is Slicer3D, GE Microview, and our new  
> project BioImageXD
> 
> At BioImageXD we are very interested in vew fast volume rendering  
> methods being implemented in VTK

Nice, so if I start implementing it on VTK, at least there is one
project interested in it.

> As far as i unserstand it, there is no reason that you could not  
> implement splatting  in VTK.

Perfect! I was worried to know why no body has implemented it before. To
be sure it is feasible.

> see out project at
> http://www.bioimagexd.net

Interesting features and interesting license (GPL)! 

> Its written mostly in python with a few custom VTK C++ classes, and  
> relies heavily on VTK for openGL graphics
> and image processing,
> and ITK for segmentation stuff.
> The project is 3 years old and maturing rapidly .
> We are about to hire another programmer, so we will then have 2  
> programmers, as well as several biologists like me helping out.

This information is relevant for me in order to choose with which
project being involved. Thanks.

> maybe we can work together?
> We are interested in all kinds of collaborations.

Good news. We can see which can of collaboration we could have.

My thoughts are: (1) implement splatting algorithm in VTK, (2) find an
"interface application" to use it.

It seems, that your project could cover the second step. So, we could
find a way to collaborate. On the other hand, do you have programmers
that could help me to start on the first step? It could be an starting
point to know each others.

> There will be a new windows beta version of BioImageXD coming very soon,
> with linux and OS X to follow.
> The current development source code is also available
> for programmers like yourself that know what to do with it!

Ok, may I have a look? I check the web page, but only the sample data
sets are currently available. By the way, I develop on linux.

I think my first focus should be step (1), but I would be important to
have a minimum of step (2) ready to test it.

> 
> I am moving to Perpignan soon, so wont be too far from you.

Good! So may be we even could meet in some moment.

> 
> cheers
> 
> Dan

regards!

jor;)i


[1] http://truja.lsi.upc.edu/movibio/soft/paraview/Workshop

> 
> 
> 
> > Message: 1
> > Date: Mon, 15 Jan 2007 21:41:15 +0100
> > From: Jordi Campos i Miralles <jcampos at maia.ub.es>
> > Subject: [Paraview] Newbie: contributing with an implementation of the
> > 	Splatting algorithm
> > To: paraview at paraview.org
> > Message-ID: <1168893675.31216.114.camel at trantor>
> > Content-Type: text/plain; charset=ISO-8859-15
> >
> > Hi all,
> >
> > I'm a PhD student [0] at Universitat Politècnica de Catalunya [1] and
> > Universitat de Barcelona [2], working on Volume Visualization at  
> > MoViBio
> > research group [3].
> >
> > The research group has its own software system Hipovis [4], but I am
> > evaluating the possibility of using other software systems. Right now,
> > I'm evaluating using ParaView/VTK to test current research  
> > approaches on
> > Focus+Context Volume Visualization based on the Splatting algorithm  
> > [5].
> >
> > As far as I know, VTK libraries does not offer the Volume Splatting
> > algorithm [6] and there are no available examples of implementing it
> > using VTK. However, I found references to works that use VTK to
> > implement Splatting approaches [7], but no code is available.
> >
> >
> >
> > Hence, I have the following questions::::::::::::::::
> >
> > A- Is there any VTK's architectural reason why the splatting algorithm
> > does not suit the VTK libraries? May be implementing the splatting
> > algorithm inside the VTK's pipeline architecture will not provide  
> > enough
> > performance to develop research activities, will it?
> >
> > B- Although ParaView offers fast volume rendering (textures), precise
> > v.r. (RayCast) and both qualities v.r. (using VolumePro hw), will  
> > it be
> > worth if I work on adding the Splatting algorithm and Focus+Context
> > features? (for me it is worth because it is the basis of my thesis  
> > but I
> > would like to know if there are other people also interested in it).
> >
> > C- If I want to be involved in VTK development to implement the
> > Splatting algorithm, which steps do you recommend me? From you
> > experience, how long does it take to a PhD student (with C++ and
> > graphics knowledge) to get involved with the project and develop new
> > code? (I know this is a generic question, but I need some  
> > estimation). I
> > already bought the two books [8][9], reviewed the coding standards  
> > [10]
> > and subscribed to the list.
> >
> > D- If I want to be involved in ParaView development to use the  
> > Splatting
> > algorithm and implement Focus+Context features, which steps do you
> > recommend me?  From you experience, how long does it take to a PhD
> > student (with C++ and graphics knowledge) to get involved with the
> > project and develop new code? (I know this is a generic question,  
> > but I
> > need some estimation). I already ordered the book [11] and  
> > subscribed to
> > the list.
> >
> > E- Which are the good and bad points of ParaView/VTK versus VolumeShop
> > [12]? It seems VolumeShop is not really open source (and we are  
> > looking
> > an open source project to get involved), it is mainly used on  
> > MsWindows
> > platforms (and we are interested in a multi-platform environment), and
> > it does not provide parallel rendering.
> >
> > F- Which are the good and bad points of ParaView/VTK versus VolView
> > [13]?
> >
> >
> >
> >
> > I would like to known your opinion about these questions and any other
> > possible important factors you think I should pay attention.
> >
> >
> >
> > Thank you very much in advance.
> >
> >
> > jor;)i
> >
> >
> 
> Dr. Daniel James White BSc. (Hons.) PhD
> Bioimaging Coordinator
> Nanoscience Centre and Department of Biological and Environmental  
> Sciences
> Division of Molecular Recognition
> Ambiotica C242
> PO Box 35
> University of Jyväskylä
> Jyväskylä
> FIN 40014
> Finland
> 
> +358 14 260 4183 (work)
> +358 468102840 (mobile)
> http://www.bioimagexd.net
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> white at cc.jyu.fi
> 
> 
>