who will talk about "Scientific case studies of Blender

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hugen
Posts: 17
Joined: Sun Aug 20, 2006 2:27 pm
Location: Stuttgart/Germany

who will talk about "Scientific case studies of Blender

Postby hugen » Tue Sep 05, 2006 12:10 pm

Hey,
I'm also working on scinentific visualization in Blender.
Who will talk about "Scientific case studies of Blender usage in simulation and research" at the conference?

thanks

fritz

ton
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Postby ton » Thu Oct 05, 2006 11:29 am

The schedule is online now:

http://www.blender.org/cms/Program.777.0.html

There are no contact details though, you have to wait for the proceedings to be put online.

Dani
Posts: 251
Joined: Fri Oct 18, 2002 8:35 pm

Postby Dani » Fri Oct 06, 2006 6:27 pm

Hum, that could have been interesting for me to attend at.

I hope there will be notes of all these meetings on the web site! They could be precious!

I used blender last year for the visualisation of results from morphometrical analysis software (Morphologika) in apes crania for my paleontology master.
However the french (sorry) paper that I wrote doesn't mention the process in Blender (this is undesired in a publication) but I still aknowledge the blender foundation at the end. Most pictures in the paper (cranial landmarks aquired using a microscribe => low-rez meshes) are done in Blender.

What made me export to blender is how painful it is in the other softwares (morphologika, morpheus, past) to have a good visualisation, well at least I found i difficult. So I exported the data (procrustes residuals) to excel and used excel to give me a wavefront *.obj. I *could* have used python, but the only module I really use is BGL, so I would have lost some time learning the other modules etc...

At the end I thought it could be great to have all the tools needed for morphometrics integrated in blender (from acquisition to visualisation)... so I changed from learning bones to learning computer programming ^^

It is good to see that blender is being used for scientific visualisations. I also beleive that it has a lot of what's needed for the treatment of raw data that is needed for morphometrics, and the visualisation of those results so it could be used as a framework for developping scientific software needing reasonably sophisticated 3D treatments/viz!

I'm looking up to reading those notes ;)

Ciao
Dani

PS: I now have moved on to a computer master as I said, with a lot of theory and practice of programming (it's java/perl/python, no C unfortunately) and I really hope to be able to tackle the Blender beast somewhere near next year ! :)

hugen
Posts: 17
Joined: Sun Aug 20, 2006 2:27 pm
Location: Stuttgart/Germany

Postby hugen » Sat Oct 07, 2006 5:08 pm

ok, I've talked to those guys.

Konrad Haenel (http://www.konrad-haenel.de) does some kind of visualization what scientists have in mind (from powerpoints) or from given CAD or OBJ data.

Albert Cardona Torrens does something similar but more in the scientific way (he can generate meshes out of image data by using ImageJ). Have a look yourself (http://www.pensament.net/java/index.html).

I think this session at the Blender Conference will be cool!

What I am trying is to connect simple simulations through a simple to handle python gui to Blender. I'm using VTK do do the visualization of the results. A pre pre pre version can be found at http://www.napshell.com/blender/. Would love to hear your comments.

bye

hugen

Leafw
Posts: 82
Joined: Sun Apr 18, 2004 10:53 pm

Postby Leafw » Sun Oct 08, 2006 5:11 pm

Just to mention we (a genetics and development lab at UCLA) are using Blender as the visualization and rendering tool for our modeling pipeline. No matter how good one can get in segmentation and thus object extraction from registered sets of 2D images (i.e. confocal stacks), the need to observe and colorize the 3D meshes is there, and Blender comes in really handy because:

- it's extendable with python, and thus it can interface basically any other program written in any language.
- the mesh edition and colorizing (materials) is just plain awesome, very useful to adjust and render models for publication.
- it's libre and free! Others are simply ridiculously expensive and/or buggy and/or incomplete and/or limited.
- it is very well documented, with many howtos and tutorials.

The ability to modify and extend blender for our needs (i.e. independence) is just what it's needed for a research environment, plus it runs on any platform that has a working GCC and can work over X sessions.

That said, we are modeling fruit fly (Drosophila) and flatworm brains, and having a lot of fun!

Related webpages:

http://www.ini.unizh.ch/~acardona/trakem2.html
http://www.mcdb.ucla.edu/research/hartenstein/
http://www.mcdb.ucla.edu/research/hartenstein/software/
( the above is the new version of http://www.pensament.net/java/CurveMorphing.html )

hugen
Posts: 17
Joined: Sun Aug 20, 2006 2:27 pm
Location: Stuttgart/Germany

Postby hugen » Sun Oct 08, 2006 6:10 pm

- the mesh edition and colorizing (materials) is just plain awesome, very useful to adjust and render models for publication.

I miss the rendering of alpha values at vertices very much.
I could do much nicer pix with that feature
- it's libre and free! Others are simply ridiculously expensive and/or buggy and/or incomplete and/or limited.

I think, that's because Blender was once commercial. That was a great start for this cool modeller. I don't care whether gui is included in the functions or not (the k3d developers always talk about that). It's working. Probably sometimes too slow (expecially on older machines it's going down while trying to move around in 3DView with > 500,000 faces).

bye

hugen

YB_Tech
Posts: 4
Joined: Thu Apr 24, 2008 7:58 pm

Postby YB_Tech » Thu Apr 24, 2008 8:37 pm

I simply wanted to know if Dani has had any new advancements in his research regards to Blender and the use of Python and other research software.

I went through Dani's search on the Aps/HomoSpacial Skulls and I thought it was pretty interesting. I also wanted to know if I would have the right to refer to his research on other projects that may have any relations to those studies.

Thank you for you input.


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