source: http://www.cg.tuwien.ac.at/research/publications/2006/bruckner-2006-ICE/

Stefan Bruckner, Sören Grimm, Armin Kanitsar, Meister Eduard Gröller
Illustrative Context-Preserving Exploration of Volume Data
IEEE Transactions on Visualization and Computer Graphics, 12(6):1559-1569, November 2006

Why? Just play the video….o…my..god. Basically played it about 1000 times last 2 years, time to share it with the world!

The application

The application I will present on the 7th of june is made to educate medical students in the subject of structural brain connectibity (SBC). As SBC cannot be seen in a human cadaver, and is hard to explain using only classical education methods as textbooks and literature slides, an interactive application could prove to be useful. As shown by Dale’s cone of experience we remember 90% of what we do, supporting the use of an interactive application. For a complete specification of the Design principles you will have to wait until I publish my final report . It will explain all educational principles as well as the principles of Multimedia learning which are kept in mind while designing the application.

The application consists of three views. Each view contains multiple visualizations except for the first one. The first view contains an Isosurface rendering of the human brain. The second view contains a volume rendering of the human brain, a fibre visualization of the (water) diffusion data, and a MRI slice viewer. All coordinate systems are overlayed meaning that the location in 3-D space is the same location in each of the visualizations in the view. The last view contains also the volume, and MRI slicer, but exchanges the fibre visualization for a glyph visualization.

This way the student can use the knowledge of known views to learn and use the new type of visualizations (the fibre view and glyph view). As students tend to be lazy, questions are posed which have to be answered using the various views. In this way the student is ‘forced’ to use the visualizations and becomes familar with them.

The question sets can be constructed by the instructor. In order to do this, the instructor puts a series of questions in a textfile accompanied with the view which has to be used (volume, fibres, glyph, combination of all) and the points received when the question is answered correctly. In a normal case the instructor will let the student first answer questions about all views seperately and in the end ask questions in which views have to combined, much like the way math books work, first learn the individual formula’s and in the end combine those to solve more complicated questions.

All results are logged and shown as feedback to the student and the logfile is made available to the instructor to enable him or her to check the student progress of the group.

DeVIDE and prototyping

To find the three correct views I have used DeVIDE. DeVIDE, or the Delft Visualisation and Image processing Development Environment, is a cross-platform software framework for the rapid prototyping, testing and deployment of visualisation and image processing algorithms. I have used it to quickly generate multiple visualizations and check those with two medical students to find the three best visualizations to put in the educational application. As DeVIDE is also programmed in Python, AND is open-source, I could 1-on-1 transfer those pipelines to my own application running on PyQt4 + vtk.

I would advise everyone using vtk for development to at least have a quick peek at DeVIDE, as it will enable you to quickly prototype various visualization pipelines without bothering for the correct code. If needed, DeVIDE provides a CodeRunner module which can be used to put python code in.

Final application screencast

I have made a quick screencast demo-ing the application which is embedded below. Have a look!

That’s all folks!

• “Dynamic Visualisation of Orbital Fat Deformation”
  - P. J. Schaafsma, S. Schutte, H. J. Simonsz, F. H. Post, and C. P. Botha
• “Combined Surface and Volume Processing for Fused Joint Segmentation”
  - P. R. Krekel, E. R. Valstar, F. H. Post, P. M. Rozing, and C. P. Botha

Next to this, this week or the next we will probably hear from Universiteitsfond Delft if they will cover part of the costs of presenting our work in Leipzig, Germany where VCBM 2010 is held. Our department already tossed in a couple of hundreds so lets hope they close the last gap so we can almost go for free …. i mean, we are still students right?

Happy as I was after like a week or two I decided to run my python application which suddenly decided to crash bigtime. The application is created for Educational Software, a course at the TUDelft. It is nearly finished and running smoothly in 9.10 Karmic. It uses VTK (edited), PyQT and vtkTeem and produces some visualizations of structural connectivity in the brain. But suddenly, in ubuntu 10.04, creating a mask with as input an vtkTeem.NRRDReader() output and VTIReader output (casted to unsigned char) produces the following error:

*** glibc detected *** python: double free or corruption (out): 0x00007f0984000990 ***

My first guess is that this only produced a warning in the previous eglibc and in the new version is (correctly) handled by throwing an error. Since ubuntu relies heavily on eglibc a simple fix is out of the question. Seems we have to either dive into the VTK source and check what is wrong or really hope I made a stupid mistake somewhere in my code ).

ubuntu 1 – 0 bastijn

Stay tuned!

“We are very pleased to inform you that your paper has been ACCEPTED
for the Eurographics Workshop on Visual Computing for Biology and
Medicine (EG VCBM) 2010.”

After a little celebration that our paper got accepted at the conference it was time to read the comments of the reviewers. Those weren’t that bad at all, of course we need to do some work but I think we can do a lot before the 1st of July. Lets hope

It all started after a meeting and presentation of our project results to researchers from the LUMC. After receiving positive response in this meeting our docent asked us if we would like to do some extra work, but get a huge gain in return; a publication. Of course, this was no choice at all, most of the work was already done so with minimum effort we could make a nice contribution to the world .  Besides, how cool is it to have your name on a publication, even before you have finished your master thesis?

André started refactoring our old code so it would be more robust (first version was made in a _big_ hurry) and I started combining two papers into one and putting everything in the correct LaTeX markup for the conference.

Last thing to mention is that we will visit LUMC again tomorrow for an informal, first meeting since we were a bit late handing them our new work (in fact, they received it today). I’m curious what the day will bring!

- Educational Principles
- Design of educational software such as electronic instruction manuals, serious gaming, VR training, drills, and tutor agents and tutorials
- Educational software for specific learners such as children, elderly, mentally or physically challenged individuals
- Evaluation of education software

Which, in the end, will be evaluated by an oral exam, some presentations, and some course work.

To pass the course work, each group has to design and implement a small but executable and usable piece of educational software. First the subject matter, the learning objectives and the user group has to be chosen. Teams are free to choose their subject, and create an outline which has to be presented in class. The next decision is to choose a didactical strategy, an instructional design and a toolset for the implementation. Although several development environment exist, the objective of this module is not learning to use these tools, but to designing and implementing the educational software.

The coming week I will spend some of my time on coming with a nice concept for a piece of educational software. If you have any ideas feel free to comment here, or tweet or email me.

The first sort of updates are the most important ones. Information, meaning I will post various topics here concerning my master thesis, field of study (some overlap here), and just simple brain noise I have to drop somewhere which contain more characters than my Twitter can handle.

The second thing I hope to do is change this simple wordpress with a basic theme into something more challenging, providing a better read. But rome isn’t built in one day, and to translate directly from Dutch to English (which gives very funny sentences): “Fast runners are dead runners”.

I hope this is enough for a first post, soon more posts will follow showing actual things you want to read……at least, I hope.