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Scientific Visualization

Course instructors: prof.dr. Jos B.T.M. Roerdink, dr. Michel Westenberg

This course is part of the master program Computing Science.
For up-to-date information, see Nestor.

Introduction

Goal: Acquisition of knowledge about the research area, the role of visualization in scientific research, and elementary visualization techniques; use of the techniques in a number of application areas.
Prerequisites: Computer graphics (recommended), linear algebra (recommended).
Cross links: Computer graphics, image processing, linear algebra, geometric algorithms, medical imaging, fluid dynamics, molecular modelling.

Course week Topic
  • 1


  • 2

  • 3


  • 4

  • 5


  • 6
  • 7
  • Introduction: Role of visualization in scientific research. History. Computational cycle. Visual metaphors. Visualization pipeline.
  • Data: Acquisition from numerical simulations and measurements. Selection techniques for data preparation.
  • Volume visualization I: marching cubes; ray casting, multimodal rendering. Applications in biology and molecular visualization.
  • Volume visualization II: splatting, Fourier & wavelet volume rendering. Applications in medical imaging.
  • Vector field visualization: experimental methods, surface particles, flow field topology, probing. Applications in flow visualization.
  • Information Visualization. Applications in bioinformatics.
  • Student presentations

Course material

Course structure

During the lecture period students work in pairs (or individually) on a final assignment, to be chosen from a list of topics. A list of topics with accompanying literature or web links will be distributed via Nestor.

Before the end of the third course week, you have to inform the lab teacher about the final assignment you have chosen.

Presentation In week 7 of the course every student (pair) gives a short presentation of the chosen topic, the problem definition, and the results obtained so far.

Goals of presentation:

Rules for the presentation

(Self)evaluation forms You can use the (self)evaluation forms for written and oral presentations.

If you plan to use a notebook with beamer for your presentation, you must transfer the file (powerpoint, pdf) no later than the day before the presentation, to the lab instructor (by email if the size is not too large, otherwise put it on a web site where it can be downloaded), so that all presentations can be put on a single notebook. Because of the very strict time allotted to each presentation, we would loose to much time if you all bring your own notebooks.

To make a schedule for the oral presentations, we must know which pairs of students are doing the final assignment together. If you did not yet inform the lab assistant about this, or if you do not plan to give a presentation, please inform the lab instructor as soon as possible by email.

Final report
The problem and results of your final assignment have to be described in a written report.

  1. Structure of the final report:
    -Introduction: Sketch the context (what is it all about), what is the application domain (some pictures usually help here). Give required background knowledge.
    -Problem definition. Give a precise formulation of the problem you will be addressing.
    -Solution method.
    -Implementation (if applicable).
    -Results.
    -Conclusions. What has been achieved? Also discuss unsolved problems, future experiments to be done.
    -References. Literature you have used.
  2. Since this course is about visualization, include some pictures (with a descriptive figure caption) of AVS networks (if applicable) and results in your report.
  3. Size: between 10 en 15 pages.

The report has to be typeset using a LaTeX or Word style. The following style files (Eurographics-UK style) are available for this purpose:

EGUKstyle.doc A Microsoft Word template (0.30MB).
EGUKstyle.pdf A PDF version of the template (0.18MB).
EGUKstyle.tgz A LaTeX version of the template (19KB).

Lab sessions

During the course a number of lab sessions with assignments has to be completed, and reported about. The lab sessions have to carried out by each participant individually.
You can sonsult the lab instructor, preferably by email, if you have questions about the lab sessions. Also, each student needs an account (csg-number) on our student computer system. If you don't yet have a csg-number, you can inform the lab instructor about it, who will then arrange an account for you with the system administrator.
The lab sessions are as follows. Of all sessions, except the first, a report has to handed in, containing (i) answers to the questions, (ii) printouts of the constructed Amira networks, (iii) images (with captions) of visualization results.
Reports have to be printed on paper, and handed in to the lab instructor.

Session Topic
  • 1
  • 2
  • 3
  • 4
  • 5
  • Introducing Amira (no report required)
  • Volume visualization
  • Medical visualization
  • Fluid flow visualization
  • Information visualization

The working directory for the lab sessions is /wing6/home/vakken/ScientificVisualisation.
Read the file messages before starting the sessions.

Final assignments

A list with descriptions of final assignments can be found on the Web (click here). Final assignments are allocated on a first come-first serve basis .... Register via email to the lab instructor.
Ideas for other topics can be proposed, provided the topic is within the area covered by the course, a clear problem formulation is given, relevant data exist, and the level of the assignment is sufficient. If you have a proposal, consult the lab instructor about it.


Literature

A selection of books on scientific visualization.


Web links

A selection of web links.


Grading

To earn the credits for the course, you have to comply with the following:

  1. Lab sessions. Handing in reports of the lab sessions (meeting the deadlines).
  2. Oral presentation in week 7 of the course period.
  3. Report of final assignment. Report (LaTeX or Word), including printouts of AVS networks (if applicable), and pictures of visualization results.
    Deadline for handing in the final assignment: see Nestor.
    The score of the final assignment will be based on the oral presentation and the final report.

The final score is determined as follows: (2*final-assignment-score + lab-sessions-score)/3.

You can only pass when the scores for the final assignment and the lab sessions are both >=5.


Jos B.T.M. Roerdink, Johann Bernoulli Institute for Mathematics and Computer Science, RuG, JBI-480, tel. 363 3931.