Category Archives: MedVis

CGV Colloquium – Thursday April 9th

You are cordially invited to attend our next Computer Graphics and Visualization (CGV) Colloquium, which will be held on Thursday April 9, 2015, 15.45-17.20, in the Dijkstraroom (HB09.150). The program this month features the following speakers:

  • Mattijs van Driel:
    • Title – Real time intersections on  Space Scale Cube data
    • Abstract – The space scale cube (SSC) model offers a new way of encoding 2D geographic data with continuous level of abstraction on the Z axis. It lacks a flexible way of visualizing intersections, which is what this work offers at its core. A SSC based dataset is preprocessed into a simple octree structure, which is then used as input for an interactive rendering system that provides a user controllable intersection surface. The system uses the octree structure to cull unnecessary chunks, and OpenGL to render the intersections themselves. In addition to rendering intersections, the approach allows for a number of enhancements on the final image, such as antialiasing and transition colorization.
  • Rob Coorens:
    • Title – Quantification of deformation and sliding of orbital fat during rotation of the eye Short
    • Abstract – When the eye rotates, the muscles contract and move through the orbital fat. This movement is a combination of sliding through the fat and deformation of the fat. The goal of the project is to quantify both types of movement from MRI data of the orbit using registration and segmentation techniques.

As a reminder, all CGV MSc students (both seminar and thesis project) are expected to attend our monthly colloquium series. All other interested colleagues are more than welcome, so feel free to disseminate this announcement. Looking forward to see you all at the colloquium!

Recent PhD defenses

Two new doctors graduated from our group at the end of 2014 in the field of medical visualization:

  • Dr. Peter Kok successfully defended his PhD. In his thesis, ‘Integrative Visualization of Whole Body Molecular Imaging Data‘, Dr. Kok present methods to map molecular imaging data to a common reference frame, to combine multiple modalities and to compare scans taken at different timepoints. The full text of the thesis is available here.
Dr. Kok with his paranymphs and the thesis committee members.
Dr. Kok with his paranymphs and the thesis committee members. tblr: Jos Roerdink, Elmar Eisemann, Charl Botha, Erik Jansen, Boudewijn Lelieveldt, beadle Rina Abbriata, Louise van der Weerd, Bernhard Preim, Noeska Smit, Peter Kok, Thomas Kroes and the head of the committee.
  • On the same day, Dr. Stef Busking also successfully defended his PhD. His thesis, ‘Visualization of Variation and Variability‘ deals with comparative visualization as a means to analyze variation or variability based on two or more specific instances of the data. The full text of the thesis is available here.

We would like to congratulate to both doctors with their accomplishments.

CGV Colloquium – Thursday December 11th

We would like to invite you to a special CGV colloquium on the 11th of December at 15:45 – 17:15 (see details below). The colloquium will be held in the Dijkstrazaal (HB 09.150) and will feature two invited talks by guest speakers: 

image003Prof. Dr.-Ing. Bernhard Preim

Title: Visual Analytics in Cohort Study Data

Abstract: Epidemiology aims at understanding relations between life style, genetics, environmental factors and the outbreak of diseases.

Recent large scale cohort studies involving a wealth of sociodemographic data and medical image data bear a great potential to identify complex interactions between different factors and non-linear relations between risk factors and the likelihood and severity of diseases. A combination of data analysis (dimensionality reduction and clustering), image analysis (segmentation and quantification of target structures) and interactive visualization supports the generation of new hypothesis.

As case study, we discuss back pain and its relation to socio-demographic and medical image data. The epidemiological data is part of the SHIP ( 


Prof.dr. Jos Roerdink

Title: Brain Patterns: Prediction of Neurodegenerative Diseases

Abstract: In this talk, I will discuss some recent work on the visualization and analysis of brain patterns obtained from neuroimaging data, and their use in the understanding of brain (mal)functioning.

The recently GLIMPS (“GLucose IMaging in ParkinsonismS”) project at the University of Groningen concerns the creation of a national database of FDG-PET scans which reflect the glucose consumption of the brain in patients with neuro-degenerative diseases. The goal is to identify distinctive structural and functional brain patterns and derived quantities like network patterns of brain activity, which display statistically significant differences in healthy subjects and patients with certain types of neuro-degenerative disease. The database will be used for clinical practice as well as for research purposes. Pattern classification and visualization methods will be developed to associate brain patterns to various types and stages of neuro-degenerative disease. First results will be shown and discussed.

MSc thesis successfully defended

On the 10th of October, Lennaert van den Brink successfully defended his thesis “HiveArcs – visualizing genome co-expression data“. In his work, he introduced HiveArcs, an interactive online visual analysis for genome co-expression data. HiveArcs visualizes modules using arc diagrams on radially placed axes. Using this lay-out accommodates display of per-gene tracks of additional information as well as relationships between modules. This allows for quick and intuitive comparison between modules as well as in depth analysis of a single module.

HiveArcs - Visualizing genome co-expression data
The HiveArcs layout with 1) the module glyps, 2) arc diagrams, 3) gene tracks and 4) module tracks.

We would like to congratulate Lennaert with his work and defense and wish him all the best for the future!

CGV Colloquium – Thursday July 10th

You are cordially invited to attend our next Computer Graphics and Visualization (CGV) Colloquium, which will be held on Thursday July 10, 2014, 15.45-17.00, in the Vassiliadis room (HB10.230).

The program this month features the following speakers:

  • Ioannis Tolios – Visual exploration and analysis of DCE-MRI using a combined semi-quantitative and quantitative approach
  • Antoine Plat – Processing upper airway endoscopic videos for sleep apnea diagnostics
  • Melos Gebrekrstos – Visualization of sleep and circadian alignment

All interested colleagues are more than welcome, so feel free to disseminate this announcement.  As a reminder, all CGV MSc students (both seminar and thesis project) are expected to attend our monthly colloquium series.

Looking forward to see you all at the colloquium!

MSc thesis successfully defended last week

Casper van Leeuwen successfully defended his thesis ‘Spatial-temporal pathline clustering based on FTLE fields‘ in our group on the 14th of May.

Casper van Leeuwen defending his thesis
Casper van Leeuwen defending his thesis

In his work, Casper worked with cardiac flow acquisition data consisting of 3D blood flow of the heart featuring 4D vector fields. These 4D vector fields of the heart are used in clinical research to gain insight in the flow patterns within the heart which in turn can be used to gain a better understanding of the pathogenesis of cardiovascular diseases. He implemented a visualization technique called Spatial-temporal Clustering based on Finite Time Lyapunov Exponents, that aims to circumvent the challenges posed by the structural complexity of the flow and give a concise and insightful representation of the blood flow patterns within the heart. Aside from the main visualization technique this works also introduces a novel probing technique that highlights the base principles of the FTLE fields to provide the user with a better understanding of how a FTLE field works.

Casper van Leeuwen receives his MSc degree
Casper van Leeuwen receives his MSc degree

We would like to congratulate Casper with his achievement and new title and wish him all the best for the future!

Two MSc theses successfully defended this week

Berend Klein-Haneveld and Cees-Willem Hofstede successfully defended their theses in our group this week.

Main interface of Berend Klein-Haneveld's RegistrationShop with two CT lung datasets. The fixed volume is visible on the left side, the moving volume on the right and the view in the middle shows the current registration result of the two volumes.
Main interface of Berend Klein-Haneveld’s RegistrationShop with two CT lung datasets.

On Wednesday, the 26th of March, Berend defended his thesis “RegistrationShop – an interactive 3D medical volume registration tool”. In his work he developed RegistrationShop as a tool that aims to make the complex process of 3D volume registration easier by providing simple interaction techniques and real-time visual feedback of the current registration results. Users are able to place landmarks in 3D either by surface picking or by tracing a ray through the volume until the desired location is reached. During the registration process they are provided with visualizations of both the moving and fixed volumes as well as the current registration result in a combined view.

The Online Anatomical Human with a 3D model of the pelvis and linked orthogonal planes containing cryosectional data and label information.
The Online Anatomical Human with a 3D model of the pelvis and linked orthogonal planes containing cryosectional data and label information.

On Friday, the 28th of March, Cees-Willem defended his thesis “The Online Anatomical Human – an online browser and annotation system for real human anatomy”. He worked on bringing anatomical education to a web browser, by creating an online environment in which a 3D anatomical model of the pelvis is linked to 2D medical imaging data. Users are able to annotate structures directly on the 3D mesh using landmark, brush and line tools and can enrich the model with their annotations.  Both theses were supervised by Charl Botha, Anna Vilanova and Noeska Smit.

We’d like to congratulate Berend en Cees-Willem on their Master of Science titles!

Recent M.Sc. Defences

At regular intervals, we will post updates concerning recent master thesis topics and outcomes.

We’ll begin with a description of the work done by Marnix Kraus, MSc. who completed his Master Thesis in the field of active multi-camera navigation in video surveillance systems, supervised by Gerwin de Haan. He designed and evaluated a prototype system for this purpose. His findings indicate that the presented system can enhance operator performance in surveillance control rooms that monitor vast and complex areas. The full thesis can be downloaded here. More information on research related to this topic can be found on the VRLAB project website.

In the game technology department, Rick de Ridder, MSc. worked on simulating urban area development for semantic game worlds for his Master Thesis. This work was supervised by Tim Tutenel and Rafael Bidarra. In his work, he expands a semantic world-generation prototype by introducing factors like resources, events and neighboring settlements in the generation process. It extends current techniques by adding more history and meaning to the procedurally generated cities. The full thesis can be found here and additional information is available on the related Game Technology project website.

Anne van Ee, Msc. developed new interaction schemes for the touch-based organization of patent collections in her thesis work. The thesis was supervised by Gerwin de Haan and it was carried out in co-operation with the European Patent Office. Anne based her work on earlier co-operative work with the European Patent Office and improved the organization system by introducing the Local Affine Multidimensional Projection (LAMP) technique to help the user while searching for patents. If you’re interested in this work, you can check out the full thesis here.

Renata Raidou. MSc. completed her thesis in the field of medical visualization as a Biomedical Engineer. In her work she successfully researched the planning and guidance of minimally invasive cement injection to combat the effects of aseptic loosening that occur after total hip replacement surgery. This work was supervised by Francois Malan and Charl P. Botha. Renata developed an integrated system for planning and guiding minimally invasive refixation. The thesis proposes new approaches to combine CT and fluoroscopy in pre-operative planning. She conducted an extensive review with domain experts to evaluate the system. Her full thesis can be found here.

MedVis overview preprint gets featured on Gizmodo and MIT Technology Review

During EuroVis 2012, we put a preprint of an upcoming Springer book chapter, titled From individual to population: Challenges in Medical Visualization by Charl P. Botha, Bernhard Preim, Arie Kaufman, Shigeo Takahashi and Anders Ynnerman, on arXiv. To our delighted surprise, the paper was featured two days later both on Gizmodo, titling their post This Is the Future of Medical Imaging, and also on the MIT Technology Review, with a rather complete paper summary titled The Future of Medical Visualisation! This led to a whole slew of other sites also mentioning this work.

In any case, we hope you enjoy reading the preprint, a very compact summary of Medical Visualization developments of the past 30 years and a hint of what the coming decade holds, as much as we enjoyed writing it!