Category Archives: MedVis

Recent PhD defense

Today Nicola Pezzotti successfully defended his thesis, Dimensionality-Reduction Algorithms for Progressive Visual Analytics, in Senaatszaal, the Aula. Congratulations to Dr. Pezzotti!

Dr. Pezzotti graduated cum laude for his high-impact work carried out during his study at TU Delft.

Workshop Visual Analytics and Applications

You are all cordially invited to workshop visual analytics and applications, which will take place on 8th of April, from 14:00-17:00 at Pulse-hall 4. Please find detailed program below.

14:00 Jean Daniel Fekete: “Exploring the Evolution of Relationships with Dynamic Hypergraphs”

14:40 Renata Raidou: “Employing Visual Analytics for the Exploration and Prediction”

15:20 Break

15:30 Cagatay Turkay: “Informed computational modelling through visual analytics”

Abstract: With
the increasing availability of computational data analysis and modelling tools
that can be utilised out-of-the-box, the route from data to results is now much
shorter. However, these advancements also come together their own limitations,
and a data scientists need to be aware of the pitfalls and act carefully to
question every observation and method used within each step of the data
analysis process. Visual analytics approaches where interactive visualisations
are coupled tightly with the algorithms offer effective methodologies in
conducting data science in such inquisitive, rigorous ways. This talk will
discuss how visual analytics can facilitate such practices and will look at
examples of research on how data can be transformed and visualised creatively
in multiple perspectives, on how comparisons can be made within different
models, parameters, and within local and global solutions, and on how
interaction is an enabler for such processes.

16:10 Thomas Hollt: Cytosplore: Visual Analytics for Single-Cell Profiling of the Immune System
Recent advances in single-cell acquisition technology have led to a shift towards single-cell analysis in many fields of biology. In immunology, detailed knowledge of the cellular composition is of interest, as it can be the cause of deregulated immune responses, which cause diseases. Similarly, vaccination is based on triggering proper immune responses; however, many vaccines are ineffective or only work properly in a subset of those who are vaccinated. Identifying differences in the cellular composition of the immune system in such cases can lead to more precise treatment. Cytosplore is an integrated, interactive visual analysis framework for the exploration of large single-cell datasets. We have developed Cytosplore in close collaboration with immunology researchers and several partners use the software in their daily workflow. Cytosplore enables efficient data analysis and has led to several discoveries alongside high-impact publications.

16:50 end

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.

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!

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!

Frits Post receives Visualization Career Award

We are proud to announce that Frits Post received the IEEE VGTC Visualization Career Award. At VisWeek 2011, the annual IEEE Visualization conference held 23-28 October in Providence, RI, he received his award. With this award, the international visualization community recognises his outstanding contributions to the research field, and flow visualization in particular. In his acceptance speech, Frits briefly discussed his 20+ years in the visualization field and expressed his gratitude for great collaborations in several organizational committees, and for the PhDs he supervised from 1989 through 2011. Earlier this year, Post also received the Eurographics Honorary Fellowship from the European association for computer graphics. Frits Post, now officially retired, indicated he will continue to visit the Computer Graphics and Visualization group at Delft University of Technology regularly to advise on ongoing research.

(Update: here is the accompanying award text and a snapshot of the award plaque itself)

Frits Post receives Visualization Career Award at Visweek 2011