Conference Report: EG VCBM 2014 Vienna (Austria)

Posted on May 16, 2015 by Noeska Smit

In the spirit of better late than never, the Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) 2014 conference report, summarizing some personal highlights. At VCBM 2014, we tweeted a picture for every talk and then some, which was arguably a bit much, but still a lot of fun. The VCBM organization also posted a great recap using Storify at their website. Given the theme of the conference, almost every talk is relevant to our medical visualization interests, but I would like to briefly summarize only a couple of them here. The benefit of delaying so long in writing this is that there are a lot of videos online by now. I will try to let the videos speak a 1000 words where available instead of getting too verbose. Onwards to the highlights!

The venue was really amazing, VCBM was held in the Universitätscampus
Altes AKH, but not just in any old lecture hall, it was the former anatomical theatre of the AKH and still has the original marble slab that was used as a dissection table:

Hörsaal D at the AKH

A day before the start of VCBM itself, the VCBM fachgruppe (working group) had a meeting with six interesting talks. This was followed by a social event, a guided tour of the Narrenturm. Built in 1874 to treat mental patients, it now serves as a museum for the Pathologic-Anatomical Collection. The Narrenturm features a huge collection of moulages. These are wax models of diseases made based on real patients and used in medical education, which is cool and slightly creepy at the same time. This tour was followed up by a delicious dinner at Unibräu for those who didn’t lose their appetite after what they had seen during the tour.

On Thursday, VCBM itself kicked off with an opening by Katja Bühler. After this we enjoyed a keynote by Anna Vilanova on the future of medical visualization. Anna presented medical visualization as a field that is between fields: computer graphics and medical imaging. She talked us through the past, present and future of medvis and going from facilitating analysis of the known to unraveling the unknown using visualization. A memorable quote from her talk:

“If the brain were so simple that we could understand it, we would be so simple we couldn’t” – Lyall Watson

Thursday featured four interesting sessions on Multivariate Data Analysis, Segmentation and Uncertainty, Microscopy and Visual Analytics for Biology:

Multivariate Data Analysis:
- Benjamin Köhler presented interesting work on “Robust Cardiac Function Assessment in 4D
  PC-MRI Data” [1]. Four-dimensional phase-contrast magnetic resonance imaging (4D PC-MRI) is a relatively new modality that can acquire non-invasive, time-resolved, three-dimensional blood flow information. Benjamin proposed robust quantification techniques to assess cardiac function in this data.
- I am obviously biased because she is from my group ;), but Renata Raidou presented her work entitled “The iCoCooN: Integration of Cobweb Charts
  with Parallel Coordinates for Visual Analysis of
  DCE-MRI Modeling Variations” [2]. She proposed a visualization application for the exploration and analysis of model-induced
  variations in pharmacokinetic parameters. For this application, she created a visual representation, the Cocoon, by integrating perpendicularly Parallel Coordinate Plots (PCPs) with Cobweb Charts (CCs). A demo video is available here.
Segmentation and Uncertainty:
- Peter Faltin presented his work on “Extracting and Visualizing Uncertainties in
  Segmentations from 3D Medical Data” [3]. He introduces a new processing chain comprising a series of carefully selected and well-matched steps to
  determine and visualize a segmentation boundary. Additionally, a novel visualization method was presented, specifically designed to simultaneously provide information about 3D morphology, confidence and possible errors.
Microscopy:
- Steffen Oeltze-Jafra delivered an excellent talk on “Interactive Labeling of Toponome Data” [4]. In this work, they present an approach for the in-place annotation of multi-channel microscopy data in 2D views, combining dynamic excentric labeling and static necklace maps:
Visual Analytics for Biology:
- I really enjoyed the talk by Nicolas Swoboda on “Visual and Quantitative Analysis of Higher Order Arborization Overlaps for Neural Circuit Research” [5]. The overlaps they are reffering to, consist of two or more neurons and indicate a potential anatomical connection. They present a novel tool for potential connectivity exploration by providing for the first time the possibility to compute and visualize higher order arborization overlaps on the fly (for fruit fly brains, well played!) and to interactively explore this information in its spatial
  anatomical context and on a quantitative level. Slides of the talk are available here and this is the accompanying video:

In the evening we hiked up through the vineyards of Vienna to the main social event: dinner at the Waldgrill Cobenzl. The view on the vineyards and Vienna itself was really stunning. We enjoyed a delicious buffet dinner accompanied by Sturm. Sturm is grape juice that has just started fermenting and is only available for a limited time every year, so we were lucky VCBM was held in Vienna exactly during Sturm time. After dinner the winners of the Karl-Heinz Höhne Award for Medical Visualization were announced:

Announcing the winners of MedVis Award at #vcbm14 social event. Congratulations! http://t.co/4aZxcPMoo4

— Eurographics VCBM (@eg_vcbm) September 4, 2014

I would love to tell you who the winner’s were, but the official announcement has not been made yet ;), so I don’t dare… Congratulations to the award winnners nonetheless, you know who you are ^^.

On the second and last day of VCBM there were sessions on Volume Visualization, Image Registration and Data Reconstruction for Medical Interventions, Visual Explanations and Display Techniques as a keynote by Nigel John entitled ‘Visual Computing in Healthcare – from the Research Lab into the Hospital”. In the keynote he presented several case studies and discussed some of the challenges
involved in deploying visual computing solutions in a hospital setting.

Volume Visualization:
- Veronika Solteszova and Åsmund Birkeland presented their work on
  “Visibility-Driven Processing of Streaming Volume Data” [6], in which they propose a visibility-driven processing scheme for handling costly
  on-the-fly processing of volumetric data in real-time for real-time volume data acquisitions:
- Stefan Lindholm gave an interesting talk entitled “Towards Clinical Deployment of Automated Anatomical Regions-Of-Interest” [7]. In his work he proposes an Automatic and Anatomical ROI (AA-ROI) approach based on the combination of automatic image registration (AIR) and distance-based Transfer Functions (DBTFs), designed for automatic selection of complex anatomical shapes without relying on excessive amounts of interaction:
  Towards Clinical Deployment of Automated Anatomical Regions-Of-Interest
Image Registration and Data Reconstruction for Medical Interventions:
- At the risk of tooting my own horn, I gave a talk on “RegistrationShop: An Interactive 3D Medical Volume Registration System” [8], developed to improve and simplify the process of volume registration with 3D visualizations and
  simple interactive tools. The source code is available here, talk slides are here, and this is a demo video:
Visual Explanations and Display Techniques:
- Steffen Oeltze-Jafra delivered another interesting talk, this time a useful “Survey of Labeling Techniques in Medical Visualizations” [9]. I especially enjoyed his proposed decision diagram, to quickly assess what the best labelling technique for your specific problem is:

VCBM wrapped up with the awards ceremony. The best paper award went to:

Best paper of #vcbm14 ! pic.twitter.com/zMOZDHuaMS

— medvis.org (@medvisorg) September 5, 2014

The honorable mentions can be found here. Our congratlations to the authors! Ivan Viola closed the conference and announced the location for next year (this year by now ^^): VCBM 2015 will be held in Bangor (UK) and will from now on be an annual workshop instead of bi-annual (once every two years, not the twice every year-type). To conclude this summary, I’d really like to thank the organizers of this excellent workshop. Interesting talks, a beautiful location, good food, great people once again!

References:

[1]: Robust Cardiac Function Assessment in 4D PC-MRI Data. Köhler, Benjamin; Preim, Uta; Gutberlet, Matthias; Fischbach, Katharina; Preim, Bernhard
[2]: The iCoCooN: Integration of Cobweb Charts with Parallel Coordinates for Visual Analysis of DCE-MRI Modeling Variations. Raidou, Renata; Breeuwer, Marcel; Vilanova, Anna
[3]: Extracting and Visualizing Uncertainties in Segmentations from 3D Medical Data. Faltin, Peter; Chaisaowong, Kraisorn; Kraus, Thomas; Merhof, Dorit
[4]: Interactive Labeling of Toponome Data. Oeltze-Jafra, Steffen; Pieper, Franz; Hillert, Reyk; Preim, Bernhard; Schubert, Walter
[5]: Visual and Quantitative Analysis of Higher Order Arborization Overlaps for Neural Circuit Research. Swoboda, Nicolas; Moosburner, Judith; Bruckner, Stefan; Yu, Jai Y.; Dickson, Barry J.; Bühler, Katja
[6]: Visibility-Driven Processing of Streaming Volume Data. Solteszova, Veronika; Birkeland, Åsmund; Viola, Ivan; Bruckner, Stefan
[7]: Towards Clinical Deployment of Automated Anatomical Regions-Of-Interest. Lindholm, Stefan; Forsberg, Daniel; Ynnerman, Anders; Knutsson, Hans; Andersson, Mats; Lundström, Claes
[8]: RegistrationShop: An Interactive 3D Medical Volume Registration System. Smit, Noeska; Klein Haneveld, Berend; Staring, Marius; Eisemann, Elmar; Botha, Charl; Vilanova, Anna
[9]: Survey of Labeling Techniques in Medical Visualizations. Oeltze-Jafra, Steffen; Preim, Bernhard

Open PhD position: Visualization at the University of Bergen (Norway)

Posted on May 16, 2015 by Noeska Smit

We have received word from Bilal Alsallakh that the University of Bergen is looking for a PhD student in visualization. The exact topic of the PhD will be decided on with the advisor, but biomedical, visual analytics and visual computing are among the list of possible topics. More information about the position is available here. Alternatively you can skip to the full advertisement here and a factsheet here. The application deadline is the June 1, 2015, so do not delay and apply now if you are interested in this amazing opportunity.

Medical Visualization PhD defenses

Posted on February 15, 2015 by Noeska Smit

I apologize for the delay in reporting this, but I heard about/attended three great medical visualization PhD defenses late 2014:

Dr. Mathias Goldau successfully defended his PhD at the University of Leipzig. His thesis is entitled ‘Multi-modal and Slice-based Visualizations of Diffusion Tractography Data’ and you may or may not already be familiar with his work on OpenWalnut, an open source tool for multi-modal medical and brain data visualization. The full text of the thesis can be downloaded here or take a look at his publications here.
Dr. Peter Kok successfully defended his PhD at the Technical University of Delft. 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. 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 successfully defended his PhD at the Technical University of Delft as well. 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.

Congratulations to all three doctors!

Medical Visualization colloquium and double PhD defense this week

Posted on December 8, 2014 by Noeska Smit

This week the TU Delft in the Netherlands will host two medical visualization events in a single week:

First up, on Thursday December 11th, we will have a special medical visualization colloquium (open to the public). This colloquium will feature two invited speakers, Prof. Dr.-Ing. Bernhard Preim and Prof.dr. Jos Roerdink, presenting recent work on ‘Visual Analytics in Cohort Study Data’ and ‘Prediction of Neurodegenerative Diseases’. More information about the colloquium and the abstracts for the talks are available here.
Secondly, on Friday December 12th, Peter Kok and Stef Busking will be defending their PhD theses. Peter Kok will present and defend his work entitled ‘Integrative Visualization of Whole Body Molecular Imaging Data‘ starting at 9.30 am in the TU Delft Aula. Afterwards, at 12:00 pm Stef Busking will present and defend his work entitled ‘Visualization of Variation and Variability‘ in the same location.

The theses that will be defended next week. Picture courtesy of Charl Botha.

VAnPIRe PostDoc position still open at TU Delft (The Netherlands)

Posted on October 6, 2014 by Noeska Smit

Previously, we reported on two open positions in the context of the VAnPIRe, Visual Analysis in Population Imaging Research, project. The PhD position has since been filled, but the PostDoc is still open. More information about the position can be found here. The closing date is at the end of the month, so apply now if you’re interested!

We’re at VCBM!

Posted on September 4, 2014 by Noeska Smit

We’re currently at VCBM in Vienna. For live updates, check out our Twitter coverage and be sure to check back for a full conference report in the near future!

Software Engineer job opening at Clinical Graphics in Delft, the Netherlands

Posted on July 31, 2014 by Noeska Smit

Clinical Graphics, a fast-growing medical visualization company, is currently looking for a Software Engineer to join their team. From their job description: “We make software for the analysis of medical 3D scans of hips and shoulders. This software is used by the company to provide online surgery plans to orthopedic surgeons. Surgeons can predict how well a patient will be able to move after surgery thanks to our analysis service. Surgeons from around the world are sending in their scans for us to analyse.

You will perform challenging development work on our diverse set of software applications, using various technologies. It should be noted that although we are pragmatic, we are not afraid to try out new technology stacks or software architectures.”

If you’re interested, check out their career page here and the full job description for more details here!

PhD Thesis Rocco Gasteiger defended with summa cum laude

Posted on March 26, 2014 by Noeska Smit

(This news was submitted by the Magedeburg Visualization group. We would like to congratulate Rocco Gasteiger with his outstanding work and his summa cum laude defense!)

Rocco Gasteiger

On February 7, 2014 Rocco Gasteiger successfully defended his PhD Thesis “Visual Exploration of Cardiovascular Hemodynamics” with summa cum laude in the Visualization Group (headed by Prof. Bernhard Preim) at the Otto-von-Guericke University (OVGU) Magdeburg. During the work on his PhD Thesis, Rocco provided new contributions to the field of visual exploration of complex morphological and hemodynamic data of cardiovascular diseases with a focus on cerebral aneurysms. In the current clinical and biomedical research, the analysis of measured and simulated blood flow data is of major importance for the examination of diseases, their courses and optimized patient-specific treatment options. The main contributions of the PhD Thesis consist of the development of an expressive visualization method for vessel illustrations with embedded flow information, the automatic extraction of qualitative hemodynamic parameters (see Fig. 1) as well as a flexible focus and context illustration for the examination of multi-parameter data of the hemodynamics (also known as FlowLens).

Automatic extracted and illustratively depicted Visualization of the inflow jet (arrow glyph) and impingement zone (contours) of the blood flow in a cerebral aneurysm.

The articles were published in the well-known Journal IEEE Transactions on Visualization and Computer Graphics (TVCG) and the Eurographics Workshop on Visual Computing in Biology and Medicine (VCBM). The articles resulted from a close cooperation with his colleague Mathias Neugebauer, the Visual Computing group at OVGU (headed by Prof. Holger Theisel) as well as Prof. Anna Vilanova Bartroli (TU Delft) and Dr. Roy van Pelt (TU Eindhoven). Besides the work for his PhD Thesis, Rocco contributed to further topic-related publications as coauthor. Amongst others, his work was recognized by the medvis award (1st price in 2012). This award is offered by the Medical Visualization group of the German Informatics Society (GI) and is sponsored by BrainLab. Furthermore, the joint works of Mathias, Rocco, Gábor Janiga (Institute of Fluid Dynamics and Thermodynamics, OVGU), Oliver Beuing (University Hospital Magdeburg) and Prof. Bernhard Preim received the 2nd Dirk Bartz Prize for Visual Computing in Medicine at Eurographics 2013.

VCBM 2014 Vienna (Austria) – Call for papers and posters!

Posted on January 26, 2014 by Noeska Smit

The “Call for Papers and Posters” for VCBM (AKA Eurographics Workshop on Visual Computing for Biology and Medicine) 2014 has been released! VCBM is an excellent venue for medical visualization work and this year it will be held in Vienna, Austria.

The deadline for full paper submission is June 19 and the posters need to be submitted by August 7. Don’t miss this opportunity to present your work at this excellent location and please take a look at this website for more details. In other news: did you know our website also features a conference calendar that you can add to your personal calendar?

Start submitting those papers and posters for VCBM 2014!

VIS 2013 Atlanta Conference Report

Posted on January 20, 2014 by Noeska Smit

(We are very thankful that Dr. Steffen Oeltze from the University of Magdeburg Visualization Group could write this short report on the medical visualization-related papers at IEEE VIS 2013 for us.)

I was very happy to see that in 2013, the IEEE Vis conference hosted again a separate session on biomedical visualization. On top of the five talks given in this session, five more interesting talks, also related to MedVis, were distributed over the conference program. Before the event started, I considered it a good omen that the inwards of the conference hotel looked like a gigantic corpus with the conference attendees accommodated along the costal arches.

Images are courtesy of Helwig Hauser ©2013.

The session on biomedical visualization was opened by Jan Kretschmer from the FAU Erlangen and Siemens Healthcare Computed Tomography, Forchheim, Germany. He gave a talk on the interactive patient-specific modeling of vasculature by means of sweep surfaces. He showed how vascular segmentations may be polished in a fast, interactive, and intuitive way such that high-precision models for blood flow simulations are generated on the fly. The modeling approach is robust, eligible for clinical on-site application, and it delivers smooth high quality results.

Xin Zhao from Stony Brook University presented a novel area-preservation mapping/flattening method using the optimal mass transport technique. Compared to previous methods, the size and area of each fold component are preserved facilitating quantitative analyses. Two interesting and very relevant applications from a medical point of view were presented: brain surface flattening and colon flattening. In the former, the correct detection and quantification of brain folds is crucial. Traditional approaches induce severe area distortions and therefore hamper these tasks. In colon flattening, the detection and measurement of polyps benefit from the new method.

A tailor-made algorithm for colon flattening was presented by Krishna Chaitanya Gurijala from Stony Brook University. In contrast to previous approaches, the algorithm is shape-preserving and robust to topological noise. It dispenses denoising the data as a pre-processing step and instead replaces the original Euclidean metric of the colon surface with a heat diffusion metric that is insensitive to topological noise. Virtual colonoscopy greatly benefits from the new approach since shape and area of polyps are preserved.

Thomas Auzinger from the Vienna University of Technology, Austria presented Curved Surface Reformation (CSR) for visualizing a vessels’ interior by generating a view-dependent cut surface through the vasculature. The approach is an advancement compared to Curved Planar Reformation (CPR) and Centerline Reformation (CR) since it handles unrestricted vessel orientation and view direction, it provides a good visibility of the vessels and the surrounding tissue, and it produces results at interactive frame rates. CSR even copes with occlusions of different parts of the vasculature.

Johanna Beyer from Harvard University, Cambridge (previously with the King Abdullah University of Science and Technology (KAUST), Saudi Arabia) concluded the biomedical session. She presented a system for the query-guided visual analysis of large volumetric neuroscience data: the ConnectomeExplorer. The system facilitates the integrated visual analysis of volume data, segmented objects, connectivity information, and additional meta data. Powerful query algebra allows neuroscientists to pose domain-specific questions on the data in an intuitive manner. Johanna’s presentation was completed by an impressive demonstration of the systems performance in typical use-case scenarios.

Moritz Ehlke from the Zuse Institute Berlin presented an approach to render virtual X-ray projections of deformable tetrahedral meshes that runs very fast on the GPU. The purpose of generating these projections is the reconstruction of 3D anatomy from a single or a few 2D X-ray images. In an iterative optimization process, the tetrahedral mesh of a statistical shape and intensity model of an anatomical structure is transformed, such that it represents plausible candidates for a patient-specific shape and density distribution. Each transformation result is then converted to a virtual X-ray projection, whose X-ray attenuation is finally compared to the clinical 2D X-ray. The best candidate provides a plausible representation of 3D anatomy which was demonstrated for the pelvic bone.

Bret Jackson from the University of Minnesota presented a prop-based, tangible interface for 3D interactive visualization of thin fiber structures. He demonstrated the exploration of fiber orientations in second-harmonic generation microscopy of collagen fibers by means of a paper prop, a depth sensing camera, and a low-cost 3D display. The paper prop is tracked and the visualization is restricted to fibers oriented in the direction specified by the prop, i.e. the user. Different gestures, one- and two- handed, are supported for filtering fibers, adjusting the fiber similarity threshold, slicing the volume, and rotating or rolling the volume.

Benjamin Köhler from the Otto-von-Guericke University Magdeburg, Germany gave a talk on the semi-automatic vortex extraction in 4D PC-MRI cardiac blood flow data by means of line predicates. The relation of blood flow patterns, e.g., vortices, and vascular pathologies is currently a hot topic in cardiovascular research. Benjamin compared various vortex extraction methods to determine the most suitable one for cardiac blood flow. He integrated several dedicated flow visualization techniques and the vortex computation in a system that is fully implemented on the GPU to provide real-time feedback. The system was demonstrated based on ten datasets with different pathologies like coarctations, Tetralogy of Fallot and aneurysms and evaluated at the Heart Center Leipzig. A video is available here.

Adrian Maries from the University of Pittsburgh presented GRACE: A visual comparison framework for integrated spatial and non-spatial geriatric data. These high-dimensional data span volumetric images and variables such as age, gender or walking speed. Their concurrent analysis is supported by a multiple coordinated view system comprising volume rendering panels, dendogram panels, and a Kiviat graph. Techniques from statistics are integrated to quantify potential neurology-mobility connections. The usefulness of the framework for generating and refining hypotheses was demonstrated on two case studies. In the paper, the authors report their lessons learned from designing visualizations for concurrently analyzing spatial and non-spatial data. Check the videos here.

Thomas Schultz from the University of Bonn, Germany gave a very good talk on the application of spectral clustering to medical image analysis. He showed a system that makes this powerful and versatile technique more accessible to users via an open-box approach, in which an interactive system visualizes the involved mathematical quantities, suggests clustering parameter values, and provides immediate feedback to support the required decisions, e.g., on the number of clusters. The system further supports the filtering of outliers and the recording of user actions and their translation to other data containing the same structures. Thomas demonstrated the system based on chest CT and brain MRI data.

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Author Archives: Noeska Smit