Python Developer job opening at Clinical Graphics in Delft, the Netherlands

Clinical Graphics, a fast-growing medical visualization company, is currently looking for a full-time Python Developer 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, designing smart solutions to complex image processing and data exchange problems. The core of our work consists of a pre-operative planning system for orthopedic surgery written in Python, using VTK and various libraries from the SciPy stack, such as NumPy and Matplotlib.

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

Introducing our new contributor: Kai Lawonn

I am happy to announce that we have found a new contributor for…  Who you might ask? It’s Kai Lawonn!
Kai Lawonn
He is currently a postdoc at the Visualization group in the Otto-von-Guericke-University Magdeburg. Last year he defended his PhD thesis in the exciting field of illustrative medical visualization. Before this he studied Mathematics at the Free University Berlin.

With this new addition to our team, expect more frequent updates, new thrilling features and a barrage of beautiful medical non-photorealistic rendering results. As a first course of action, he has added a grand total of 15 new spectacular header images to the site. Hit refresh and see if you can catch them all ^^

VCBM 2015 Chester (UK) call for papers and posters: Deadlines imminent!

The “Call for Papers and Posters” for VCBM (AKA Eurographics Workshop on Visual Computing for Biology and Medicine) 2015 was released a while ago. As you probably already know, VCBM is an excellent venue for medical visualization work and this year it will be held in Chester, UK.

The deadline for full paper submission is June 21st and the posters need to be submitted by August 7th. Don’t miss this opportunity to present your work at this excellent location and please take a look at the website for more details.

Open PhD position at Aviz-Inria (France)

There is an open position for a PhD at Aviz-Inria in France. They are looking for someone to work on a project on the interesting topic of Structural and Functional Visualization of Brain Connectivity. The project combines the best of both worlds with a mix scivis and infovis approaches. Does this sound like your type of project? If so, keep in mind the application deadline is August 1, 2015 and start working on your application. More information on the project and the position can be found in this pdf.

Karl-Heinz-Höhne-Preis (MedVis-Award) 2014: And the winners are…

Every two years the VCBM group awards the Karl-Heinz Höhne Award for Medical Visualization (medvis-award for short) to a young scientist in the MedVis field. Candidates for this award focus their innovative research on visualizations clearly related to medical questions.

The official website has not been updated yet, but we have received a tip from Frank Heckel that there has been a press-release announcing the winners (in German). Last year at VCBM, three contestants got awarded for their medical visualization work:

  • In third place: Cees-Willem Hofstede (Delft University of Technology) for his work on the Online Anatomical Human: an online anatomy browser, which allows combined display of medical images and reconstructed 3D models of various anatomical structures.
  • In second place: Frank Heckel (Fraunhofer MEVIS) for his work on interactive correction of segmentation results, such as delineated tumors in CT-scans.
  • In first place: Benjamin Köhler (Universität Magdeburg) for his work on the quantification and visual representation of blood flow data in cardiovascular disease.
 2014 Karl-Heinz-Höhne Award (MedVis- Award)  winners

Karl-Heinz-Höhne Award (MedVis- Award) winners: from left to right: Cees-Willem Hofstede, Benjamin Köhler and Frank Heckel in the front row. Dr. Stefan Zachow and Dr. Dorit Merhof in the back row.

We would like to congratulate the winners with their well-deserved awards!

Advanced Medical Visualization tutorial at MICCAI 2015!

(Cross-posted from The go-to resource for all things related to the book ‘Visual Computing for Medicine – Second Edition’. Original post written by Charl Botha.)

Bernhard Preim (University of Magdeburg, DE; author of and driving force behind the MedVis book) and Anna Vilanova (Delft University of Technology, NL) are organizing a tutorial on Advanced Medical Visualization at MICCAI 2015, one of the most important technical medical imaging conferences in the world today.


Judging by the list of topics and especially the list of speakers, I expect that this is going to be a great tutorial. If you’re going to MICCAI 2015, don’t miss this!

Conference Report: EG VCBM 2014 Vienna (Austria)

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

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:
  • 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:
  • 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:

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.

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

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!


  • [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)

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

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

  1. 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.
  2. 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.

    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.

  3. 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

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

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

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