Category Archives: science

Sometimes, being in academia rules. [Weekly Head Voices #25]

Kids!  It’s now truly summer over here, which means as much as possible time outside, which means less time available for writing blog posts. However, weeks 24 and 25 of 2010 contained such newsworthy items, that I’m simply forced to trade some sun-light for a bit of TFT exposure. In this post, we talk flowers, PhD defences, scientific talks, funny Js and finally stick figures, so please stick around!

I took this photo of the Oude Kerk in Delft as we were taking a walk with one of our esteemed guests. So it's really relevant to this post, ok?

Last week we had our department’s yearly BBQ at the Blue Lagoon at Scheveningen.  In a not altogether surprising turn of events, I’ve been working at the TU for 10 years, and I now have the bunch of orange flowers to show for it! Time is really fun when you’re having flies.

Five of my MedVis (that’s IN4307; if you’re at the TU, make sure you take this life-changing course! :P ) students presented their final project work. Between the visualisations of coronary stents from optical coherence tomography data, the 3D lung volume reduction surgery (LVRS) planning tool and the real-time X-Ray simulator, I was hugely and pleasantly impressed.  Expect to see a large part of this functionality in a future release of DeVIDE. This was energy-producing event #1 of the past two weeks. Energy-producing event #2 was a M.Sc. defence that I opposed just this past Friday, where the candidate presented and defended, in a highly-entertaining and convincing fashion, his thesis on investigating 3D synthetic aperture radar construction on multi-core architectures.

Energy-producing event #3 was when the now freshly minted Dr Eric Griffith defended his PhD thesis on Visualizing Cumulus Clouds in Virtual Reality in stellar fashion.  Dr Griffith did a superb job of maintaining an eloquent discussion with all 7 of his opponents. The offence of Prof Jos Roerdink (Visualisation, Groningen) also deserves mention: The multi-level questions and typically professorial delivery were most entertaining.

The final energy-producing event that I’m going to mention has been named #4 for mysterious reasons, and, for other reasons that will soon become clear, was for me the most significant. Jorik Blaas, close collaborator and friend for the past seven (7!) years, defended his PhD on the Visual Analysis of Multi-Field Data, on Thursday June 24. To take part in the offence, we were extremely honoured to welcome three luminaries of my research field (that’s Visualisation, for those of you who’ve just joined!): Prof.dr. Jack van Wijk, Prof.dr. Anders Ynnerman and the Viennese-Bergenesque Prof.dr. Helwig Hauser. Having all three of them in Delft was just WOW, you just have to trust me on this. In any case, for the first time at the TU, I was also allowed to take my place in the PhD committee. :)

Of course, Dr Blaas sailed through the defence, his usual understated yet verbally effective hyper-intelligent self. Invited lectures by our guests, much late night discussion on the nature of (visualisation) science and of life in general and finally a PhD party that stress-tested all glandular resilience helped to turn this into one seriously wonderful and life-affirming week. I am thankful to all involved.

In completely unrelated news:

  • Have you ever wondered what that funnily isolated ‘J’ character is doing at the end of sentences in emails?  Well, wonder no more! (5-second-version: it’s supposed to be a smiley, but Outlook on the sending side substitutes it with a character from the Wingdings font that is rendered at the receiving side, if that font is not available, as a ‘J’)
  • My 4-year old daughter recently made a drawing with two stick figures standing next to each other. Not significant as such, but the one stick figure was wearing a bow tie, while the other stick figure had a thought bubble above its head with a bow tie in it.

Thank you for joining me again for this edition of the Weekly Head Voices, and please feel free to kick-off completely unrelated discussions in the comments.  Next week (actually this week, I’m late), four of us will be going to Leipzig for the bi-annual Eurographics workshop on Visual Computing for Biology and Medicine (VCBM), which I’ll probably be reporting on in a future blog post (and hopefully on twitter with hashtag #vcbm2010). Stay tuned for much fun and excitement!

EuroVis 2010 [Weekly Head Voices #24]

Welcome all to the latest edition of the Weekly Head Voices!  In a bid to get more numbers into my titles (oh who am I kidding, I’m clearly trying to slightly injure or preferably frighten two birds with a single stone, splitting infinitives as I go along), this WHV is dedicated to the EuroVis 2010 conference, which on its part is the reason I spent most of last week in Bordeaux.

Château Faugères, youngest of the chateaux. Photo by Peter Krekel.

EuroVis is definitely the most important European scientific conference on Visualisation. For detailed and complete coverage, see T.J. Jankun-Kelly’s (he was also the uncontested tweetmaster of the conference) detailed blog posts on the first, second and third days of the conference. The post you are reading now is my very own extremely biased and mostly incomplete view of the conference and of conferences in general, which can sometimes be interesting.  Or just very misleading.

Let’s start with the basics: A scientific conference is where a bunch of mostly scientists get together somewhere in the world, ostensibly to present recent results of their research to each other. Work certainly gets presented, and in some cases it’s a treat seeing a gifted orator giving a superb presentation.

However, in my mind the primary reason to go to a conference is not to discuss work that was submitted half a year ago, but to meet with colleagues and friends and to discuss important things, such as life, science in general and the research that has not yet been published or even started up yet. It is a hugely important element of the social goo that keeps a research field coherent and cooperative.

There are numerous overlapping interest and social groups that continuously split off to discuss something or just socialise, and then merge back into the larger group. The various attendees each has their own character and associated mode of operation: Some flit around, speaking to all and sundry, some stick to and act as the backbone of the subgroup that they belong to, some walk around and think, sometimes being approach by yet another type of agent. It’s interesting to watch from the corner of one’s eye whilst one is also enjoying taking part in this system. Sometimes the backyard anthropologist in me wonders how exactly the nature of this social fabric affects the performance of science. I imagine that it would be cool to put together a taxonomy of social conference types and even map their behaviour during a single conference such as this.

In any case, at EuroVis there were, the same as last year in Berlin, 190 attendees.  Three days of presentations, with a poster session and a visit to Saint-Émilion thrown in for good measure.

With regard to the presentations, I seemed to notice an ever-so-slight upwards trend in the number of papers accompanied by open source software implementations (both MotionVA and ShapeSpaceExplorer by respectively our very own Peter Krekel and Stef Busking are open source, but there were more examples). This is really a great development, as it is an important component of the whole open science idea. With the implementations available, colleagues can reproduce one’s results and thus have a greater chance of being able to improve on them. Also, new implementations can be directly compared to existing ones, something which is currently incredibly hard.

Two of my favourite presentations were the following:

  • Visual Support for Interactive Post-Interventional Assessment of Radiofrequency Ablation Therapy by Christian Rieder, Andreas Weihusen, Christian Schumann, Stephan Zidowitz, Heinz-Otto Peitgen: I really like this genre of solutions, where complex 3D problems are reduced to normalised 2D representations. A previous example is the work of Neugebauer et al. at EuroVis 2009. In this case, the authors presented “tumor maps”, a 2D map-style representation of the tumor and its surroundings which greatly facilitates the post-therapy tumor assessment. The fulltext paper will hopefully be linked on Christian’s website soon.
  • Estimation and Modeling of Actual Numerical Errors in Volume Rendering by Joel Kronander, Jonas Unger, Anders Ynnerman, Torsten Möller: Although this is not my personal favourite type of research, I think the work (and work like it) is tremendously important. The authors meticulously measure the impact of different precision and sampling strategies on the volume rendering pipeline, and, as if that wasn’t enough, derive a mathematical model with which the role of these variables can be predicted in unseen volume rendering problems. In my view, this is a great example of research towards deriving elements of that elusive visualisation theory. Just to help ram the point home, the presentation was extremely well executed.

On a slightly higher level, what I’ve also started noticing is the different styles of visualisation.  Many research groups have a distinct style of visually representing their data: One can easily recognise a Viennese design, and sometimes even notice how elements thereof have been subtly adapted by a faction of ex-Viennese scientists in Bergen.  The Bergenesque style is still quite young, but will probably soon spread to different groups.  Of course not all groups are that easy: Our own style is heterogeneous, although I’m glad to see at least the blue-to-yellow more-or-less perceptually linear colour-scale starting to permeate our work. It would still be interesting to start a kind of genealogical tree showing the various styles and also how they spread along with the persons practising them.

On the topic of Saint-Émilion: 1000 vineyards covering 95% of the available land, oldest of the vineyards 2000 years old, number of beautiful old Chateaux (castles man, castles!) each having on average 6 hectares of land. 5 different classes of wine produceds, ranging from 5 euros per bottle (hello there!) up to 7000 euros per bottle. It’s a beautiful piece of country.  In fact, it reminded me very strongly of the Western Cape in South Africa,where I grew up.

My group ended up visiting Château Faugères, by far the youngest of the chateaux, but awesomely cool nonetheless, as it was designed by a Swiss-Italian architect by the awesomely cool name of Mario Botta. We got to taste one (1) wine. This was slightly less reminiscent of the vineyards of the Western Cape in South Africa, where one can taste wines until one starts developing very entertaining coordination problems. Fortunately, this very small oversight was more than compensated for by the subsequent visit to the town of Saint-Émilion, its monolithic church and the catacombs, all narrated by an extremely gifted and humorous guide, and finally by the marvelous concluding dinner, done as only the French can.

So kids, that it was it for this week’s lecture on Further Mystifying Scientific Conferences!  I have to go, as I have to start thinking about the next Weekly Head Voices.

I’m on a boat! [Weekly Head Voices #20]

Welcome all, to the 20th edition of the Weekly Head Voices, now with ever so slightly updated title style!  Let’s just call it Rotterdam-style for now. In any case, this edition looks back on weeks 14 and 15 of the year 2010, with news about a boat and the people on it, two more accepted student papers (I’m just SO proud at the moment), and the International Symposium on Biomedical Imaging (ISBI) 2010 that took place this past week in, you guessed it, Rotterdam.

Below is the boat on which the conference social event took place on Friday evening:

The actual boat that we were on Friday.

It is a nice boat, full of food and drink and happy people. After a while, I was feeling like the protagonist in one of my all-time favourite music clips (the version embedded below has bleeped out swear words, for the uncensored version, click here):

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(Certain people have claimed that there is a certain resemblance between me and aforementioned protagonist. I hope that nobody is being undeservedly insulted or flattered.)

I’ll get right back to ISBI in about a paragraph or two, but first allow me to wax ecstatic about three of my master’s students who just had their first papers accepted at VCBM 2010 in Leipzig: I am so fantastically proud at the moment! A ton of hard work went into these two master-pieces (student names in bold):

P.J. Schaafsma, S. Schutte, H.J. Simonsz, F.H. Post, and C.P. Botha, “Dynamic Visualisation of Orbital Fat Deformation using Anatomy-Guided Interaction,” Eurographics Workshop on Visual Computing for Biology and Medicine, 2010. (8 pages)

A. Van Dixhoorn, B. Vissers, L. Ferrarini, J. Milles, and C.P. Botha, “Visual analysis of integrated resting state functional brain connectivity and anatomy,” Eurographics Workshop on Visual Computing for Biology and Medicine, 2010. (8 pages)

Click on the title for the fulltext PDF and more.  As always, remember: Cite them soon and cite them often!

Back to the the ISBI conference: FrancoisM, man of multiple blogs (fpixel, fvoxel and finally francoism.  have I forgotten any?) and all-round hip guy (harr harr) got us in with the following paper and (beautiful) poster:

D.F. Malan, C.P. Botha, R.G. Nelissen, and E.R. Valstar, “VOXEL CLASSIFICATION OF PERIPROSTHETIC TISSUES IN CLINICAL COMPUTED TOMOGRAPHY OF LOOSENED HIP PROSTHESES,” Proc. ISBI, 2010, pp. 1341-1344. [link to paper page will be added soon]

Besides the chock-full scientific programme of paper presentations and posters, there were a number of special sessions and keynotes, all of them definitely keynote-worthy. However, there are two meta-lessons I took home (for those of you not paying attention, that means that these are by definition take-home messages, harr harr), apart from all the valuable scientific content:

  1. By a very rough count, I saw at least a billion rainbow colour maps. I know that these are well-loved by scientists all over the universe, primarily because they’re available everywhere and because they’re easy to make (hey, let’s vary the hue between 0 and 1!).  However, think twice next time you opt for the rainbow, and whilst you’re thinking, read this: D. Borland and R.M. II, “Rainbow Color Map (Still) Considered Harmful,” IEEE Computer Graphics and Applications, vol. 27, 2007. (I myself have sinned before and still do sometimes…)
  2. More importantly: It’s really very hard to give a good talk if you’re going to discuss more than two or three different topics. In spite of experienced and skilled speakers, many talks suffered due to this. An illustrative counter-example is that of Dr. Roderic Pettigrew, head of the National Institute of Biomedical Imaging and Bioengineering (one of the National Institutes of Health in the US), who presented the work of a number of NIH grantees. A master-orator, it was wonderful to see Pettigrew integrate various different projects into a single coherent presentation by regularly going back into overview mode, describing how the just-described or the next project fit into his grand vision. The bottom-line is: Either limit yourself to a maximum of three different topics, or put a great deal of effort into the integration of your topics.

My personal favourite talk of ISBI 2010 was that of Prof. Bram van Ginneken in the special session on computer-aided detection, during which he deftly illustrated one way of reaching the next level in one’s chosen research speciality: It seems that transcendence is possible by Revolution Through Competition! Oh, just go read the page and make sure you’re there next time the good professor gives a talk.

Finally, during a pleasurable but perhaps far too late night somewhere in the city, I was convinced by two BIGR members (all the BIGR people I know are extremely pleasant, so watch out!) that the Weekly Head Voices title style should be slightly upgraded, with the post title in front and the weekly head voices branding at the end. At the time, it seemed like terribly logical advice. Although somehow I don’t recall exactly why I thought that, I did promise to give it a try.  So what do you all think?

Someone might also mentioned that my posts were too long…

Weekly Head Voices #20: A Lamarckian Knot.

Welcome dear fellow-monkeys, to the 20th edition of the Weekly Head Voices, exceptionally vaguely associated with the 13th week of the year 2010. In this post, nothing much happens, except that I tell you about the bowline (the king of knots), present the usual GTD analysis, spiced up with some perspective gravy and conclude with a brief introduction to epigenetics, something that I’ve also very recently learned about for the first time.

Here is the knot I promised, as well as one of this post’s major visual elements:

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I just love the gentleman’s wooden delivery! It somehow suits the knot. It turns out that the version below, albeit of exactly the same knot, is a more correct or accepted execution (but the delivery is not as cool):

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This is the knot I use to tie my keys to my James Bond-small 8G USB stick and to my iButton with a length of diabolo string (that’s seriously good stuff!), as a sort of makeshift and extremely space-efficient key-ring. With the bowline knot, you can make a fixed-size loop at the end of a rope that won’t slip and is also easy to untie. It turns out this is often called the King of Knots, which is kind of nice, as it’s dead simple to make and extremely useful. To my few sailing friends this is probably old news, hopefully to some of you it’s not.

During week 13, consisting of only 4 work days (we had us a nice long weekend here in NL, hence also the lateness of this post), I had about 15 hours of regular meetings and managed to complete 26 GTD tasks spread over 9 projects.

As part of my new high-priority theme of keeping things in perspective, I’ve been revising my work strategy in a number of regards. Importantly, I’ve taken a hard look at my work-at-home policy. Somehow, I’d forgotten about my rule of only working at home on the fun parts of my job, and otherwise only in case of a looming deadline. However, there had been so many deadlines, that I had gotten into the bad habit of simply continuing at home with my work day, without applying the fun-filter. That’s all over now. The fun-filter is back on ultra-strict, thank you very much. I just have to remember next time deadline-season comes along again.

Further, my GTD-brainwashed inbox-emptying compulsion had reached pathological proportions. I wasn’t able to open up my work inbox without stressing out and immediately going to work emptying the thing out again by processing all mails, a situation that would occur at the most inopportune and unsuitable times. I’ve now got this in check as well, and I’m able to stare at my inbox when it’s not mail processing time without breaking down. (So what if I have to bite down and have those bulging veins on the sides of my head!) This is a refinement of the first of my three rules of stress-free email productivity, in that sometimes one has to check mail for other reasons than processing the whole inbox, and in those cases it’s important to remember that it’s not an inbox processing moment.

In a slight variation of the usual backyard philosophy theme, I’d like to tell you briefly about epigenetics, something that I’ve recently heard about for the first time. This weekend’s Volkskrant had a good article on the topic by Frank Grosveld (professor of Cell Biology and Genetics at the EMC in Rotterdam) and Jos de Mul (professor of Philosophy of Man and Culture, also at the EMC). Epigenetics is the study of external influences by the surroundings, feeding and habits on gene expression. The DNA itself is not modified, but how the DNA code is read and reacted upon: This happens through chemicals that attach to the nucleotides in the DNA. In this way, there’s an extra regulatory layer, allowing the environment to influence gene expression.

Sounds reasonable, until one ponders the implications: A number of studies have shown that this mechanism makes it possible for environmental effects to be inherited, even being passed on for example from grandparents to grandchildren! The Volkskrant article mentions a number of examples:

  • Men who were underfed during their pre-adolescence have grand-children with a significantly lower risk of cardiovascular disease whilst grandfathers who lived in times of plenty have grand-children with a significantly higher risk of diabetes (Pembrey and Bergen 2006).
  • In gestating rats, exposure to an anti-fungal agent used in wine-making affects offspring three generations down the line (Skinner 2008).
  • Mice placed in a stimulation-rich environment have offspring with a similarly improved memory, even when they grow up in a stimulation-poor environment (Feig 2009).

Besides shedding new light on the whole Nature vs. Nurture debate, this has the profound implication that we live in a kind of post-existentialist reality, where your actions and experiences affect not only yourself, but also your future offspring, and even the offspring of those around you, in more direct ways than hitherto recognised.

Think about that for a while, ok?

(P.S. Figuring out the first part of the title of this post is left as a simple but gratifying exercise for the reader: You too will be able to use this impressive-sounding qualifier in full sentences at cocktail parties.)

Weekly Head Voices #14: My Week Was A Wormhole.

In this week’s post, documenting the 7th week of 2010, I wonder about perceived business, mention two of our most recent open source releases and give to you, my readers, two screencasts about the DRE, in addition probably highly effective in the treatment of insomnia.

Screenshot of the FoBVis system. This is just one of our many attempts to take over the world, subtly.

Just before bedtime on Monday, I had still managed to make a note in my special top-secret Weekly Head Voices journal.  I usually do this every day to make sure I don’t forget anything by the weekend, when I usually have some time to write these posts.  Thursday night’s entry simply says “WTF, where did my week go?!” — There had been no other entries since Monday. I’m still not quite sure why it felt that way, as my breakdown of activities is similar to that of the previous week: 2 hours of lecture preparation, 3 hours of lecturing, 15 hours of scheduled meetings and 20 tasks completed (one more than last week!!) across 10 projects. Perhaps those four extra hours of meetings don’t scale linearly in the amount of business they cause, due to the number of extra context switches that they bring. I have to add that a number of truly exciting projects are brewing, but I can’t say more about them until I can say more about them, if you know what I mean.

We (The Group, of course) recently released two new open source software projects:

  • FoBVis is a tool for the real-time acquisition and visualisation of human motion: Currently it supports the Flock-of-Birds electromagnetic acquisition system, we are currently working to integrate Optotrak optical tracking system. We should also shortly have a version of the DRE that can run the FoBVis on YOUR computer as well.
  • HistoVis is a client-server system for the visualisation of large collections of (registered) histological sections.

It’s all very exciting that more products of our research are entering the big bad outside world!  The FoBVis is already being actively used by the LUMC Laboratory for Motion Analysis (we hope that more labs will start using this soon), and HistoVis will soon go live from the visible-orbit.nl server. Of course these have both been released under the new BSD license, as the GPL sucks.

Screencasts: Video Performance Art of the Nerdily Inclined. That’s where one makes a recording of one’s computer screen whilst demonstrating some or other procedure, optionally narrated by oneself, and then proceeds to upload said recording (called a screencast) to YouTube or similar. See a previous post of mine for one possible (and free) way of doing this on Windows. This weekend I produced and uploaded two such pieces, both demonstrating aspects of the DeVIDE Runtime Environment, or DRE, that paradoxically do NOT involve DeVIDE itself. Especially the second is really soothing, one could even say mildly sleep-inducing.  I just say: (1) Try (2) it.

To conclude, I give you a track from the new Massive Attack album Heligoland, called Paradise Circus. It should make your brain sit and scratch its chin stubble, not unlike the usual dose of backyard philosophy:

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