Coursera course on anatomy of the abdomen and pelvis

I recently mentioned a certain OAH webviewer short paper that was accepted as a EuroGraphics Education paper, but I now have some more news to share: the webviewer will be used in a Coursera course on anatomy of the abdomen and pelvis that starts this week, entitled ‘Anatomy of the Abdomen and Pelvis; a journey from basis to clinic.’! This course is a Massive Open Online Course (MOOC), a free online course aimed at unlimited participation, and organized by highly qualified people at the Leiden University Medical Center.

So far, already 7,796 people signed up. If you also have an interest in anatomy, why not sign up yourself? It’s completely free and completely awesome, I promise! I do have to add, it is not for the faint of heart, since it features live anatomical dissection videos. I am following the course myself and really enjoying the classes. I even just passed my first quiz with 100% correct answers. Try and beat that 😉

Soon, you could be playing around with this yourself:

Looking forward to seeing you as my virtual classmates in the course 🙂

Comic Book-Inspired Illustrative Medical Visualization

Medical visualization isn’t always about rendering data in the most realistic way possible. In fact, quite often it isn’t. Illustrative rendering techniques have been developed that present medical data to the viewer in a style that is more abstract, often emphasizing important features, while taking emphasis away from the less relevant. Illustrative rendering techniques can even make data originating from medical imaging scanners such as CT, look hand-drawn. Check out for instance the works by Tobias Isenberg, Stefan Bruckner, Ivan Viola and Kai Lawonn to name a few. As you may recall, last year’s VCBM paper I had the pleasure of co-authoring also involved illustrative rendering:

Illustrative rendering of a CT scan
Illustrative rendering of a CT scan

So what you see here kind of looks like a sketch hinting at the shape of the human body on a table right (well with some limbs missing ;))? Actually it’s a rendering of a CT scan combining toon shading and feature lines without any artists involved. Here’s another example by Roy van Pelt:

Roy van Pelt's blood flow visualization
Roy van Pelt’s blood flow visualization

He visualized blood flow using particles that get elongated as they move faster in combination with speed lines indicating the direction and speed of the particles. This style is reminiscent of something you could see in comic books or cartoons. In fact, I think there is a lot we can learn from comic book artists that we can apply to medical visualization.

For this reason, I asked Gerrit Rijken, AKA Iosua, a freelance illustrator as well as comic book aficionado, to write about the basics of inking, and more specifically the do’s and don’t’s and why’s of it all. In his elaborate post, which you can find here, he talks us through many things that are of interest in illustrative rendering as well. He describes how inking techniques are applied to create textures, the importance of line weights, spotting blacks, screen tones, feathering and cross-hatching. He provides explanations of these techniques combined with examples illustrating the concepts.

I see many parallels to visualizing techniques. For instance, focus-and-context techniques and depth cues are relevant for both comic books and medical visualizations. There are also some interesting rules on line thickness that I had not considered before. Furthermore I see techniques that have already been adopted in medical illustrative rendering, such as stippling and hatching, while I did not see researchers using feathering yet (correct me if I’m wrong ^^). I hope you find this as interesting as I did and if you have further questions, do not hesitate to contact him!

On Research Visits, Paper Writing and Club Mate

First up: a little In Memoriam for The ‘Weekly Status Update’. Remember those? I vaguely recall wanting to post weekly updates with five bullet points each. Ain’t nobody got time for that! I’m following up on excellent advice by cpbotha:  “when under-achieving, lower your standards”. I’m no longer setting any expectations here, I just post whenever I want, whatever I want from now on. So what’s cooking?

  • Last week I briefly visited the University of Koblenz · Landau, in, you guessed it, Koblenz to work on a EuroVis STAR paper (time to shine) with the newly minted J.- PROF. DR. KAI LAWONN, who you may remember from:
  • I’m currently visiting Bernhard Preim‘s excellent visualization group in Magdeburg to:
    • Meet the lovely group members
    • Work on the aforementioned paper (deadline: 14th of February, I can’t even…)
    • Oh and I also gave a talk last week. It was all over the news ;), but in case you missed it, check the group website
  • We are writing the aforementioned paper in Overleaf. Which is pretty awesome. I might do a little comparison post on ShareLatex vs. Overleaf when deadline season is over (estimated timeframe: never).
  • I’m getting a notification for a EuroGraphics Education paper I submitted next week on Monday. Will this end my paper rejection streak? Time will tell 🙂
  • I should probably get back to, oh writing a paper or two, but I’ll leave you with a nice action photo:
Club Mate
Drinking Club Mate and writing a paper. Kind of a big deal!

I didn’t realize when I bought it, but apparently, Club Mate is/was totally the hacker tech-startup drink of choice and I am now officially totally cool for drinking that.

Did I just write out five bullet points? Is this a Weekly Status Update in disguise?

2016 is here! A time for looking back and looking forward.

If cpbotha can post after a four month hiatus, then so can I ^^.  First of all, all the best for 2016 to all of you! I hope it’s a good one.  The start of a new year is as good a time as any (if not better) for a look back, or review if you want to get fancy about it, of the previous year and to look forward to things happening in the time ahead.

First up, looking back:

  • I didn’t blog so much, because a) I was crazy busy (final year of the PhD anyone?), and b) personal issues that I will not discuss here. Maybe I will increase the update frequency, maybe I won’t. Wait and find out?
  • In September, I presented at VCBM! My favorite conference in the world (eat it, VIS!). It was in Chester, UK this year (full report here) and I presented work festively entitled “Illustrative Multi-volume Rendering for PET/CT Scans”, which does exactly whatever you think it does. To make sure it does, check the full paper and pretty pictures here.
  • In September/October I went on a month-long research visit to the Bergen Visualization group in Norway, which was great for several reasons:
    • I met soooo many cool new people as well as cool people I knew from conferences before. It’s really an excellent group in all ways possible.
    • Bergen itself is really heaven on earth. It has it all, mountains within walking distance, a harbor, waffles and lots of metal. Also, VCBM 2016!
    • A little more on these mountains…. I’m not much of a sporty person, but on my first weekend there, I was invited to hike up Ulriken (only the highest of the Seven Mountains they have, luckily):
      Ulriken Bergen
      Ulriken as viewed from the airport bus

      Talk about life-changing experiences… Mind=blown by the view, experience and sheer exhaustion.

      View from Ulriken, Bergen
      View from Ulriken, Bergen. Hi, Bergen!

      It’s quite addictive really. I hiked up there once more during my stay. I could definitely see that becoming sort of just a thing to do on the weekends while living there.

    • I presented at a medviz seminar, check the flyer here. Yes, there was a flyer with my face on it!
    • I got some great PhD advice and started collaborating on a paper together. I can really recommend a visit like this, if it is at all possible, to anyone doing a PhD.
  • 2015 was definitely the year of collaborations. Good ones too (for me at least ^^)! I worked with people from Leiden, Magdeburg, Bergen and recently Koblenz, and they are all awesome and I hope to do more of that in 2016.

Then for the looking forward bit:

  • I hope to have more awesome collaborations in 2016.
  • I have approximately a million, ok four-ish, papers to wrap up and then…
  • I don’t want to alarm you or anything, but 2016 could be the year I get my PhD (correction sent in by cpbotha: get doctorified) . After which I’ll have to change the subtitle of this blog into something yet unknown. I’m not the world’s biggest fan of change, but let’s just say, ‘it is time’. I’ve been walking around at the TU Delft since 2005 (yes, really…), first as a bachelor student, then master, then PhD, and a decade is more than enough for me. I’m looking forward to starting something new somewhere else. Anywhere else 😉

Alright, I just spent my full two week holiday working interspersed with family visits, the first part of which is not really my style, but hey, desperate times, desperate measures. So I guess I’d better go finish 1 out of those million papers. Till next time!

How scientific conferences are like music festivals

Fresh out of the nightly brainfart department, a short look at the similarities between scientific conferences and music festivals as well as some tips and tricks that apply to both:

  • The bigger conferences often feature parallel sessions not unlike how music festivals can have multiple stages and concerts at the same time.

    Tip:  Take a look at the schedule beforehand and choose the talks/concerts you really must see beforehand, so you don’t miss out on anything important during the event.

  • The keynote speakers are like the headliners at a festival: big names in the field who are allowed more time to present their work.

    Tip: Keynotes and headline shows got that spot for a reason, while there are exceptions, in general you can expect high quality content and good delivery, so be sure to attend.

  • Big conferences and festivals can span multiple action-packed days and therefore be really exhausting.

    Tip: Eat and drink well to maintain your energy levels and just hang in there. Big conferences/festivals only come around once a year and you might not get the chance to go every year, so make the most of your time there!

The new MedVis bible is available :)

The new MedVis book is available! I’ve already seen a copy and wow, it is glorious! Filled with beautiful imagery and all the latest and greatest medvis developments in many interesting research areas. My name is even in it somewhere 😉 Check the companion website for details on where to order and exclusive online content!

The new MedVis book
The new MedVis book cover

My PhD supervisor left me

This post is of a more personal nature than most, but I would still like to write about this. Last September I took a course called ‘Achieving your goals and performing more successfully in your PhD‘ (a serious contender for the longest-course-name-ever-awards). Among other things, the course had us thinking of potential threats to getting our PhD-degree in the given time. The first thing that came to my mind was the thought of my supervisor leaving me. And guess what, that totally happened: my PhD supervisor left me!

Continue reading My PhD supervisor left me