What is love? [Weekly Head Voices #64 no #65]

I’ve been dealing with a spot of blog writer’s block, hence the lateness of this post. I’d forgotten that these monthly instalments were initially intended to be extended status updates, with a spot of backyard philosophy every so often. Trying to come up with worthwhile backyard philosophy every week is just plain hard. This week I’m going for half a status update along with a list of possibly interesting sciencey tidbits.

  • I’ve managed to release a stable version of DeVIDE, my Frankenstein-Borg software system for visualization and image processing, only about 2.5 years after the previous stable release. Go get yours fresh from the oven, it’s completely open source!
  • It seems like yesterday when I got to design and teach the first MedVis Ninja course at the TU Delft. The fourth generation of students have just started with the course (partly the reason for pushing out a new DeVIDE release). The previous generations are kicking ass as we speak, and I’m proud of ’em all.
  • I had the privilege of giving another invited talk, in Dutch, at the yearly conference of the Dutch Anatomical Society. In my talk, titled Data Visualization: Driving the human visual system for fun and profit, I introduced data and medical visualization, and then discussed three illustrative examples in more depth: high quality volume rendering (work by Thomas Kroes), diffusion tensor imaging (work by Jorik Blaas) and fMRI connectivity visualization (work by André van Dixhoorn).

That’s it for the status update. The sciencey bits I thought were worth mentioning are:

  • There’s been some press lately about the letter to the Wall Street Journal, signed by 16 scientists, in which they try to make the case that climate change is really not such an issue. Climate change denialists everywhere rejoiced, I cringed. I really don’t like denialism. Fortunately, it turns out that I’m not the only one, and that there’s a story behind the story: The WSJ editorial board is severely biased against climate science.  Another letter, signed by 255 real scientists (all members of the US National Academy of Science), dealing with the realities of climate change, was flat-out rejected by the WSJ. It’s a shame that the first factually dubious letter got so much of the press. Read more about the whole debacle in this Forbes article.
  • A recent Psychological Science article contains the results of a study  on more than 15000 UK inhabitants, as well as on a group in the US, that shows that lower cognitive ability predicts greater prejudice, manifesting in for example right-wing ideologies or homophobia. Ha ha.
  • In another not-so-surprising turn of events, it turns out that alcohol does indeed make you more creative.  FrancoisMalan.com sent me, albeit indirectly, this Consciousness and Cognition article, titled Uncorking the muse: Alcohol intoxication facilitates creative problem solving. Note the creative title, draw your own conclusions about the state of intoxication required for authoring a successful scientific article. Ahem.

Good science should be reproducible. Judging by the blood alcohol content and weight tables on Wikipedia, I should be more creative between 3 and 4 beers, a result I will certainly try to confirm during my next WHV writing session. It is left as an exercise to the reader to calculate my body weight based on this information.

Weekly Head Voices #17: The Eternal Foreigner.

In this edition, looking back on the 10th week of 2010, I report briefly on the lack of blog-worthy events in my life, noting that my life is undoubtedly extremely exciting, just not always in that special blog-worthy way, before concluding with some backyard psycho-philosophy on my perception of the greenness of grass as a function of its distance from the observer.  Skip to just after the YouTube clip if you want to get right to the backyard part of this blog.

Work-wise, last week was good for 2 hours of lecture preparation, 3 hours of lecturing, 12 hours of meetings, including an inspiring visit to Real Scientists at the EMC, and finally some quality time catching a monday night paper deadline in the nick of time with one of our MedVis Ninjas, whom I’m coincidentally extremely proud of at the moment.  I completed only 16 GTD tasks, down 6 from last week.

Besides not having hot water for two days due to my boiler’s operating system (yes, it has a frikking operating system) refusing to switch on the heat exchanger, forcing me to take a bath in 15 litres of hot water boiled, cowboy style, on the stove, and also experiencing first-hand the surprisingly high actual efficiency of my house’s Super Environmentally Friendly heat-retention system (everything is insulated, air is mechanically circulated at about 100 cubic metres per hour, extra heat exchanger transfers warmth from expelled air to fresh injected air) which managed to keep the internal temperature at a comfortable 18 C (outside between 1 and 8 C) without any hot water in the radiators, and also managing to write one of the longest sentences in a blog post since last Tuesday, the only other blog-worthy artifact I have to offer you is this YouTube screencast I made the other day, demonstrating how to perform a rudimentary segmentation on DICOM CT data and extract STL surface meshes using DeVIDE:

You can add this to your growing list of natural non-ingestible sleep medicine.

Last week I heard that I’d passed my Korte Vrijstellingstoets. This is a test that you, foreigner in The Netherlands, can take to demonstrate that you have sufficient knowledge of Dutch language and culture and thus don’t have to take bunches of other compulsory courses and/or exams that are far more time-consuming. This is not such a significant happening, were it not for the fact that it’s another very concrete symbol of my growing affinity with and attachment to this little patch of the planet. I can hardly avoid thinking seriously about the future of this relationship.

Further, this weekend I missed the wedding of one my best friends due to the niggling matter of 10000 kilometres conspiring with sundry but unavoidable work-related constraints. I would really have loved to be there… There will always be drawbacks, no matter where you choose to live. Especially if you choose for the excitement of a country-skipping adventure and do so for any significant length of time, you will always long for That Other Place, that special coordinate that you currently can’t occupy, and the people associated with it.  Even if you go back to where you started, irrevocably tainted with a strange culture, you don’t quite fit in and long for your acquired home. The grass is and will remain greener on the other side.

I had the good fortune of meeting a wise and well-spoken French man shortly after starting my European adventure. This man, who had done quite some country skipping, finally ending up in Lugano (one can end up in worse places than Lugano), introduced me to the concept of the Eternal Foreigner. This is what one becomes when one simply embraces the idea that, once having moved country and culture, one can never ever be at Home again. Instead of struggling to blend in, struggling to be more like one’s neighbour, or struggling to retain and manifest some warped version of one’s own culture in an environment where it’s doomed to wilt, simply accept Being From Elsewhere.

The Eternal Foreigner misses Home, but smiles, and is at peace.

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:

Recording screencasts on Windows with free software

(This post was first written in May of 2008, but I’ve been updating it periodically. See also the updates right at the end.)

Screencasts refer to video recordings of screen activity, often with narration. These can be used to demonstrate software or to serve as a kind of visual HOWTO. We often make screencasts of software we design in the Medical Visualisation group at the TU Delft to use in presentations at conferences or to distribute online.

On Windows, Camtasia Studio ($300) or Camtasia SnagIt ($40) are probably the best options your money can buy. Most of the free alternatives suck quite badly: This includes the Windows Media Encoder, thank you very much. In fact, the Windows Media 9 Screen Capture Codec has been fine-tuned to create the worst possible quality movies you can imagine. Another problem with the free options is that they often can’t sustain writing the video stream to disk, hence resulting in dropped frames and unusable screencasts. When they are able to sustain writing, it probably means that the compression is completely killing video quality.

Fortunately, it turns out that there is a free option which offers comparable performance to the Camtasia products, and for good reason. It’s called CamStudio, and it’s even open source! It’s terribly important that you also install the lossless CamStudio Screen Capture codec, it’s this that makes all the difference. This codec compresses all frames with the fast LZO lossless compression algorithm, so you get the highest possible quality without dropping frames due relatively slow disc writing.

Using CamStudio, I made a 3.5 minute screencast, with live audio recording, show-casing some of the new DICOM browsing functionality in the next DeVIDE release. After capture, I transcoded the CamStudio screen capture codec AVI to XVID using MediaCoder, and then uploaded to YouTube (play at your own risk!):

Update on 2010-02-21:

I’ve made two more screencasts and learnt some time-expensive lessons:

  • DON’T encode with H.264, in spite of YouTube’s recommendation. This screws up captured text elements extremely badly. I had much more success with XVID at 1500 kbit/s and MP3 audio using MediaCoder, and THE MOST SUCCESS OF ALL just directly uploading the lossless codec screencast to YouTube, without any transcoding.
  • DO capture at 640×480 or at 1280×720 (HD).  For example 800×600 is NOT worth it, it gets downscaled by YouTube. By capturing at 640×480 or 1280×720 you have much more control over what finally appears on YouTube.
  • If you get audio / video sync problems (I experienced them with a 10 minute screencast), try activating “Use MCI Recording” in the CamStudio “Audio Option for Microphone”.
Update on 2011-10-22:

With CamStudio 2.6 r294 getting the codec working on Windows 7 64bit is not straight-forward. You first install the codec in the normal way (with the exe installer), then you have to do TWO things. First copy camcodec.dll from Windows\System32 to Windows\SysWOW64. Second, create a reg file with the following contents:

Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows NT\CurrentVersion\drivers.desc]
"camcodec.dll"="CamStudio lossless codec [CSCD]"
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows NT\CurrentVersion\Drivers32]

Install it by double-clicking the reg file, or doing right-click and then selecting Merge. After this, you should be able to select the camstudio codec from Options | Video Options | Compressor.

Furthermore, you can upload camstudio-encoded movies directly to Google Picasa, it Just Works(tm)!

Update on 2013-02-13:
If CamStudio 2.7 complains about MSVCR100.dll being missing, you should install the MS Visual C++ redistributable (32bit, because CamStudio is 32bit).