Category: Uncategorized

Sheep Brains – 2013

Students in PSY 348 (Research in Behavioral Neuroscience) had the opportunity today to dissect sheep brains – enhancing their understanding of neuroanatomy.  This is one of my favorite labs.  Typically the students begin the lab unsure of how to approach it, and by the end they feel much more confident.

These photos are cross-view 3D images – to see the 3D effect cross your eyes and create a fused central image.  This image will appear to be in 3D, much like your favorite ViewMaster images from your childhood.

The original Lytro images that were used for thed 3D pictures, as well as a few other pictures from the lab, appear here (click on icon in lower right corner and select “SEE ON LYTRO.COM” to see all the images):

For info about how these 3D images were created, see this earlier blog post.

Time Lapse Photography

I spent last summer examining the circadian activity of earthworms (with a student who did all the hard work).  Rather than watching worms for 2 days straight, we decided that we should use technology to help us out.  We could have simply “filmed” the worm for 2 days, which would have resulted in very long movies showing long periods of inactivity.  Instead we decided to create time lapse videos.

Time lapse photography is simple: aim a camera a something and take images at fixed intervals over a period of time.  This requires a camera that can be triggered automatically at designated intervals – the device that does this is called an intervalometer.  Most point-and-shoot digital cameras lack this capacity, but I was fortunate in that my trusty camera is a Canon, and some industrious hackers have provided an alternate firmware called the Canon Hack Development Kit (CHDK).  CHDK replaces the camera’s own operating system with a far more capable one, and because this new OS lives on the memory card the camera is essentially unchanged – remove the card and the camera is back to its original state.  CHDK gives my Canon a built-in intervalometer (in addition to allowing ultra-long exposures, saving RAW images, and many other cool features).

So we set up the camera, plugged it into an AC adapter, ensured that there was lots of space on the memory card, and shot worms for 48 hours at a time.  Here’s an example of what we saw:


After analyzing the movement of a dozen worms we saw little evidence of circadian rhythms shared by the worms – although it is possible that careful analysis of more worms might reveal individual rhythms.

Now that I had this technology, I wanted to apply it to something more fun, if not more practical.  “More fun that worms?” you ask in disbelief!  Yes – good music and people eating chili immediately come to mind.  I applied my new-found time-lapse ability to the annual Blues Jam and Chili Cook-Off at the Marshall (MI) United Methodist Church.  This event involves local musician playing the blues, while people eat chili that is competing for the prized Championship Ladle, all the while making donations to the Haven – a homeless shelter.  I set up the camera on a beam above the crowd, aimed at the stage, and set the intervalometer to take a picture every 3 seconds throughout the event.

At the end of the night I had a full memory card, about 6,000 photos, and an arduous photo processing task ahead of me.  Within a day the 6,000 shots had been combined (using ffmpeg) into four sequential time-lapse videos totaling about 10 gigabytes of hard drive space.  Next I used GIMP to create title and credit slides from a still photo advertising the event on Facebook.  Kdenlive was used to reduce the size of the four video files by turning them into mp4 files, and then to combine the title shots with the four sequential videos, and to add a soundtrack that had been recorded during the final open jam session at the event (recorded to CD by the sound techs at the event, CD loaned to me and ripped to my laptop using grip and CDParanoia).  Kdenlive then rendered the entire project into another mp4.  The resulting video was only about 50 megabytes, and was considerably coarser than the original photos.  You can see it here.  To come up with a higher quality final product, I used kdenlive to crop the original high-res videos, zooming in on the stage area.  Then I re-combined these videos, the title slides, and the soundtrack into a lossless MPEG version – still about 10 gigabytes in size.  Finally, I had kdenlive re-render this file into a more manageable mpg file (about 450 megabytes), which was uploaded to YouTube.  Here’s the final product:

This was a project that taught me a lot about time-lapse photography, video-editing, and file compression.  Now I find myself looking for other venues where time-lapse might create an enjoyable short film.

I guess this post falls into the category of “Other Stuff that Matters,” at least to me.

Starting Over

With the beginning of the Spring semester comes the opportunity to reflect on our purpose.  College offers an opportunity to expand one’s interests and gain additional knowledge.  These are admirable goals, and can be achieved easily if one follows these guidelines:

  1. Show up.  Woody Allen said that “80% of success is just showing up.”  This is certainly true. Attend class regularly, and you’ll be 80% of the way there.
  2. Be prepared.  “Chance favors the prepared mind,” as Louis Pasteur said.  By doing the assigned readings and coming to class having thought about the material you will find the favor of which he spoke.
  3. Be open.  True education requires a level of openness that we do not all possess.  There is, however, a balance that must be maintained: “By all means let’s be open-minded, but not so open-minded that our brains drop out.” – Richard Dawkins
  4. Confront your ignorance.  You don’t know everything, nor do I.  Recognize the material that you don’t understand and ask questions about it. “What the mind doesn’t understand, it worships or fears.” – Alice Walker

Looking forward to a great semester as we grow together.

(Now – begin to confront your ignorance: if you do not recognize the people I have quoted, get to work.  Knowledge is only a Google away.)


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