Thursday, 21 February 2008

Epalxella dinner party

A new microbiology movie is up, and with it a lot of firsts: the first I did with the new iMovie, the first I'm putting up on YouTube (a direct result of the "publish to YouTube" option in iMovie), and the first which I've done since receiving D.J. Patterson's excellent Free-Living Freshwater Protozoa: A Colour Guide.

In case I sound like I'm building it up, though, I'm not: my narration in this movie is terrible, and my explanations are so brief that it will probably be incomprehensible to anyone not already intimately acquainted with the subject matter. Still, practice makes perfect, and through the magic of Web 2.0 I can publish my practice movies just as easily as not.

If one prefers to watch the movie just to observe the epalxella, I recommend turning down the sound and listening to appropriate music instead (viz. Nefertiti from the new Herbie Hancock album).

Posted by jon at 10:46 PM in Microbiology 

Monday, 7 May 2007

First microbiology movie

I've put together a quick little minute-long video of a few highlights of my observations of the past couple weeks. It's been astounding to watch the ecosystem evolve since I captured some very lively pond water into a small glass vase kept outside our appartment window. I've seen a lot of things I haven't been able to identify, but in this video I point out two classics of microbiology, the amœba and the paramecium.

Click here to watch the video.

Posted by jon at 11:14 PM in Microbiology 

Sunday, 28 October 2007

How cool is this?

I was immensely pleased to receive an unexpected comment the other day on my second microbiology film, "Hunt for Paramecium". While I make these films more for my own benefit than anything else (it gives some added direction to my microscopy), I publish them openly, since there's no good reason to make them private. But still I never really expected anybody else to watch them, much less enjoy them. Yet lo and behold, not only has my film been enjoyed by someone else, but by a whole class of sixth graders! It's quite rewarding when something you do almost on a lark turns out to be useful, for education and for communicating an interest in the hobby.

The irony is that right after publishing "Hunt for Paramecium", I was somewhat unhappy with it, since I thought that it gave the impression that microbiology was too difficult. In fact with a slightly more mature sample I had some sixty paramecium swimming around in a single drop, and so I planned a follow-up film, "Paramecium party", to show the other side of the coin. With the move and new job (and with the chance to use my telescope again) though, I haven't used the microscope for a few months now. So this new comment from the other side of the world was just the thing to get me inspired again!

Posted by jon at 10:24 AM in Microbiology 

Sunday, 20 May 2007

Hunt for paramecium

My second effort at a microbiology film is up, entitled "Hunt for paramecium." I play around with a few more editing techniques, and do at least manage to do what I set out to (film a paramecium at high magnification), but overall I think this falls well short (in quality and educational value) of what I'll be able to do when I get the hang of this more. (It didn't help that I had a fairly boring specimen tonight.) But this is a "learn by doing" endeavour, after all, so I'll have to work through this amateurish stage before I can become a true microbiological Jacques Cousteau :-)
Posted by jon at 11:12 PM in Microbiology 

Saturday, 21 April 2007


When I was a kid, during summer vacation, I often went to these "Mini-courses" that the Des Moines Public Schools put on. Unlike regular classes in "boring" subjects like Math and English, these were a lot more diverse and interesting, with subjects like rocketry and aviation. The one I found the most interesting though is one I had always meant to get back into: microbiology. This was such a fun hobby that I have continually been amazed that it doesn't seem to be that popular (so far as puttering around on the net and seems to indicate). But at long last I have decided to forge ahead despite the lack of the handy field guides that spoil the ornithologists and minerologists, and just get back into it anyway. Wikipedia now seems to have enough information about kingdom Protista that I should be able to classify and understand what I see reasonably well, even if left to my own means.

The mini-course in question, like my intended hobbyist activity now, was basically formed around the following: we would hike out to a pond, collect a sample of pond water (there is a technique for doing this to get the best concentration of amœbids), and then observing drops of the sample under the microscope and cataloguing the unicellular organisms we found. At the same time, to get the most out of the viewing, one learns about the various traits and species of amœbids, flagellates, and ciliates, as well as the parts of their cells, and how they live, eat, and reproduce. So it amount to an activity similar to bird watching, except that it is done in a microscope and the species observed are a lot wierder. And, phagocytosis is somehow more interesting to watch than pecking worms :-) In addition, I find that the study of unicellular organisms leads to much more thought-provoking introspection on the nature of life and the universe. In this the rewards of the hobby closely parallel those of amateur astronomy.

My reasons for renewing my interest in the hobby after such a long hiatus are pretty easy to explain: In Montreal I didn't have any easy access to ponds that might harbour any interesting unicellular organisms, and in Natick the conditions were good for astronomy, so I gave more of my time to that. But now in Valenciennes I find myself unable to use my telescope conveniently (even though at long last I finally have it with me), yet I could easily put a microscope to good use. So if I can't study and contemplate the astoundingly big, I might as well explore the astoundingly small.

I am so happy about the microscope I purchased that it will certainly deserve an article of its own as soon as I have the time to write one; I cannot remember the last time I bought something that so surpassed my expectations. It is a really, really good microscope!

The first fruits are already available with this post, however: the scope came with a USB webcam attachment, which means on the one hand that I can view images on my computer screen instead of squinting through an eyepiece if I so choose, and on the other I can capture images and movies to publish on my blog (caveat lector :-)). The very fact that I am able to post this with images of my own creation so quickly is very rewarding. Yes, the images accompanying this first article were taken by yours truly, using one of the prepared slides the microscope was delivered with, displaying the cellular wonders inherent in a microscopic bit of pine wood. And given that these photos were captured in the first 10 minutes of me using my new microscope, I think this is an auspicious beginning, and I hope there will be many more and more interesting images to come.

Posted by jon at 12:24 AM in Microbiology 

Sunday, 22 April 2007

The Bresser "Erudit" microscope

I decided about a month ago to get a microscope, but the decision on which one to get was not taken lightly. I already knew a thing or two about the importance of quality optics from amateur astronomy (enthusiast photographers will already have the same insight). So I wasn't at risk of being suckered into a toy store rip-off.

On the other hand, this is just one hobby among a lot of others that I have, so I wasn't about to spend $6,000 on a microscope either! My primary interest is in protists, which means I'd be interested in specimens 10-50 µm in size; being able to zoom in close to view cellular nuclei and organelles would be a plus though. Still, I didn't need anything fancier than what I used in school. At 100x a small 10 µm protist would appear like 1 mm to the naked eye, getting up to 1000x would fill out the field a lot more but the quality (given what I'd be willing to pay) would be sub-par. I've since discovered this page that does a very good job of clarifying magnification requirements for various tasks.

I also decided right away that a good way to keep the price down would be to stick to a monocular microscope; I was already used to observing with one eye from my telescope, and the extra optics would be sure to drive up the price.

Armed with this general picture of what I was looking for, hunting around I found a German site,, with a big catalog of serious microscopes, most of which were well beyond my price range. Looking at the link now, I see that I was very lucky as the microscope I bought is already out of stock! Anyway, the Bresser Erudit was listed as a best seller, and also had a number of accessories, which meant I could expand if needed later on, without having to buy a whole new microscope. Best of all, the scope was sold in a kit with everything I'd need to start right away: three eye pieces, a Barlow lens (all told that means I can view at 15 different magnification settings, from 20x to 1024x). It also came with five prepared slides and five empty slides, and best of all, a USB web-cam. Besides letting me post images on my blog, I'm hoping that by post-processing the images on the computer I'll be able to bring out more detail, without having to resort to the hassle of phase-contrast or staining. (Time will tell if that will play out in practice, though.) Also if I do get tired of looking through an eyepiece, I can just watch the image on screen. At €200, it was a deal for a respected German brand-name microscope with such a complete kit. (Compared to telescopes or prosumer camera lenses, microscopes are cheap.)

And when the thing arrived I was blown away: look at what a solid case this thing comes in! No danger of shipping damage here! The scope is as solid as I had hoped, and even has excellent fine-tuning controls for moving a specimen; even at 400x I was able to move up, down, left, and right without jerkiness.

In the USA, I believe that Meade distributes Bresser mircoscopes; judging from the photos on the Meade site the Erudit seems to be most like the Meade 9460, although the lens configurations are different.

Posted by jon at 12:00 AM in Microbiology 
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