An interesting offer from ASPEX

I had my doubts about this; I got an offer from ASPEX corporation to let people get free scanning electron micrographs of just about anything. They make a desktop SEM, and all you have to do is fill out a form and mail it in with your sample of a dead bug or a microchip or bacon, and presto, within a few weeks they’ll have it scanned in and the image available on their website.

I asked them if they knew how many readers I have, and they said no problem, they can handle it.


Well, you heard them. Scavenge your trash cans, dig into your local sources of vermin and oddments, and send them in. I’m thinking this could be really fun for any school teachers out there — you could have the whole class looking for interesting specimens to zoom in on. You can see their current galleries for ideas.

Weird Bug Ladies are the nicest kind, I think

She sounds like a nice person: a zoology student (I was one of those, once! Zoology departments are disappearing everywhere, though), with the hobby of making cuddly, squishy plush beasties of all sorts, especially of lots of invertebrates. I think it’s time that the teddy bear hegemony in the world of children’s toys be broken — you can start there, and support a science student at the very same time.

Watching every cell of the developing zebrafish

Blogging on Peer-Reviewed Research

How can I respond to a story about zebrafish, development, and new imaging and visualization techniques? Total incoherent nerdgasm is how.

Keller et al. are using a technique called digital scanned laser light sheet fluorescence microscopy (DSLM) to do fast, high-resolution, 3-D scans through developing embryos over time; using a GFP-histone fusion protein marker, they localize the nucleus of every single cell in the embryo. Some of the geeky specs:

  • 1500×1500 pixel 2-D resolution

  • 12 bits per pixel dynamic range

  • Imaging speed of 10 million voxels per second

  • Complete scan of a 1 cubic millimeter volume in 3µm steps in 90 seconds

  • Efficient excitation (5600 times less energy than a confocal, one million times less than a two-photon scope) to minimize bleaching and photodamage

Trust me, this is great stuff — as someone who was trying to do crude imaging of fluorescently labeled cells in the 1980s using a standard fluorescence scope and storing stills on VHS tape, this is all very Buck Rogers. Just load your embryo into the machine, start up the scanner, and it sits there collecting gigabytes of data for you for hours and hours.

But wait! That’s not all! They’ve also got sophisticated analysis tools that go through the collected images and put together data projections for you. For instance, it will color code cells by how fast they are migrating, or will count cell divisions. Similar tools have been available for C. elegans for a while now, but they have an advantage: they’re tiny animals where you might have to follow a thousand cells to get the full story. In zebrafish, you need to track tens of thousands of cells to capture all the details of a developmental event. This gadget can do it.

Here, for instance, are a couple of images to show what it looks like. The right half is the raw embryo, where each bright spot is a single cell nucleus; the left is one where the pattern of cell movement is color-coded, making it easier to spot exactly what domains of cells are doing.

Cell tracking and detection of cell divisions in the
digital embryo. (A) Microscopy data (right half of embryo:
animal view maximum-projection) and digital embryo (left
half of embryo) with color-encoded migration directions (see
movie S9). Color-code: dorsal migration (green), ventral
migration (cyan), towards/away from body axis (red/yellow),
toward yolk (pink).

I grabbed one of their movies and threw it on YouTube for the bandwidth-challenged. It’s not very pretty, but that’s the fault of reducing it and compressing it with YouTube’s standard tools. This is an example with color-coded migration (blue cells are relatively motionless, orange ones are moving fast), and you can at least get the gist of what you can detect. You can see the early scrambling of cells in the blastula, migration during epiboly and blastopore closure, and convergence in the formation of the body axis fairly easily. Well, you can if you’re familiar with fish embryology, anyway.

This crappy little video doesn’t do it justice, however. Take a look at the Zebrafish Digital Embryo movie repository for much higher resolution images that are crisp and sharp and unmarred by compression artifacts. It contains DivX and Quicktime movies that are somewhat large, 10-40M typically, that represent visualizations of databases that are several hundred megabytes in size.

What can you do with it? They describe observations of early symmetry breaking events; patterns of synchrony and symmetry in cell divisions; direct observations of the formation of specific tissues; and comparisons with mutant embryos that reveal differences in cell assortment. It’s fabulous work, and I think I’m going to be wishing for a bank of big computers and lasers and scopes for Christmas—only about $100,000 cheap! Until then, get a fast internet connection and browse through the movies.

Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EHK (2008) Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy. Science 2008 Oct 9. [Epub ahead of print].

Honey, where’s my Super-Suit?

The new Speedo LZR Racer suit, that is. Designed with all the power of science and technology behind it, the LZR Racer is being credited with imparting enhanced, record-breaking athletic performances to its wearers.


It was designed using the same technology applied to reducing drag on the Space Shuttle, with the goal of diminishing the friction and skin movement that normally occur during swimming, thus improving overall hydrodynamics. It’s a cool story from the scientific perspective, to be sure, but the public reaction since its unveiling in February 08, and now with the Olympic Swimming competitions coming up, has been just a teensy bit hysterical.

I have to hand it to the Speedo marketing team. Dropping ‘NASA’ into any conversation about your product is sure to get people’s attention, and beyond that, the look and promise of the suit is truly reminiscent of something Edna Mode might have whipped up.

So you get a bunch of top tier athletes, adorn them in the best suit technology can buy, extoll its performance-enhancing properties, and have them all feeling like superheroes going into a race. Is there a psychologist in the house who can predict the probable effect here? And is it any surprise that the competitors who don’t have LZR rocket super-suits are pretty much shitting bricks about this?

Oh yes, the competition is crying foul heading into the Olympic games. Entreaties have been made to FINA, the international governing body of organized aquatic sports, to ban the suit from competition, to no avail. In a stellar display of hyperbole, Italian swim coach Alberto Castagnetti has declared the suit tantamount to “technological doping.”, but his complaints have garnered little sympathy.

Don’t get me wrong, I’m all for fairness in competitive sports. I hate doping, not only because of the unfair advantage it can confer but because of the short-sighted greed it denotes–greed for both the victory and the spoils. Spending hours and hours on conditioning to improve performance is one thing; intrusive meddling with one’s body chemistry through injecting hormones or proteins targeted to increasing red blood cell density, etc. is a different proposition entirely, and reveals an ugly, desperate side of professional athletics. The line blurs a little bit in situations where medically necessary reconstructive surgery (of, say, a baseball pitcher’s shoulder) ends up enhancing performance by imparting increased joint mobility. It would be a shame to ban athletes who were able to return to peak performance after such a procedure, but it would be deeply disturbing if athletes were compelled to undergo this surgery without need with the express purpose of gaining a competitive edge.

This, however, is a merely a swimsuit. An externally applied and fully removable garment that anyone in the world, at least in principle, can purchase and use. A product with such dramatic hype attached that it will be virtually impossible to determine how much of the resulting performance enhancement is due to the power of suggestion, rather than the superior crafting. Get over yourself, Italian coach. Let the Games begin!
I neglected to note that this post was authored by Danio. I apologize for the omission.


Ahhh…in case you hadn’t heard, Apple came out with an new machine yesterday, the MacBook Air. I want. It’s one of those superslim portables, with the usual Apple elegance — this would be a perfect travel machine.

Except for the price: a bit less than $2K for the low end model, over $3K for the high end, all solid state model. I think I’ll have to wait a few years for the price to drop significantly.

Go, squid, go!


We can learn from nature:

Inspired by the sleek and efficient propulsion of squid, jellyfish and other cephalopods, a University of Colorado at Boulder researcher has designed a new generation of compact vortex generators that could make it easier for scientists to maneuver and dock underwater vehicles at low speeds and with greater precision.

In addition, the technology — seemingly inspired by the plots of two classic sci-fi films — may soon allow doctors to guide tiny capsules with jet thrusters through the human digestive tract, enabling them to diagnose disease and dispense medications.

(The two films, by the way, are Fantastic Voyage and Inner Space; I think only the former classifies as an SF classic.)

While the details are awfully thin, there are more pictures and movies online. Hint—don’t waste your time with the mpgs, they only show the titles; you’ll have to watch the ugly wmv files.

I guess I chose wisely


Foreign Dispatches posts some digital camera recommendations, with explanations. I just went through a fair amount of research before going out and getting a new camera myself a few weeks ago, and it’s all good—most importantly, his best choice is the same camera I got for myself, the Nikon D50. Whew, what a relief. Don’t you hate it when you dump a bucket of loot on something and then you find a good review that tells you you should have got something else?

As he notes, how many millions of pixels you’ve got are no longer the most important criterion for a good camera. What settled me was that I finally wanted some good optics—the teeny-tiny cheap lenses on your standard point-and-shoot have always bugged me, and I wanted a camera body where I could actually mount some good lenses. Since my working camera for film (which I have hardly used in years now) was a Nikon 6006, that pretty much settled it for me, so I went with the camera body that would handle my Nikkor lenses.

One other thing Abiola didn’t mention in his review: a good camera is useful, but it isn’t the most important thing in good photography. I don’t consider myself a good photographer, but I’m not bad as a microscopist, and know by analogy what works. On a scope, you get the best objective you can afford, but when you’re working at micrography, you just sort of aim that at the specimen and forget about it. Where you put all your effort and fuss and tweak is in the illumination, and what you learn to appreciate is a condenser with all the knobs and dials and filters. Same with a camera; you want to be able to point a good light collector at your subject, but the difference between a blah picture and a great one is the lighting.