A virtual camera lucida

Sometimes, the scientific literature sucks at getting information to you.

I was looking at the table of contents of a new issue of The Journal of Crustacean Biology and saw an article about how to photograph soft-bodied crustaceans. Hm, I wonder why photographing soft-bodied crustaceans is difficult, I thought.

And the abstract mentioned software to deal with short focal planes by merging several pictures. The software is Helicon Focus.

Yes, I should be happy that I have found something useful, but... dagnabbit, why didn’t I know about this years ago?

For instance, here’s part of Figure 3 from a paper a few years back (Espinoza et al. 2006) on the left, compared to a new picture processed with Helicon Focus (click to enlarge).

These are neurons stained through a technique called backfilling. The best backfills are really superb, and you can see a lot of detail. But they’re often in thick tissue, and neurons go all over the place through it, making it hard to see all the relevant detail. The way people usually got around this was to get a camera lucida attached to a drawing tube through a microscope, then trace the axons as you focused up and down.

I was actually very pleased with the pictures in Figure 3 as published, which had dark cells against a very clear background. But the one shown here on the left shows the problem of getting all the relevant detail in the shot. The cell bodies on the right are okay, but the ones down a little deeper in the ganglion on the left and their axons are already blurring out.

The processed version on the right is better.

Having played with this a bit, sometimes there are things you can see in the individual frames that do get lost in the processed version. The biggest problem is when there is some detail underneath something else. You can often see it under the scope and in the individual frames, but not so well in the composite image.

This was so startling and so useful to me, I briefly entertained the thought of trying to turn this into a neuroscience methods paper. Then I looked and found short references that it had been used in the invertebrate neurobiology literature a couple of years ago (Scanell et al. 2008) in a journal I read. D’oh! Another shrewd Faulkes scheme bites the dust.

But at least I can spread the word through a blog post. A slightly more recent paper by Berejnov and company (2009) has nothing whatsoever to do with biology, but gives a better example of what you might get from this kind of software.

As I was writing this, I read an interview with Neil Gaiman, where he said this, mostly in relation to book publishing in particular genres:

Information used to be gold: hard to find, expensive, the equivalent of going off into the desert and coming back with a perfect lump of gold. Now, it’s the equivalent of going off into the jungle, in which there is information everywhere and what you are trying to find is the piece that is useful, while ignoring the noise.

I do wish the process of finding useful things was a little less jungle-like.

References

Berejnov, V., Sinton, D., & Djilali, N. (2010). Structure of porous electrodes in polymer electrolyte membrane fuel cells: An optical reconstruction technique Journal of Power Sources 195 (7), 1936-1939. DOI: 10.1016/j.jpowsour.2009.10.050

Espinoza SY, Breen L, Varghese N, Faulkes Z. 2006. Loss of escape-related giant neurons in a spiny lobster, Panulirus argus. The Biological Bulletin 211: 223-231. http://www.biolbull.org/cgi/content/abstract/211/3/223

Hegna, T. (2010). Photography of Soft-Bodied Crustaceans via Drying, Whitening, and Splicing Journal of Crustacean Biology 30(3): 351-356. DOI: 10.1651/09-3253.1

Scannell, E., Dell'Ova, C., Quinlan, E., Murphy, A., & Kleckner, N. (2008). Pharmacology of ionotropic and metabotropic glutamate receptors on neurons involved in feeding behavior in the pond snail, Helisoma trivolvis Journal of Experimental Biology 211(5): 824-833. DOI: 10.1242/jeb.011866

Rise from the ashes

A while ago, while cleaning out a storage closet, I came across a couple of boxes filled with cassette tapes. I’ve been slowly converting them to mp3 files over the last couple of weeks. Almost every time I comment on Twitter of Facebook about digitising old cassette tapes, someone asks how I’m doing it. So maybe this will be of interest to a few blog readers...

It’s pretty simple: it’s just a tape deck with a USB interface and a bit of software. The software “EZ Audio Converter” is pretty simple, which is both blessing and curse. There’s about one important option for recording: automatically separate tracks or not. It does a fairly good job of recognizing tracks for basic rock and roll songs, but not great for things like spoken word recordings. sometimes you have to go in and use another audio editor to split tracks.

You can’t pick the audio format (you will get mp3 and you will like it!), no fiddling with equalizer settings, and it assumes you have iTunes software.

There are other ways of converting cassettes to digital audio files, but some of them require you still have a tape deck, and I imagine a lot of people got rid of theirs sometime around the turn of the century. This one is nice because it’s a all in one package.

I also have a USB turntable for digitising vinyl from the same manufacturer. I haven’t used it yet, because it requires more table space, and I haven’t found a place to put it.

I have gotten spoiled, though, by ripping CDs. You can rip a 70 minute CD in a few moments, but with tapes and vinyl, you have to play the whole thing through at regular time... It’s also fun to look at some of the graphics, particularly for cassette singles (which were short lived, ephemeral things).

It’s nice to get back some music that I thought I’d never hear again. Obscure Canadian pop from the heyday of MuchMusic or The Q. Except maybe in a dodgy YouTube video that you can’t put on an first gen iPod nano.

Fashion! Turn to the left! Fashion! Turn to the right!

Dr. Becca was singing the praises of her new lab coat. It apparently references Lost.

Well, Dr. Becca, you are not the only one to have a cool partner. For not too long ago, I received as a gift, this:

Now, I will admit Dr. Becca’s lab coat may have a bit of an edge in the artistic department. The embroidery is more substantial. But, Dr. Becca, Ph.D., I will see your lab coat and raise. Do you have...

TEH GOGGLEZ?!?11?1!!?

(My people get me. The crazy, geeky, me.)

I hate shopping

At least, I hate shopping for my lab. It's taken up most of my time for the last several days. And it's a pain, for two reasons.

One is that the purchasing is complex. When I personally want something from most internet based businesses, I give them a credit card or just click on PayPal, and away I go. Not with science shopping. Since it's the university, we have to go through a convoluted purchase order arrangement, which differs depending on how much money you want to spend (among other factors).

The second is that the websites of science suppliers are really disappointing in their ability to locate items. If you want pipette tips, suppliers have a huge range of them, and not many options to sort them. The clunk solution? To look through the well-organized -- but clunky -- print catalogs (pictured), which are faster to browse. Of course, the prices in those are out of date, so you have to find the item you want, type in the catalog number into the website to get the correct, current price. If the item hasn't been discontinued.

Even worse, it's nearly impossible compare items. You can't do anything like you can on many shopping websites to compare features of different products. So you have to look at each one individually, which takes a bloody long time for many common supplies. Let's say you type in "HCl," the chemical formula for hydrochloric acid. You get 2,794 hits from one supplier. Even if you just look at the best matches, you still have to wade through 40 separate entries, from different suppliers, different amounts, different purities, and so on.

And try to figure out how much shipping will cost you. You probably can't. One of the reasons I use one supplier in particular is that they don't charge for shipping, which means they get a lot of business from me because they have reduced the number of things I have to worry about in my order by one.

It's such a pain that it routinely goes on the bottom of my "to do" lists, which is not a good thing. So if you're running a scientific supply company, consider looking into what your customers do so that you can help them do it better on your website.

Bagging a roc with a slingshot

We got one.

After so many tries in the department to get external funding solo, my collegue Anita has managed to pull down a six-figure equipment grant from the National Science Foundation.

Let there be much praise sung and much chocolate purchased for our mighty hunter, who brought down seemingly impossible prey.

As it happens, I also submitted a proposal to the same program at the same time. I should be hearing news on my proposal "Real Soon Now."

Where’d it go?!

So here it is, a day with very little teaching, one phone interview (done), so I went into my lab and started to set up to do an experiment. I went down the hall to get some ice...

And the flipping ice machine is gone! Blast it! Apparently, it was taken away this time because it was leaking.

I am persevering and trying to continue with the experiment.

Threes

After two straight days of receiving equipment packages, I'm pretty excited to see if good things really do come in threes...

Christmas in June!

Yesterday, paper. Today, plastics. Tomorrow, the WORLD!

Just kidding about that last one.

Yes, another bunch of boxes of equipment arrived this afternoon. Mostly plastics and glasswear: beakers, graduated cylinders, carboys, disposible pipettes, petri dishes, and so on.

The biggest arrival, both literally and figuratively, was my new lab computer. It's got plenty of computing power, decked out in black and silver (you gotta approve of a colour scheme that matches much of your wardrobe), CD burner, DVD player, and a slim, flat screen. My techno-geek side is pretty excited about all this.

I'm still a long way from recording that first action potential, but the lab is starting to look like someone works there. And that someone is me. Which feels pretty good.

Microscope after all

After feeling a bit bummed yesterday about the start-up cash flow, I rethought the situation this morning.

Fortunately, the quote I had received for my microscopes were really two quotes for two microscopes. A "fancy" one with a digital camera and a couple of other bells and whistles is still going to be out of reach for a while. But the cost of another scope is within my current available funds. I'm resubmitting the request for that one.

At least I'll be able to look at some small things, even if I can't take pictures of them.