Cool scientific instruments: the NORUSCA II hyperspectral camera

Thumbnail image of two NORUSCA II 1st Generation
hyperspectral cameras. For full-size image see Optics InfoBase.

Up north in Svalbard, at the Kjell Henriksen Observatory, something very cool recently happened: the first hyperspectral images of the Northern Lights were taken. The NORUSCA II is the instrument developed to take them.

The Aurora Borealis and Aurora Australis—the Northern and Southern Lights respectively—occur because of the interaction between the solar wind and the Earth's magnetic field.

The Earth has an iron core, the inner part of which is under such pressure that, despite having a temperature of 5430 °C, it's a solid ball. The outer part, meanwhile, is cooler but under less pressure, so it remains liquid. Thanks to a combination of convection currents in the molten iron, the Coriolis force, and induced magnetic and electric fields that isn't totally understood (see Wikipedia or Gary A. Glatzmaier's page for more detailed descriptions), the geomagnetic field of the Earth is created and sustained.

Hundreds of kilometres from the Earth's surface, this field is met by the solar wind, charged particles that stream away from the Sun, through its own magnetic field. The solar wind distorts the Earth's magnetic field into the shape shown below:

Artist's rendition of Earth's magnetosphere, from Wikimedia Commons.

The charged particles, as well as ultraviolet radiation from the Sun, ionise the outer layer of the atmosphere to produce a plasma shell known as the ionosphere. (The ionosphere also has a dynamo region of its own, producing electric fields and magnetic effects. There are a lot of interrelated feedback systems at work here!) Accelerated along the lines of the distorted magnetic field, charged particles from the ionosphere and the solar wind are funnelled towards the poles.

When they get there, they can ionise nitrogen atoms by kicking out one of the atom's electrons, and excite both oxygen and nitrogen atoms that absorb their extra energy, moving an electron up into a higher-energy state. These states can't last, though—the atoms naturally tend to the lowest-energy state possible. When the nitrogen atom regains an electron, or the excited electrons drop back down to their ground states, photons are emitted—that is, light.

The wavelengths of the light emitted depend on the exact events that generated it. For the human observer, that means breathtaking displays in green, red and blue. For scientists, measuring the spectra of the aurora additionally makes it possible to discover a lot about the interplay of the upper atmosphere with the magnetic fields of the Earth and the Sun and the solar wind.

Northern lights over Nybyen, Svalbard, by Torbjørn Taskjelle,
shared on Flickr  under a Creative Commons licence.

Finally, this brings us to the NORUSCA II!

The ideal scientific image of the aurora would show us the whole sky at a high resolution, and for every pixel we could see each different wavelength of electromagnetic radiation that came from that part of the sky. To get this, some way of separating out the spectrum into bands is necessary. This can be done using prisms, diffraction gratings or, most usefully for our purposes, filters. The type used in the NORUSCA II is a kind of Lyot filter, a piece of birefringent material. The two perpendicular components of the electromagnetic radiation travel at different rates through the material and usually, when they recombine, their intensity will be reduced. Only for specific wavelengths will the intensity be preserved. This effect is increased by directing the light through a polariser before it gets to the
camera, thus picking out only the intended wavelength.

It's possible to scan through multiple bands of wavelengths with a Lyot filter, by switching out plates, but this takes too long to give really good results. Instead, the NORUSCA II uses a tunable liquid crystal filter. The birefringence of the liquid crystals can be tuned by adjusting the electric field across the filter, allowing NORUSCA II to scan through 41 wavelength bands in a matter of microseconds and with no moving parts. A fisheye lens allows the whole of the night sky to be seen at once and an EMCCD (electron-multiplying charge-coupled device) captures the image.

Thumbnail image of the lens mechanics and
optical diagram of the NORUSCA II all-sky lens:
(1) focusing mechanism and collimator lenses,
(2) filter box - chamber,
(3) camera lens, and (4) camera head.
For full-size image see Optics InfoBase.

Tunable liquid crystal filters have poor transmission of blue light, which is why they haven't been used for this type of application before, but the combination of high-throughput lenses and the EMCCD in NORUSCA II compensate for this well.

In the 2011-12 aurora season at Svalbard, not only did the Norwegian/Russian team successfully take the images they wanted, but they might already have discovered a new phenomenon.

Part A – The aurora as seen as a color composite image from the NORUSCA II camera. Three bands were combined to make the image. Each band was assigned a different color -- red, green, and blue – to enhance the features of the aurora for analysis.

Part B - The red arrow points to the unidentified low-intensity wave pattern, which the researchers suspect is an auroral-generated wave interaction with airglow. For contrast, the blue arrow points to the faint emission of the Milky Way. (Credit: Optics Express - image taken from UNIS). 

The red arrow on the image to the right shows a wave pattern picked up during a coronal mass ejection, when a particularly strong burst of high-energy particles hit the Earth's atmosphere. The researchers believe this could show an interaction between the aurora and airglow, normal light emission from the upper atmosphere (shown beautifully here).

You can read more about NORUSCA II here, and the full paper on its design and early results is available here. I'm very excited to see what it can discover in future aurora seasons.

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Bonus material:

• The great solar storm of 1859 produced huge and splendid auroral displays, as well as widespread disruption of telegraph lines. Some lines, however, were just the right length and in just the correct position that they functioned better under auroral power than with their batteries!
• I'm currently reading Thomas Keneally's novel Victim of the Aurora, a murder mystery set in an imagined British Antarctic expedition in 1909. The aurora so far hasn't played much of a role but there is plenty of discussion of ice phyiscs, Arctic marine biology and Edwardian scandal. I thoroughly recommend it.
• Here you can see the students at Kjell Henriksen Observatory demonstrate new ways of removing the observatory's dome covers: both scared and safe turtle methods.

Science Blog Saturday: Science You Can Love and In the Pipeline

Well, I said I wanted Science Blog Saturday to be fortnightly, but I seem to have missed out on last week's post. It's been a busy week, though—I've just started my first (part-time) programming job—and to make up for it, here are two quite different recommendations.

Science You Can Love

Science You Can Love, otherwise known as Wissenschaft und Deutsch, is a science tumblelog. I find the differences between the tumblog and blog formats very interesting, and I'm also very impressed by this blog in general. Written by a 20-year-old Nigerian student in the USA, who's studying (you guessed it) German and science, specifically chemistry, SYCL is a mixture of reblogged articles from a wide range of sources and original posts, with a few personal entries sprinkled in. SYCL posts a torrent of information of entomology, astronomy, particle physics, virology, scientific ethics, scientific illustration, geology and almost everything else: it's always interesting and always has beautiful pictures.

The curator of SYCL is even more prolific than Chris Quigley, whom I wrote about previously, posting several times a day. Reblogging is certainly less work than creating the same amount of original text each day, but it's obvious that she puts a lot of effort into finding and presenting scientific news and curiosities. At the same time, due partly just to the Tumblr format, the blog feels very personal and the blogger's passion for science shows clearly. She's had some of the social justice controversy for which Tumblr has become a byword and handled it gracefully. (For those unfamiliar with Tumblr formatting: the first, indented paragraphs are the text of the original post; the next paragraph is a response from another Tumblr member; and the final paragraph is SYCL's response to that.)

Science You Can Love is, in my opinion, a must-read for anyone with a raging curiosity about the world. You can expect to be amazed, awed, fascinated or disgusted—maybe all of those— at least once a day. For me today, it was this post on the parasitic plant Hydnora africana. (In case SYCL's theme makes it hard to read, I would recommend using a Readability app or bookmarklet, or just joining Tumblr and following it there.)

In the Pipeline

In the Pipeline, by Derek Lowe, is in many ways the opposite to SYCL. For one thing, it's so well-known that I feel a little silly linking to it here. Lowe is well-established in his career and writes original posts, with few pictures, mostly in a comparatively narrow range of topics around pharmaceutical chemistry.  The content at In the Pipeline is much wider than first meets the eye, however, and it's deep too. There are over ten years' worth of posts here, with commentary on chemical and biological news, graduate school and getting a pharma job, Alzheimer's disease and cardiovascular disease.

The route by which I discovered In the Pipeline, however, was a friend relating a series of anecdotes from Things I Won't Work With to me, one evening in a nightclub. (Yes, I'm cool.) In this series of posts, you can read Lowe's heartfelt grounds for refusing to enter a chemistry lab with small, smelly isocyanides:

. . .well, I've never actually been downwind of the Abominable Snowman's armpit or been had my eyeglasses fogged up by a Komodo dragon with stomach trouble, but those are the examples that come to mind.

—dioxygen difluorine:

And yes, what happens next is just what you think happens: you run a mixture of oxygen and fluorine through a 700-degree-heating block. "Oh, no you don't," is the common reaction of most chemists to that proposal, ". . .not unless I'm at least a mile away, two miles if I'm downwind."

—or straight dimethyl zinc:

A colleague of mine made some in graduate school, and came down the hall to us looking rather pale. He'd disconnected a length of rubber tubing from his distillation apparatus and seen it go up in immediate, vigorous flames. "This stuff makes t-butyllithium look like dishwater" is the statement I remember from that evening.

If you can't get enough of terrible ideas, you may also enjoy the sections Things I'm Glad I Don't Do and How Not to Do It. A harmless but hilarious example: bromine.

Finally, I appreciate Lowe's coverage of the dark side of research, publishing and drug manufacture, which is both mordant and moral. If you're interested in any part of the world of the professional (bio)chemist, there's something here for you.

Cicada surface science

Photo of a clanger cicada by Arthur Chapman,
shared on Flickr under a Creative Commons licence.

The east coast of the USA is greeting the latest emergence of the Brood II 17-year cicadas this month, and it reminded me of some interesting science I read about earlier in the year.

The wingcases of the Australian clanger cicada have the special property of killing bacteria that touch them, using just their physical structure—that is, there's no chemical reaction going on. Now an international team of biophysicists have developed and tested a model for how this happens. Their paper was published in the Biophysical Journal this February.

It's been known for a while that the cicada's wingcases are covered in a hexagonal array of nanopillars, up to 200 nm high. You might expect that the pillars pierce the soft walls of the bacteria to kill them. In this model, however, the high surface area that they give the wingcase is more important. The bacterial cell wall adsorbs onto the surfaces of the nanopillars from the top down, stretching the sections of wall in between until they rupture. You can see how this works in the animation below.



Since the model predicts that bacteria with more rigid cell walls will be resistant to death-by-nanopillar, the team could test it by microwaving resilient strains of bacteria, to soften their walls, and observing their survival on the wingcase surface. As expected, softened bacteria were destroyed by the surface, even if the unsoftened strain could survive it.

This work should contribute to developing antibacterial surface treatments that don't need extra cleaning agents to be kept hygienic. I do wonder, though, just which bacteria would be affected by such a surface and which would be resilient against it. Altering the height and spacing of the nanopillars could make them effective against a wider range of germs, as could playing with the chemical makeup of the surface to increase bacterial adsorption.

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Some bonus cicada titbits:

• These insects are gluten-free, high in protein, and taste a bit like asparagus. If that tempts your tastebuds as much as it does mine, the National Geographic has a selection of recipes for you.
• After seventeen years underground, how do the members of Brood II know that the time is now to emerge? New research suggests that they count the spring blooms of the trees whose roots they snuggle up against.
• The Washington Post takes a look at the evolutionary pressures that led to North American periodical cicadas 13- and 17-year lifecycles.
• Scientific American covered the Biophysical Journal paper in March, with an article on nanopillars and a disinfected world.

Science Blog Saturday: Quigley's Cabinet

Science Blog Saturday is a new fortnightly feature. I want to share some of my favourite science blogs and tell you why they're so great. Enjoy!

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Quigley's Cabinet is a one-woman effort that covers an impressive range of subjects.

Chris Quigley blogs mostly about her research interests, death and the anatomical body; she has written six books on these topics, including The Corpse, Modern Mummies and Dissection on Display. The Cabinet is by no means a gorefest, though. It has recently featured posts on the smell of death, the exhumation of a luckless member of the Franklin expedition, and mass grave simulation at the University of Tennessee's 'Body Farm' (note: each of these posts contains a picture of human remains), but Quigley's tone when writing about these topics is matter-of-fact and not exploitative.

There is a new post to the Cabinet every single day (perfect for insatiable readers like me!). Common topics include fossils, animals of all kinds, and archaeology. I would like to point out these posts in particular:

• Yesterday's ingredients: a 150-year-old doctor's store room answers questions about patent medicines
• Stone Age studio: about the discovery of a 100,000-year-old artisan's studio
• Beefy builders: how much livestock was needed to keep the Pyramid builders fed?
• Dragonflies are monsters: I don't think so, but if I were a fly, I'd be terrified of them

Quigley's Cabinet is a recent discovery of mine and I'll be checking it daily for the foreseeable future. I hope you find something interesting there too.

Cool scientific instruments: the nine-lens camera

The curious picture above crossed my Tumblr dashboard this morning, with this caption:

Nine-lens camera fully assembled. This camera was designed by Oliver Scott Reading in the early 1930’s. It was the state-of-the-art aerial camera for many years. (1938)

-NOAA

I wanted to find out more about it, and a quick Google search turned up this description in a 1936 issue of Popular Mechanics. You can see its size much better in their picture, with a man standing next to it. The camera was used for aerial photography and photogrammetry by the US Coast and Geodetic Survey, now part of the National Ocean and Atmospheric Administration. There are thousands of historic photos from the Survey here.

The nine-lens camera was capable of photographing 600 square miles in a single picture. The eight lenses around the edge of the central one were focussed on angled mirrors "of an astronomical type", broadening the area that could be covered. All nine images were projected on a single piece of film, which was held flat by a vacuum pump.

The complex engineering of the nine-lense camera was a great improvement on the five-lens camera that was previously used. It was designed by Captain Oliver Scott Reading of the US Coast and Geodetic Survey, a "mechanical genius" who had joined the Survey straight out of high school and subsequently educated himself in this type of work. Read more about his interesting life here (PDF) and in his obituary (PDF). You can learn more about aerial photogrammetry in this very accessible presentation (PDF).

Incidentally, the nine-lens camera was tough. Even after a fatal plane crash onto Mount Moffat, it was able to be reconstructed, as shown below.

Oliver Scott Reading with components of nine-lens camera. Reassembling camera after Mount Moffat crash.

- NOAA

Scratching the surface of Ancient Greek and Roman painted statues

When you think of an Ancient Greek statue, is the picture above what springs to your mind? If you're like most people, you imagine classical sculptures more like Apollo Sauroktonos, below. (I picked him as my unpainted example because of the cool lizard he's about to catch.)

Archaeological research shows, however, that the Romans and Greeks preferred their statuary to wear all the colours of the real world they mimicked so well. The minimalist look we know springs from thousands of years of weathering, not to mention the cleaning efforts of restorers and curators. Marble sculptures with visible remains of colour were found in the 19th century but neglected during the 20th, according to the Stiftung Archäologie (Google translation here).

Modern scientific techniques have a lot to offer in reconstructing the original appearances of these works of art. For example, energy-dispersive X-ray spectroscopy can reveal the chemical nature of pigments that have been absorbed into the stone. Raking light (light shone across the surface at an oblique angle) shows up changes in surface texture and structure. This is useful because painted patches of stone may have protected by the wax or egg base of the paint, and so have weathered differently from the other parts. Meanwhile, reflected ultraviolet light imaging shows fine surface details that can be hard or impossible to see in visible light.

In the photo above, you can see a UV image of the cape of a statue of Athena from the Temple of Aphaia on Aegina (image from here). To the left is a reconstruction by the Stiftung Archäologie.

The Stiftung's work has been on display since 2003 in the travelling exhibition Gods in Colour (Bunte Götter). Here is the English-language gallery guide (PDF) from its stop at Harvard. It can currently be seen in Vienna, until September 2013. I wonder if I can find the excuse for a trip this summer...

As a fan of historical fiction, I find this work fascinating. It completely changes my vision of Roman and Greek cities. In comparison to the icy and dignified white marble figures we know now, these sculptures make the artists seem much more relatable.

My favourite discovery, though, is that the mysterious figurines made by the Cycladic civilisation were also coloured. Mind you, the mystery is not cleared by the revelation that some of them were covered in apparently randomly-placed eyes.

These two pictures are from Elizabeth Hendrix's article Painted Ladies of the Bronze Age (PDF), which has much more detail on the science of colour reconstruction and the significance of the Early Cycladic figures. It includes this paragraph:

The examination the figures in the collection of the Metropolitan and in other museums makes it clear that most, if not all, of them were covered with strong colors in patterns that are not always comprehensible to viewers today. When recognizable anatomical features were painted in locations that make sense to us (such as the mouth centered below the nose), we are prepared to see the traces of the painting in those areas. It is a greater challenge to accept similar evidence for asymmetrical designs or familiar shapes in the "wrong" locations (such as several eyelike almond shapes on one side of the face). It may well be that symmetrical patterns have been retained more often since they are easier to recognize, thus inspiring more care on the part of the handler, whether curator, dealer, owner, or restorer.

There are more stunning pictures and more information on the coloured gods at Archaeology.org, Harvard Magazine and ColourLovers. (Via.)

The Kakapo and the Wood Rose

Today's entry is something a bit different: a comic I drew to summarise this article, Strange Species Alliance by Stephen Luntz, in the December 2012 issue of Australasian Science magazine. You can click to see it at a larger size.