Light vs. Microscopists

Light vs. Microscopists, my research comics feature in OUBS Phenotype, trinity term 2012. Everything you wanted to know about superresolution light microscopy in one fun package. Including a cute kitten. Check out the full issue here.

Software used
Inkscape: Document design and layout.
ImageJ: Micrograph simulation.

Diatomaceous Anaglyphs

I was trying to work out what the least friendly, most jargon rich blog title I could possibly write something interesting about... I think "Diatomaceous Anaglyphs" is a pretty good effort!

Diatomaceous means "of diatoms"; a type of single celled organism which grows beautiful shells made of silica. In this case these are the shells of dead diatoms from millions of years ago which settled out of the sea, made beds of diatom shells then got compressed into a soft rock. This rock is mined and processed for use in various areas of industry and is called diatomaceous earth.

Anaglyphs are the name of the red/blue 3D images you get which can be looked at using some glasses with coloured celophane instead of lenses. With the surge in 3D films at the cinema you can find more and more 3D stuff online using anaglyphs.

When I combined the I made diatomaceous anaglyphs, which are just plain beautiful (you can also view the whole album on my Flickr):

For those of you not geeky enough to have red/blue 3D glasses this is an animated version:

Software used:
ImageJ: Image alignment and processing

FatFonts

FatFonts are a great new concept by Miguel Nacenta, Uta Hinrichs, and Sheelagh Carpendale for presenting numerical data in an easy to understand way, but while leaving the numbers readable.

The idea is that numbers with a large value appear fatter and darker than numbers with a small value which appear thinner and lighter. This means that if you want to plot something like a height map, where each pixel has a value equal to its height, you can just write out the numbers and they build the image for you. The really clever bit is that if you have a multiple digit number, like 8242, the 8 (8 thousand) appears biggest, the first 2 (2 hundred) appears a bit smaller, the 4 (4 tens) appears even smaller and the last 2 (2 units) appears tiny.

It is always easier to explain concepts like this with a picture, so here is some data:

It is hard to look at this and see the shape of the data, but if you use a FatFonts presentation (this font is called Miguta):

You can now actually see the shape of the data, where the bigger numbers are and where the smaller numbers are. This example is of the number 8242 I mentioned above:

The 8 is biggest (8 thousands), the 2 is nested inside it (2 hundreds), then the 4 (4 tens) and finally the last 2 (2 units) is too small to see.

I have coded a couple of fonts (Miguta and 7 Segments) for Miguel Nacenta to make this technique really easy to use. Check out the FatFonts 'how to use' guide for more information.

Update: 17/05/2012
And here is an example of my FatFonts 7 Segments design in action; http://studiolakmoes.nl/datavisualisatie-met-fat-fonts/

Software used:
Inkscape: Managing Miguel's glyph designs
Fontforge: Font preparation and contextual alternates coding

Diatomaceous Zoom

[watch in higher quality here]

I posted a video before about the magnification range of a scanning electron microscope... This is the update with a slightly more interesting sample! Last time I was using 10 micron beads to confirm the calibration of the scope, this time it is fossilised diatoms; tiny single celled plankton with beautiful shells.

The video starts at 25x magnification, the whole field of view is about 2mm across.



And it starts zooming in...



And in...



And in...



Until it gets to 200000x magnification, nearly 1000x greater than at the start of the video. Now the whole field of view is only about 2um across. That is 100 times narrower than a human hair.

Then it zooms back out again so you can see what you were looking at!

Software used:
ImageJ - Generating zoom series, converting individual images to a video.

Sublime - video

Sublime is a video combining music with science. Awesome.
 

[watch in higher quality here]

The story of this video is the phase of matter and how it changes. You will know the common phase changes of water; boiling, condensing, freezing and melting. These phase changes all involve a liquid step, and in this video liquids are not involved at any stage.

The phase changes here just involve solids and gases, either deposition (changing from gas directly to a solid) or sublimation (changing from a solid directly into a gas). The actual substances in the video are common, just dry ice (solid carbon dioxide) and water frost, the reason no liquids are involved comes down to the temperature and pressure. At normal atmospheric pressure dry ice does not melt, liquid carbon dioxide is not stable, so it changes directly into a gas. Dry ice is also very cold (-78°C/-108°F) meaning water vapour (a gas) in the air coming into contact with the dry ice directly deposits to form frost. In some places it also hits the cold carbon dioxide gas and solidifies from the air to form tiny snow particles.

The frost looks black and the dry ice looks white because of the way the sample was illuminated. It was lit up from the back and frost (which has lots of tiny crystals) scatters the light away from the lens, making it darker. Dry ice scattered the light less, i.e. light got transmitted straight through to the lens, so appeared lighter.

Over time the carbon dioxide gradually sublimates and the water frost gradually forms. Because the surface the frost is trying to grow on is constantly disappearing the frost constantly moves. As the carbon dioxide sublimates it also increases greatly in volume, blowing the frost about!

This video is of a microscopically small sample. The region the video shows is only about 1mm across, depending on the size of your screen you are seeing the frost and dry ice at 100× to 1000× its actual size. This high magnification lets us see individual ice crystals growing as the frost spreads. Initially the crystals in the frost are very small (5μm or so). Gradually as the dry ice sublimates the temperature increases and the water vapour in the air can take longer to deposit onto the growing ice crystals. Slower crystal growth leads to bigger crystals (up to 100μm).

Ice crystal shapes also vary depending on temperature and environment, in this video you can see both needle-shaped and flat ice crystals.

The frost grows and the dry ice sublimates quite quickly. All the clips in the video are at 4× real life, if you imagine everything happening at a quarter of the speed that is how fast the frost was growing and changing.

Software used:
ImageJ: Image editing, alignment, cropping and video making,
Audacity: Audio editing.
Windows Live Movie Maker: Final sequencing, adding captions.

Things Never Change...

There has grown up in the minds of certain groups in this country the notion that because a man or corporation has made a profit out of the public for a number of years, the government and the courts are charged with the duty of guaranteeing such profit in the future, even in the face of changing circumstances and contrary to public interest. This strange doctrine is not supported by statute or common law. Neither individuals nor corporations have any right to come into court and ask that the clock of history be stopped, or turned back.

Robert A. Heinlein: Life-Line (1939)

Treatise - my first professional font!

It was about time I started to try and make some money from my plethora of hobbies... Today my first professional standard font goes on sale! You can take a look at the interactive previews at myFonts.com:

http://new.myfonts.com/fonts/zephyris/treatise/

Treatise is serif (with the sticky-out-bits (: ) font with some fun quirks. It has very big round terminals on the top of letters like r, c, k and s and a big blob in the top of the o. These all work together to make it look a bit more handwritten. It also uses the single storey a and g (i.e. like you write them, not like you type them) which also helps maintain the handwriting feel. Treatise uses some fancy Opentype features which let you adjust the way letters appear depending on what neighbours them. I have used this to make the long tail on the capital R and Q nestle neatly around curved letters like u, e, a, etc. It also means that letter combinations like ff and fl where the f can crash into the top of the next letter are replaced with a nicer looking character combination.

While it has some cheeky little design features which make it very unlike most serif fonts it is still subtle enough to sit happily in a paragraph of text. Having said that it also has enough character to make a title interesting. All in all I am pretty happy with it as a design!

The software used to design and code this font was entirely free and open source:
Sketching - Gimp
Outline design - Inkscape
Glyph coding and font generation - FontForge