Scientific Icons

If you have ever searched for scientific icons (unlikely but possible) you will have found it is nearly impossible to find decent ones...

I thought it was time to change this; download my new set of 22 scientific icons here: SciIcons

Software used:
Inkscape

Eggs, eggs, eggs.

(Sigma 18-200mm f/3.5-6.3 DC @ 200mm)
So for anyone up for a challenge... Whose eggs are these?

(Canon 18-55 mm f/3.5-5.6 EF-S on 2cm extension rings @ 35mm)

 They were laid on a cherry tree leaf, neatly covering the lower half of it, and were seen on the 14th Aug.

(Canon 18-55 mm f/3.5-5.6 EF-S on reverser mount @ 18mm)
They are very small, around half a millimetre each, and a blue-grey colour with a slight hint of iridescence... They are definitely a moth or butterfly's eggs, but which species?

Software used:
UFRaw
ImageJ

Colouring SEMs

Scanning electron microscopes (SEMs) are the source of some of the most iconic science pictures... The problem is that they only work in black and white.

SEMs don't use light to create the image, instead a beam of electrons is fired at the surface and the ones which bounce back or are reemitted are detected. This gives a (very cool) looking picture that would be impossible to get with light but means that colours aren't detected...

The distinctive look of SEM images is because of the way edges of objects in the image appear; unlike most visible light photos the edges of objects are lighter than the middle. By detecting which way the slopes in the image are facing we can fake different coloured light falling onto the sample, I use a red light from the top, a green light from the bottom left and a blue light from the bottom right. This makes the image really come alive and gives it an even stronger sense of 3D.

Technically this colourisation method is mapping hues to the angle of orientation edges in the micrograph. The saturation of the illumination is based on the roughness of the texture at that point in the image and the value (brightness) is simply copied from the original micrograph.

The ImageJ macro I wrote to do this can be downloaded here.

Software used:
ImageJ

Image credit:
http://commons.wikimedia.org/wiki/File:Coleus_leaf_trichomes_SEM.jpg (public domain)

Spoiled Ballot

Trendy and Elemental

You can explore the properties of the periodic table interactively here, and you each one of the periodic table images links to an interactive version showing the same data.

The periodic table is an amazingly elegant arrangement of the elements based on the electron configuration of the atoms... Its power lies in its predictive abilities; clusters of elements in the periodic table have similar properties and there are distinctive trends across the table. This inspired me to make a website where you can explore these trends interactively.

Some of the classic trends are:
Atomic radius (darker colours indicate smaller atoms)
Thermal conductivity (darker colours more conductive, this reflects metallic character)Ionisation energy (darker colours indicate less energy is required to remove an electron)These are just the boring "classic" trends though... You can look at lots of other properties of the elements. The stability of the nucleus (linked with radioactivity) also gives some interesting patterns:
Radioactive decay half life (darker colours indicate more unstable elements, greyed out elements are not radioactive)
There is a clear pattern, only elements with a large number of protons are radioactive, with two exceptions; Tc (Technetium) and Pm (Promethium) which fall out of this sequence... What causes this? We can work it out by looking at the number of stable isotopes for each element, i.e. the number configurations of neutron number for an element which are not radioactive.

Number of stable isotopes (darker colours indicate less stable isotopes, light colours indicate more stable isotopes)The number of stable isotopes shows a distincive striped pattern where alternating columns have either few or many stable isotopes... Notably Tc (Technetium) and Pm (Promethium) fall in columns where the elements have few stable isotopes. These patterns show how an even numbers of protons makes the nucleus more stable, and odd numbers make it less stable. The effect of this can be extreme; Sn (Tin) with 50 protons (an even number) has 10 stable isotopes with 62, 64, 65, 66, 67, 68, 69, 70, 72 or 74 neutrons. Tc (Technetium) with 43 protons (an odd number) has no stable isotopes.

In turn the stability of the nucleus influences how abundant an element is in the universe...
Abundance in the universe (darker colours indicate more rare, light colours indicate more common)Only non-radioactive elements are common in the universe, radioactive heavy elements quickly decay after they are produced (by nucleosynthesis). There is also an obvious general trend that elements with smaller nuclei are more common.

If you look closely at the abundance of columns of elements you can, however, see trends which mirror the number of stable isotopes; elements like Cu (Copper, 29 protons), Ag (Silver, 47 protons) and Au (Gold, 79 protons) are more rare than elements like Ni (Nickel, 28 protons), Pd (Palladium, 26 protons) and Pt (Platinum, 78 protons)... Elements with more stable nuclei are more likely to be formed in supernovae.

There are always exeptions to the rule though, Li (Lithium), Be (Beryllium) and B (Boron) are much less abundant than you might expect from the "smaller nuclei are more common" trend... Turns out these are not produced in large quantities by stars, unlike carbon, oxygen and nitrogen, and were instead produced by cosmic ray spallation, but that's another story...

If you have enjoyed exploring the properties of the periodic table you can carry on, interactively, here. This is an example screenshot showing the heat capacity of the elements (in the colour hue), atomic radius (in colour saturation) and melting point (in colour brightness):
Software used:
HTML5 (canvas) & Javascript

Tube Map Metabolism

Have a look at this:
Does it look familiar?

Look closer:
It's a metabolism map, tube map-style!

Metabolism is the complex network of enzymatic chemical reactions that go on in all living cells. Many thousands of chemicals and enzymes are involved and metabolism maps are normally extremely complex. This one is a lot simpler, and a lot more light-hearted... You can download a higher resolution version or buy a print here.

Software used:
Inkscape
Creature House Expression 3

Visualising Large Data Sets - Exoplanets - The Video

Exoplanet discovery, from 1988 to 2010...

Watch it on YouTube! Over a decade of data, 300 planetary systems and 50 million cubic light years in just over 2 minutes.

Software used:
ImageJ - scripting and rendering of the video frames
FFMpeg - video transcoding