Cell Picture Show

One of my scanning electron microscope images from my research into the division of Leishmania parasites is currently featured in the Cell journal picture show on parasites and vectors. You can check it out (image number 11) here.

A montage of seven scanning electron micrographs of L. mexicana.

"Leishmania mexicana promastigotes, which normally inhabit the gut of the sand fly vector, are shown at different stages of the cell cycle. Cells are arranged by cell-cycle progression, increasing in a clockwise direction. L. mexicana mainly causes a mild form of cutaneous leishmaniasis, forming ulcers at the bite site of an infected sand fly."

Software used:

ImageJ: Micrograph processing

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

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)

SEM Zoom!

Scanning electron microscopes have an amazing range of magnifications, from around 20x to 20000x! It is very hard to give a sense of this range of scales, so have a look at this video instead... It starts at 25x, about 6mm across the whole field of view, and zooms in to 12000x, about 12um across the whole field of view. The circular objects are glass beads 10um across, for comparison a red blood cell is around 8um across.

Software used:
ImageJ - video generation from a series of SEM images
FFMpeg - video transcoding