Tuesday, 13 July 2010

Extended Depth of Field

One of the tricky things with microscopy and macro photography is the depth of field, as you start magnifying a sample you need to collect as much light as possible to generate the image with a sensible exposure time. Unfortunately this requires a large aperture, and this creates a very shallow depth of field...

This micrograph of a diatom clearly shows the problem, it is impossible to get the whole sample in focus in one image. Fortunately there are ways around it; by analysing the image for sharp edges it is possible to find which image is the most in-focus and the whole image can then be reconstructed only using the in-focus patches. This process is called focus stacking and generates an extended depth of field. Good free implementations of focus stacking are hard to come across, so I wrote one; you can download the ImageJ macro here.
Using the same technique on macro photography (processing the red, green and blue channels separately) gives a similarly impressive result. The three starting images:

And the extended depth of field result:
Software used:
Image processing: ImageJ

Monday, 12 July 2010

Diatomacious Earth

This is a picture of diatomaceous earth, also known as diatomite or kieselgur, as viewed under bright field illumination on a light microscope. View the full image (7000px wide) on Wikipedia and explore it! The diatom particles are in water and the image is covers a region of approximately 1.13 by 0.69 mm.

You won't have heard of diatomaceous earth, but you will have used it! It also looks amazing under a microscope. Diatomaceous earth is a soft, siliceous, sedimentary rock made up of the cell walls/shells of single cell diatoms and readily crumbles to a fine powder. It is used for cleaning (scouring), filtration, heat-resistive insulation, killing headlice and as an inert absorbent substrate. Its most famous use was by Alfred Nobel who developed dynamite; a mixture of diatomaceous earth and nitroglycerin! Diatom cell walls are bivalve, i.e. made up of two halves, and are made up of biogenic silica; silica synthesised in the diatom cell by the polymerisation of silicic acid. The two main groups of diatoms are centric (radially symmetric) and pennate (bilaterally symmetric).

Make sure to explore the image properly, there are so many fossils to see!