Types

... in which we present some technical information about the types pages


Background

In a publication it is usually only possible to illustrate a specimen with one or sometimes a few photographs. Because of the very limited depth of focus of high-magnification optical microscopy, a single photograph is usually not enough to show all the detail that can be seen by focusing up and down through a specimen.

This part of the website was designed so that whole specimens can be viewed by the use of carefully-prepared stacks of optical sections that your browser opens sequentially. What you see is rather like this one on the right, except that the others don't loop automatically – you get a focusing control so that you can look through the whole specimen interactively.

Scroll down past the picture to see some of the technical details.



Photographs

The photographs were taken on a Reichert Polyvar 2 compound microscope using a Polaroid DMC2 digital camera, with a resolution of 1600 x 1200 pixels. Individual optical sections were taken at an actual vertical interval of 0.2 µm, but since the refractive index of the naphrax in which the specimens were mounted is higher than that of glass, the apparent vertical interval is more than 0.2 µm.

Focusing between shots was done by hand using a home-made vernier scale attached to the fine focus knob of the microscope (we'd love it if someone would buy us a computerized microscope stage with z-control, but until that happens we have to improvise).

A scale bar was added to each photograph using the image-analysis program Optimas. The scale bar includes a 1 x 1 µm square to enable one to check whether or not the pixel aspect ratio has been changed at any stage in the display process (if the 'square' is not square, then the pixel aspect ratio is wrong). Brightness, contrast and image size were all adjusted using Adobe PhotoShop.

Web pages and focus bar

The focus bar was created using a JavaScript program available on the web (thanks to Christiaan Hofman for having the imagination and ability to produce such a thing in the first place, and to Paul Rosen for finding it and helping me implement it here). Unfortunately, it does not seem to work using some browsers (especially Mac ones, I'm afraid), so I've had to present an alternative way of viewing each focus stack. I have created a .avi movie file of each stack [using VideoMach software (available from www.gromada.com) and the Cinepak Codec by Radius], which can be played on any movie player like QuickTime. QuickTime is a good one for it, since the progress button can be grabbed and moved with your mouse, just like the JavaScript slider.


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