CoccoBiom
This macro set is designed for working with a light microscope system consisting of microscope and CCD camera to produce images, together with a framegrabber in a computer to capture the images. Our standard procedure is to first collect composite mosaic images of specimens then to carry out measurements on them.


MOSAIC CREATION
The first stage of all our work with coccoliths is to collect sets of coccolith images into larger composite mosaic images. For assemblage analysis this process is rather similar to picking forams into assemblage slides and we routinely use for this type of work. The mosaics are also similar to published plates and by sub-selection of the best specimens they can be used to produce plates to document assemblages for reports and publications - for instance they are used in Young (1998) to document Neogene nannofossil taxonomy.

Macro functions for mosaic creation include

• Mosaic image creation - the number of tiles per mosaic and the size and shape of individual tiles is completely variable.
  
• Automated saving of coccolith images - from the camera window to the mosaic window. This is a one-key operation, allowing rapid collection of large mosaic images. In addition during automated saving the images can be transformed to remove any linear distortion produced by the camera-framegrabber combination (a very common problem).
  
• Cut, copy and paste - individual tile images can be rapidly rearranged within or between mosaics.
  
• Scale setting and display - after calculation of scale calibration for the microscope the scale of images can be automatically calculated for any lens combination and is stored in the image header. Scale bars can be drawn automatically.
  

• Context sensitivity - the behaviour of individual macros depends on the location of the cursor within the image. In particular biometric macros detect which mosaic tile the cursor is over and use this to write measurements to the appropriate line of the measurements file.
  
• Display of results - the measurements file can be seen using standard routines within NIH-Image, in addition our macros always produce a graphical display on the image, for instance if the long axis is measured then it is drawn on the coccolith image. This allows the user to check that measurements are meaningful and correct mistakes.
  
• Minimum user input - all macros are designed to run with the fewest possible mouse movements and keystrokes.
  
• Customisation - different species require different solutions. We have developed a range of different measuring routines for different coccoliths, a selection of the simpler routines is included in the macro set given here, additional macros are available from us.
  
• Robust basis - they are based as far as possible on intelligent knowledge of coccolith ultrastructure, optics and geometry, based on other aspects of our research (e.g. Young 1989, Young & Westbroek 1991,Young & Bown 1991, Young 1992, Young et al. 1992)
  

• Manual measurement - using the mouse and cursor to directly measure lines on the specimen.
  
• Semi-manual axis measurement - using the mouse and cursor to fix the long axis of a specimen with image analysis being used to detect the edges of the specimen, and measure the long and short axis. (separate routines have been developed for use with cross-polarised light and phase contrast images).
  
• Automated measurement - for Emiliania huxleyi we developed a fully automated routine based on recognition of distinctive features of the cross-polarised light image, these measure measure coccolith length, width and rim width. This application is described in Young et al. (1996), and results are given in Young (1995) and Paasche et al. (1996).
  
• Semi-automated measurement of rim widths - most coccoliths show concentric cycles of elements. After the long and short axis of one cycle has been measured our routines allow the widths of additional concentric cycles to be determined by placing the cursor anywhere on the cycle.
  
• Element counting - in a few species the elements are visible in light microscope images. We have developed macros to count such elements, this is applicable for instance to Calcidiscus, multi-element discoasters and Nannoconus. It can also be used for counting striae on diatoms.
  
• Angular measurement - the angle of features such as the bar of Gephyrocapsa can be measured, the macro for this requires a line to be drawn along the feature, it then records the angle between the feature and the long axis of the coccolith.
  
  

• Mosaic making macros multi purpose macros for making mosaic images (we use these all the time). You do need to learn how to use these before doing anything with the measuring macros.
• Semi-automated macros general purpose measuring macros, for use on mosiac images.
• Automated macros specialist routines for use with E. huxleyi (more interesting programming but less general use)
• Demonstration mosaic image use this to practice making mosaic images.
• Demonstration microscope image use this to test the automated Ehux macros. (load those macros into NIH-Image; open image; put cursor over red square in corner; press key '5')