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.
MEASUREMENT OF SPECIMENS
The main purpose of
the CoccoBiom macro set is to allow efficient measurement of coccoliths
for analysis of intraspecific variation and quantification of
microevolutionary trends. For this purpose mosaics of typically 60
specimens of a species are collected for each sample. Measurements of the
specimens are then carried out with varying degrees of automation
depending on the properties of the particular species under
investigation.
General features of our biometric routines
- 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)
Techniques include:
- 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.
MACRO SETS FOR DOWNLOADING
- 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')
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