NIH - IMAGE MACROS FOR COCCOLITH RESEARCH
1. These macros are research tools not commercial software, we try to
make them robust and easy to use but...
2. This set of WWW pages to provide some documentation, but they are not a comprehensive guide. Please do contact us if you need help.
Digital image capture provides a range of opportunities for
micropalaeontological research. We have been using the image analysis
program NIH-Image extensively over the last few years in coccolith
research and have developed macro program solutions to a range of
problems. Our current work is focussed on development and application of
these macros in the CODENET project. A selection of these macros are
made available here.
What are coccoliths? - Advice to workers who use NIH-Image but
have no interest in coccoliths
- Coccoliths are cute little calcareous plates produced by a group of
planktonic algae, for more information see the INA Web site.
- The mosaic-archiving macros might be of use in any Image application
were the individual objects being studied are small (<100 pixels).
- The biometrics macros are specialised but might give ideas or even a
macro framework for other biometric applications.
- Advanced biometrics is not really possible on coccoliths, essentially
these macros are used for measuring a few simple size and shape
parameters. Numerous studies have shown that these types of measurements
are valuable, but this is not comparable to the types of advanced
morphometric analysis used on many other organisms.
What is NIH-Image? - Advice to coccolith workers who have never
used the program
NIH-Image is a widely used image analysis program developed by Wayne
Rasband of the National Institutes of Heath (USA) and available as public
domain software. The program was developed for Apple Macintosh computers and our macros only work reliably on Apple MacIntoshes.
A version for Windows - Scion-Image- is at an advanced stage of
development... but the macro language does not work predictably so we cannot recommend it for our type of use yet (late 1999). It is freely available from Scion Corporation.
Image for OSX - unfortunately NIH-Image does not work in OSX, even in OS9 emulation, however, Steve Barrett of Liverpool University, England, is developing a version of NIH-Image "Image-SXM" for OSX. At present (July 2003) it is at beta testing stage with some bugs, but basically it works. To obtain a copy contact Steve by email - S.D.Barrett@liv.ac.uk
NIH-Image works with pixel based images, and has many similar features to
image manipulation programs such as Photoshop. In addition:
- It has the ability to directly drive a range of framegrabbers so that
it can be used for image acquisition.
- It contains a suite of morphometric routines allowing measurement of
features on images, with results being saved typically to a spreadsheet
program such as Excel for analysis.
- It incorporates a Pascal -like macro programming language allowing
automation of tasks and development of custom applications (see also notes on the NIH Image Macro Language).
How to use our macro sets
We have developed our applications as sets of macros. Within each macro
set individual macros carry out specific tasks, these appear as
individual commands within a menu of NIH-Image, and can be called via the
keyboard. Different macros within a macro set complement each other to
provide a customised solution to a particular research task.
To use the macros provide here it is necessary to:
See also -Notes on downloading the macros and microscope calibration.
- Download and install the program NIH-Image or Scion Image. Homesite
for NIH-Image (Mac
versions only). Homesite for Scion
Image (Windows and Mac versions).
- Download the relevant macro sets (N.B. Download as text and avoid
adding extra carriage returns).
- Run the program and load the macro set.
- Experiment - we have included some demonstration images on this site
to aid experimentation.
OUR MACRO-SET APPLICATIONS
This is the main macro set we have developed, it 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. The macros within the set provide a range of
functions for image capture and measurement. See separate page for details.
Routines are being developed, in association with colleagues at
ETH-Zurich for use with nannofossil images captured from digital Scanning
Electron Microscopes. These include:
1. Macros for counting frequency of specimens in a set of images captured
by an automated electron microscope. The images are automatically opened
in sequence and different species can be enumerated separately.
2. Macros for automatically printing out
reference sets of images at convenient magnification for
Queries on these to Markus Geisen.
Volume of rotation calculation
Coccolith volume/mass estimates are valuable for analysis of sediment
trap data - to calculate coccolith carbonate fluxes. Since coccoliths
have a high degree of rotational symmetry their volumes can be calculated
from cross-sections. We have used NIH-Image to perform such calculations.
The macros take as their input cross sections and axial ratios and
calculate volumes and masses (assuming the coccolith is formed of
calcite. This application is documented in Young & Ziveri (in press). The
macros used are provided here.
Rock colour measurement
Rock colour is increasingly being used as a very readily measured
proxy for carbonate content. Most such work is based on scanning of
slabbed cores, this is for instance becoming a routine tool in analysis
of ODP cores. From outcrop sections similar data sets can be generated
(1) Collecting closely spaced sample sets.
(2) Grinding a smooth surface on the samples.
(3) Oven drying them.
(4) Placing the samples on a flat bed scanner and scanning them.
(5) Measuring the rock colour using an image analysis program.
We have applied this technique to rhythm analysis in pelagic sediments
showing Milankovitch cyclicity using simple greyscale variation (Gale et
al submitted). The technique is documented in detail in Young et al.
(submitted).The macro set used for the greyscale measurement is
given here, this is a very simple macro set, but perhaps a useful introduction to the macro language.
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This page is based on work primarily of Jeremy Young and Markus Geisen
Comments and queries are always welcome