Coccolith Biometrics macros - a set of macros for NIH-Image developed by Jeremy Young (Natural History Museum, London), with much assistance from Michal Kucera (Geology Dept., Prague, Goteborg Univs.) and Hsiao-Wen Chung (Bioegineering, Pennsylvania Univ.). Purpose measuring Emiliania huxleyi coccoliths from cross-polarised light images. Queries to jy@nhm.ic.ac.uk. Some macros require Image version 1.54. Availability I am posting these archives to zippy.nimh.nih.gov and to the ftp site at the Natural History Museum - IP number 157.140.2.2, directory incoming/jryoung. Minor updates will probably only be posted on the latter archive. Like NIH-Image this application is freeware, available without charge to anyone who can find a use for it - but please get in touch with me before publishing results. I am writing up the application as a paper for publication. Advice to workers who use NIH-Image but have no interest in coccoliths Ą Coccoliths are cute little calcareous plates produced by a group of planktonic algae, (Young et al. 1992, Nature 356, v. & 516-519 is an easily accesible article with some more information on them). Ą The mosaic-archiving macros might be of use in any Image application were the individual objects being studied are small (<100pixels). Ą The biometrics macros are really specialised but might give ideas or even a macro framework for other biometric applications. Advice to coccolith workers who have never used NIH-Image Ą Give it a try NIH-Image is a fine program and Image capture is a powerful tool in the study of coccoliths. Ą Read on - most of the rest of the documentation is aimed at you. WHAT YOU HAVE GOT - a series of self extracting archives produced by CompactPro (=compacted folders, with suffix .sea). Double click on the archives to extract them. You will then find.... A. THINGS I HAVE WRITTEN Ą CoccoBiom Macros 1.01 - the macro set I have written. Ą CoccoBiom user notes - a description of what the macros do, and how to use them. This file is meant as a concise manual. This is a text file created by the Image text processor (as are the next two files) , it can be opened by any Wordprocessor. Ą CoccoBiom reference Card - a list of the macros, printing out a copy of this will make life simpler. Ą CoccoBiom program notes - a documentation file which parallels the macro file, consists of a list of variables, procedures and macros with brief notes on each of them. This file is meant to assist in rewriting/editing the macros. Ą Image Macro notes (JRY) - some notes by me on relevant aspects of the Image macro language. Ą demo microscope image - a specimen field of view of Emiliania huxleyi, as captured from my microscope. Ą demo Mosaic image - a specimen mosaic (i.e. composite) image produced from microscope images using the image archiving macros in this set. Ą displayed data - an enlarged portion of a mosaic image after measuring with labels for the various coloured lines and pixels that are used to display data. Ą Parameters measured fig - a PICT figure (produced in MacDrawPro) show the parameters that are measured on the Ehux specimens by the biometric macros in this set. Ą Hardware setup - a PICT figure (produced in MacDrawPro) showing the hardware setup I use. Ą Grey+4thinramps - a LUT (look up table) that I find useful when working with cross-polarized light images (& called by one of the macros). B. FREEWARE PROGRAMS FROM THE zippy ftp site (N.B. These archives are the standard ones on the zippy site - if you have not got them from me it will be because I reckoned you already had them) Ą NIH-Image 1.55 - this is an Image analysis program developed by Wayne Rasband at the National Institutes of Health in the USA. Additonal documentation of Image, updated versions, etc. are available at the zippy.nimh.nih.gov ftp site. (N.B. This version does not need an fpu co-processor. An fpu version is available but does not speed up my macros noticeably). The archive includes a manual, macros, LUTs, kernels, etc. Ą PlugIn Digitizer 1.1 sea-2. This self-extracting archive will produce a folder containing a "plug in" for use with AV Macs (e.g. Centris 610-AV) this will allow NIH-Image to grab images directly into the AV Macs. GETTING NIH-Image WORKING NIH-Image should work OK on any Mac with a 256 colour/greyscale monitor, but you will probably have memory problems if you have <8Mb of RAM. - Image likes to have at least 3.5Mb allocated to it. I find 5Mb is ideal. But you can still get a feel for the program, and the CoccoBiom macros even on 4Mb of RAM. There are two main ways to juggle the memory 1. Change memory allocated Image - from the finder. a. Quit Image, and ALL other open applications. b. Find out how much memory you have (Apple Menu, About this Macintosh...). Note "largest unused block" size. b. Get information on Image (select the program icon, then File Menu, Get Info). c. Adjust memory allocation (to "largest unused block" size less about 200k) d. Reopen Image. 2. Change clipboard buffer size (the bigger this is the less memory there is - all you need for the macros to work is a 50k buffer - which is much less than the initial setting). To change this a. Open Image b. Change buffer size (Options menu, Preferences dialog box) c. Save preferences (File Menu, Record Preferences) d. Quit Image e. Reopen Image.