Hide
Colophon
The initial contents of this guide have been retrieved in 2009 from the ImageJ website using html2text. Since then, it has been complemented and updated using informations posted on the ImageJ mailing list, ImageJ Documentation Portal, Fiji, ImageJ, and ImageJDev websites and Tony Collins ImageJ for Microscopy manual. Nevertheless, because there has never been accompanying documentation for some of the 350+ described commands, several sections have been written from scratch based on the relevant ImageJ source code and authors own experience. Legacy nomenclature that became obsolete with version 1.46 has been intentionally omitted.
The guide was typeset with TeXLive 2012 on Mac OS 10.6.8. All illustrations were created with ImageJ/Fiji, loaded with G. Landini’s IJ Robot and J. Schindelin’s Tutorial Maker plugins. Screenshots were produced by the screencapture shell utility controlled by the following IJ macro:
exec("screencapture -ciWo > /dev/null 2>&1 &");
run("System Clipboard");
setLineWidth(1); setForegroundColor(111, 121, 132);
drawRect(0, 0, getWidth, getHeight);
The HTML version was produced with eLyXer 1.2 and formatted using CSS code from Alex Fernández and Michael Hüneburg; JavaScript code from Ciarán O’Kelly, Stuart Langridge and Tiago Ferreira. It uses SyntaxHighlighter and icons from the Tango Desktop Project.
Getting Involved
Your help is needed to improve ImageJ. Even if you are not a programmer, your participation is important:
- Are you a skilled ImageJ user?
You might want to help out with the documentation effort: Write a FAQ, How-To, Tutorial or Video Tutorial on the ImageJ Documentation Portal; Help us updating the ImageJ User Guide; Share the add-ons you may have created with the community; Subscribe the mailing list and help answering the questions raised by other users. - Are you know knowledgeable in image processing?
Please join the mailing list and participate in the discussions. You could also write a Tutorial on the ImageJ Documentation Portal. - Do you have a strong scientific background?
Frequently, the most demanding tasks in scientific image processing relate to experimental design. Even if you do not have special expertise in image processing, by participating on the mailing list discussions, your experience will be valuable to others. - Do you want ImageJ to improve?
You can report bugs or request new features using the mailing list. - Do you have experience in graphic/web design?
If you are able to to improve the look and feel of the guide we welcome your skills.
The ImageJ Icon
The Hartnack microscope (ca. 1870’s) depicted on the front page inspired the ImageJ icon for Mac OS X. It is based on a photograph by Tom Grill at arsmachina.com.
Edmund Hartnack (1826--1891) was a renown microscope manufacturer that pioneered the use of correction collars in water-immersion lenses and the adoption of the substage condenser [K] [K] Merico, G. Microscopy in Camillo Golgi’s times. J Hist Neurosci, (2003) 8(2):113--20. The precision and robustness of Hartnack optics played a pivotal role in the groundbreaking research by the Nobel laureates Robert Koch [L] [L] Brock, TD. Robert Koch, A life in medicine and bacteriology. ASM, 1999, Camillo Golgi [M] [M] Brenni P. Gli strumenti di fisica dell’Istituto Tecnico Toscano — Ottica. IMSS, 1995 and Santiago Ramón y Cajal [N] [N] DeFelipe & Jones. Santiago Ramón y Cajal and methods in neurohistology. Trends Neurosci, (1992) 15(7):237--46.