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xyz.gif (5471 bytes)ImageJ

In many respects, this web page is superfluous because of the comprehensive ImageJ web pages at http://rsb.info.nih.gov/ij/.   Almost everything is exceptionally well documented. 


There is one link not obvious from the contents on the ImageJ page, and this is the link to upgrade the software.  Installation is a two step process.

  1. Download and install ImageJ from http://rsb.info.nih.gov/ij/download.html.
  2. Upgrade to the most current version at http://rsb.info.nih.gov/ij/upgrade/.  [You should upgrade constantly; there are always new nifty features, improved functions and fixed bugs.]

But for the complete installation instructions, including how to allocate more than the default 80MB to the software, see http://rsb.info.nih.gov/ij/docs/install/.


We have a few of our own macros and we write macros on as as needed basis.   However, even our macros or plugins include chunks directly lifted from the extraordinary libraries of macros and plugins at http://rsb.info.nih.gov/ij/macros/ and http://rsb.info.nih.gov/ij/plugins/index.html.

Most of our macros are here:  http://www.aecom.yu.edu/aif/instructions/imagej/macros/
Some of these are general purpose macros that you may find useful, some are for very specific applications which you'd have to figure out before trying to use them, and not all of them work(!).  In brief, we recommend that you don't use them without first having instruction from an AIF staffmember in proper usage, etc.  And if they do work for you, please cite us.

Also, we do have some instructions pages, such as on how to make AVI movies for your PowerPoint or web presentations.

To make a set of macros load automatically on startup of the software, the macro file must be named "StartupMacros.txt" (note the upper case 'M') and it must be in the macros folder inside the ImageJ folder. There is an example at http://rsb.info.nih.gov/ij/macros/StartupMacros.txt. This is really useful if you have a library of macros that you use commonly.


To load your favorite macros automatically at software startup:

From: Wayne Rasband <wsr@NIH.GOV>

The easiest way to have a plugin automatically loaded when ImageJ starts up is to pass a one line macro to ImageJ on the command line. For, example, to load the IP Demo plugin plugin at


use the command

java -jar ij.jar Run_IP_Demo.txt

where "Run_IP_Demo.txt" is a macro in the ImageJ folder containing the line

run("IP Demo");

On Mac OS X, add an "Arguments" key with the value "Run_IP_Demo.txt" to the "Info.plist" file in the ImageJ application:

<key>Arguments</key> <string>Run_IP_Demo.txt</string>

On Windows, with ImageJ 1.32 and later, add " Run_IP_Demo.txt" to the third line of ImageJ.cfg . jre\Bin\javaw.exe -Xmx128m -jar ij.jar ij.ImageJ Run_IP_Demo.txt

On Windows, with ImageJ 1.31 and earlier, add " Run_IP_Demo.txt" to "Target:" field of the ImageJ shortcut.




From: Wayne Rasband <wayne@CODON.NIH.GOV>

How should I cite ImageJ in a scientific paper? Here are two possible ways to reference ImageJ:

  1. Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda,
    Maryland, USA, http://rsb.info.nih.gov/ij/, 1997-2005.
  2. Abramoff, M.D., Magelhaes, P.J., Ram, S.J. "Image Processing with ImageJ".
    Biophotonics International, volume 11, issue 7, pp. 36-42, 2004.

For updates:  http://rsb.info.nih.gov/ij/docs/faqs.html#cite


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