OS X Installation

To install ImageJ, download the Mac OS X .tar.gz file and double-click on it to extract the "ImageJ (OS X)" folder. To run ImageJ, open this folder and double-click on the ImageJ icon.

Memory
To make more than 128MB of memory available to ImageJ, edit the line 

com.apple.mrj.application.vm.options=-Xmx128M
in the ImageJ.app/Contents/Resources/MRJApp.properties file, where ImageJ.app is the directory (bundle) that the Finder displays as the ImageJ application. You can view the files and folders in the ImageJ bundle by control-clicking on the ImageJ application and selecting "Show Package Contents". Another way to make more memory available to ImageJ is by running from the command line and using the -mx option.

Upgrades
To upgrade to the latest version of ImageJ, replace the ij.jar file in the ImageJ application with a newer one from http://rsb.info.nih.gov/ij/upgrade/. To do this, control-click on the ImageJ application, select "Show Package Contents", and then drag the newer ij.jar into the Contents/Resources/Java folder.

Known Problems

  1. Two clicks are required to select a tool and two more are required to use it. (Fixed in OS X 10.2)
  2. The "rubberband" is sometimes not visible when using the freehand and polyline tools (java.awt.Graphics.setXORMode() bug). (Leaves trails in OS X 10.2).
  3. OS X requires a lot of memory for each open window. Converting a 1024x1024x10x8-bit stack (10MB) to separate images requires 58MB of additional memory!
  4. Text quality is poor due to antialiasing. (A workaround is in v1.28d.)
  5. Zoomed images are blury (java.awt.Graphics.drawImage() bug). (Fixed in OS X 10.2)
  6. The cross hair cursor is invisible in dark areas. (Fixed in OS X 10.2)
  7. Tab support is broken in Plugins/Edit (java.awt.TextArea bug).
  8. Arrow keys don't work in Plugins/Edit (java.awt.TextArea bug).
  9. Mouse wheel doesn't work in Plugins/Edit (java.awt.TextArea bug).
  10. Dragging and dropping image files on the ImageJ icon only works when ImageJ is already running.
  11. There does not appear to be a way to unselect an ROI in the ROI Manager (java.awt.List bug). As a workaround, press the "Select All" button twice (v1.28d and later).
  12. Buttons are HUGE, messing up the layout of some windows (e.g., Image/Adjust/Threshold). There is a work around (using the TrimmedButton class) in v1.28o and later.
  13. Labels in the optional "Outlines" plot created by Analyze Particles are gray instead of red due to antialiasing.
  14. 8-bit image drawing is very slow. Try opening an 8-bit image and running the Image/Benchmarks/Waves benchmark or the Plasma plugin, or try running the Plasma2 applet.
Running from the Command Line
To run ImageJ from the command line, open a Terminal window, cd to the ImageJ directory, then use the java command to run ImageJ. The easiest way to do this is to drag the ImageJ folder to the Terminal Window, type return, then type: 
java -jar -mx256m ImageJ.app/Contents/Resources/Java/ij.jar
(or java -mx256m -cp ImageJ.app/Contents/Resources/Java/ij.jar ij.ImageJ)
Or if you have a Mac OS 9 ImageJ folder, type: 
java -jar -mx256m ij.jar
(or java -mx256m -cp ij.jar ij.ImageJ)
The -mx256m switch specifies that ImageJ will have available a maximum of 256MB of RAM.

Here is a simple AppleScript that sends commands to Terminal to have it automatically launch ImageJ: 

tell application "Terminal"
    run
    do script with command "cd /Applications/ImageJ 
        java -jar -mx350m ./ImageJ.app/Contents/Resources/Java/IJ.jar"
end tell
With OS X 10.1 or later, you can also run ImageJ by double-clicking on ij.jar.