Main ImageJ website http://rsbweb.nih.gov/ij/
ImageJ Documentation http://rsbweb.nih.gov/ij/docs/index.html
click on “ImageJ User Guide” (not the PDF) http://rsbweb.nih.gov/ij/docs/guide/index.html
See sidebar on left for all of the menu commands and their descriptions.
For overview of basic image manipulation: 25 Image
includes Brighness/Contrast, Thresholding, Color thresholding, Splitting/Merging channels, Stacks, ie maxProjections, reslicing, 3D volume etc
For overview of basic image processing: 26 Process
This is a great introduction to basic image processing methods available in ImageJ and how they work. It's a great starting point. The next step is then to go to the plugins page and look around what other tools are already available (http://rsbweb.nih.gov/ij/plugins/index.html)
For overview of the ImageJ Editor to run macros, scripts, and plugins: 21 ImageJ Editor
On main ImageJ Documentation website, click on “resources” http://rsbweb.nih.gov/ij/developer/index.html
Introduction to Macro Language: http://rsb.info.nih.gov/ij/developer/macro/macros.html Includes the syntax for inf/else statements etc and other general useful information. Worth reading through!
Built-in Macro functions http://imagej.nih.gov/ij/developer/macro/functions.html
This is one of the most important pages. It lists all of the functions available to write macros. If you have the time, it is worth reading/skimming through all of them to know what is possible.
Introduction into Macro Programming (via FIJI) http://fiji.sc/wiki/index.php/Introduction_into_Macro_Programming This is Fiji's Macro intro. It is also relevant for those of you running ImageJ proper.
Example Macros http://rsb.info.nih.gov/ij/macros/
Fiji website: http://fiji.sc/wiki/index.php/Fiji
6. Other macro functions of use that came up during class, all described on the MacroFunction list webpage: