NIC Wiki

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

• “Fiji is just imageJ” except that the macro-editor is different
• if open a macro written in ImageJ or text editor in FIJI, need to tell FIJI what language it is
• FIJI also has MIJI capability: combine ImageJ and Matlab!

• always duplicate your file before playing with it. Will allow you to keep the original file open and repeat if you make a mistake. And will ensure you don't accidentally alter the original data
• command-shift-T for threshold window
• command-shift-C for the brightness/contrast window
• command-shift-D for duplicate
• command-shift-E for “remake previously selected shape”
• T to add a shape to the ROI manager
• command-R inside macro editor to run a macro or a selected line in the macro
• up and down arrows to mag up or down
• left/right arrows to scroll through a one-color z-stack

6. Other macro functions of use that came up during class, all described on the MacroFunction list webpage:

• getFileList(path)
• listname.length
• listname[i]
• substring(string,start,stop)
• indexOf(name, firstInstanceOf)
• roiManager(cmd)
• runMacro(name)
• setAutoThreshold(method) and getThreshold(lower, upper)
• setResult(“Column”, row, value)
• SetPixel(x,y,value)
• …and many more