ImageJ, getting started
To install ImageJ on your computer, go to http://rsbweb.nih.gov/ij/download.html.
Install it with the version of Java it is packaged with; this will minimize bugs.
Do not install in the Programs Files directory or Applications (on Mac) unless you are sure you have permissions to read/write/edit in this folder.
Install in a location where you have unlimited read/write access such as My Documents. More details on installation here: http://rsbweb.nih.gov/ij/docs/install/windows.html.
An Alternative is to use Fiji which comes with a lot of nifty plugins. Get it at fiji.sc/
When you run ImageJ the first time, follow the drop down menus to Edit > Options > Memory & Threads and set memory as you need.
When you run ImageJ the first time, follow the drop down menus to Help > Update ImageJ... to get the latest version. Scroll to the bottom of the versions list and choose Daily Build.
If you have problems installing on Mac, please look here.
You need to install the LOCI Bio-Formats so that you may open files saved in different formats.
As of 15 April 2015 you may download the most recent version from http://downloads.openmicroscopy.org/bio-formats/5.0.8/
As of May 2016 you may find the most recent version at https://www.openmicroscopy.org/site/support/bio-formats5.1/users/imagej/installing.html
Find bioformats daily build and download to the plugins folder within the ImageJ folder. (If you installed Fiji, you do not need to do this step; LOCI plugins are included in Fiji.)
If the firewall won't let you download from the open microscopy website, try downloading this version of the BioFormats plugin that works with ImageJ 1.50.
Other plugins you may find useful are at http://rsbweb.nih.gov/ij/plugins/. http://fiji.sc/Fiji is another great resource. We are (slowly) building a library of macros here too, ../index.html, but they aren't necessarily user friendly or well documented. Most need customization for individual datasets.
Want to know more about the history of ImageJ and how it is pioneering in the field of image analysis, way ahead of commercial products? Read this article in Nature Methods.