ImageJ is a powerful image analysis program that was created at the american National Institutes of Health. It is used widely throughout the scientific imaging community due to it's universal compliance with most microscopy formats and customs. It is also very versatile due to it's variety of plugins and macros. It can:
About 95% of the image processing tasks neaded in our labs can be solved with ImageJ.
FIJI is just ImageJ. It includes a large ammount of plugins and some tweaks that make it a bit more user friendly. We advise you to use FIJI over ImageJ simply for the fact that, with it, you will not need to look for whatever plugin you need since it probably already includes it (including Bio-formats/LOCI, mentioned below).
This is the official website for FIJI and we recomend that you browse it a bit to find out more about it.
To read most of the microscopy file formats you need to use the LOCI Bio-Formats library plugin. It is already installed in Fiji, to install it while using standard ImageJ, just download bioformats_package.jar and place it in ImageJ's "plugins" folder.
Please note that the UIC develops ImageJ/FIJI macros that are aimed at making your life easier. You can check some of them at our macros webpage. If need be, you may also request us to create one for you (depending on the complexity), however, take into account that macros can be complex and take plenty of time to optimize and work properly and are not done overnight, it should be done if it is needed.
Since ImageJ is freeware we recomend that you use it on your own computer. There are computers with a high memory buffer for image processing on the workstation room (speak with UIC personnel for directions), where you can use this software for large data sets.