There are many programs that can be used to analyze your confocal images. The Zeiss software itself offers many options (see the Zeiss Manuals for detailed information). The full version of the Zeiss software requires a USB dongle to run, and costs >$4-5k, so we do not have copies for each lab. There is an extra copy on the Luo PC should you need it. There is also a free image viewer (or Zeiss ZEN) version available compatible with the WindowsXP platform that performs many of the basic functions available in the Zeiss software. Note that you can add accurate scale bars to all of your images using the Zeiss software and export images with this scale bar for publications.
Many people also use the ImageJ application. ImageJ is a modern (& open source) cross platform Java Application and can run on Windows, MacOS and Linux.
Loads of useful plugins are available at the ImageJ website. You can directly open Zeiss .lsm files by downloading the appropriate plugin called LSM Reader. There are many additional plug-ins available on the ImageJ plugins website. You can make substacks, thumbnails, volumetric (4D) stacks, etc. etc.
You can find some additional ImageJ plugins written by former Luo lab member Greg Jefferis in this folder, or download the whole lot in one zip file (note, however, that some of these plug-ins have been incorporated into the core ImageJ operating system in the most recent releases).
Plugins can be installed by copying the .class files into your ImageJ/plugins folder and restarting ImageJ. The .java files are the source code and are not required to use the plugins, but you can have a look if you are interested.