Data Analysis

NIS-Elements - Nikon's image acquisition and analysis software. The same software we use to run most of the microscopes, this is also an easy-to-use tool for routine data analysis.
MetaMorph - Another program for interactive data analysis.
MATLAB - A popular commercial programming language and interactive environment for data analysis. Useful links to microscopy tools for Matlab are collected here.
Huygens - Huygens is a powerful and easy to use deconvolution program.
Slidebook - 3i commercial software package for image acquisition and analysis.

ImageJ and Variants - One of the most commonly used free image analysis programs. Has a large and active development community.
Nikon Viewer - Free viewer for Nikon's file formats.
CellProfiler - A free, open source image analysis tool designed for analysis of image-based screens.
Allen Cell Explorer - Resources from Allen Institute for Cell Science. Includes the Cell Feature Explorer, Cell Catalog, and Allen Cell Structure Segmenter.
Napari - Multi-dimensional image viewer for python
IOCBioMicroscope - A free, open source Lucy-Richardson deconvolution tool, written in Python.
Farsight Toolkit - Sophisticated packages for image alignment, segmentation, and neuron / vessel tracing, among other things.