- 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.
- Ilastik- Machine learning algorithms to segment, classify, track and count your cells or other experimental data.
- Use ilastik and cell profiler together! Check out the Cell Profiler and Ilastik: Superpowered segmentation blog entry and the How to use Pixel Classification in Cell Profiler, which has important instructions for the export of images from ilastik to get them into Cell Profiler!