Free software for analyzing and processing image data

Fiji: ImageJ plus a large bundle of plugins, all packaged together in one easy-to-download application. Runs on Mac OS, Windows, and Linux. Very handy for new users who don't want to download individual plugins. Includes utilities for 3D viewing, video editing, measuring colocalization among others. Recommended for all CDB Micro Core users.

QuPath:  Free, open-source software designed primarily for annotation and analysis of large-format whole-slide images (color brightfield and multi-channel fluorescence)

CellProfiler: Free, open-source software from the Broad Institute for segmentation and quantitative analysis of microscope image data.

Ilastik: Free software that uses machine learning for interactive object recognition and segmentation.

Imaris Viewer: A free version of Imaris with limited capabilities; useful for quickly viewing Imaris files or raw data.

ZEN Lite : Free software from Zeiss to open .czi files. Windows only.

LAS X Core: Free software from Leica to open images acquired on the Leica SP8 confocal or any microscope controlled by LAS X. Scroll down the linked page to find the version appropriate to your operating system. Windows only.