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.

VLC: VLC media player is a free and cross-platform multimedia player that plays most multimedia files as well as DVDs, Audio CDs, VCDs, and various streaming protocols.  It's absolutely necessary for playing videos created using our Core's version of Arivis Vision4D at the Lightsheet workstation. 

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.