Files with the .CZI extension contain image data saved by microscopes - image stacks, frame-by-frame photo series, and images of plates captured by the Carl Zeiss microscope.

These files are used to generate video sequences and for medical research. Carl Zeiss ZEN software enables analysis and visualization of CZI files. A special ZeissCZIReader API has also been developed for the Java programming language and made part of the Fiji suite, which is included in ImageJ image processing libraries, enabling the reading of CZI file contents.