The data format for MUSE cubes is a three dimensional FITS image, with two spatial and one spectral axis in the first extension; see the ESO Science Data Products Standard (in particular the addendum dedicated to cubes) for a description of the data format and metadata information. The wavelength scale is in the heliocentric reference system. All 3D data cubes come with error estimates (in the second extension) and a calculated 5σ limiting AB magnitude, in terms of the total flux of an unresolved source. There are a number of files associated at download time to each 3D data cube: the broad-band image, also known as "white-light" image, plus graphical (preview) files and the complete pipeline log. The MUSE data collection will grow with time, with new reduced 3D data cubes being added as soon as they are processed. MUSE 3D cubes acquired before November 2014 will also soon be added to the collection.

The MUSE 3D cubes tagged "MUSE" can be queried and downloaded using the Phase 3 generic query form which provides access to all Phase 3 data, or the Phase 3 spectral data query form with query parameters suited to harvest 3D cube data. The MUSE data cubes are normally stacked at the Observation Block (OB) level, unless there is no overlap between the individual exposures. Shallow data cubes from the SKY observations are also processed.

More details about the MUSE data are available in the associated Phase 3 data release description. Instructions on how to read and display 3D data cube spectra in the 3D FITS image format can be found, for example, on the QFitsView page.