As noted above the file structure of the collected data is normally saved in a format known as FSC (Flow Cytometry Standard). This was originally proposed by Murphy et al (ref) to encourage all manufacturers and software engineers to comply with the standard to allow relatively easy data exchange between users of different instruments. Most manufacturers comply with a reasonable extent and a number of conversion utilities exist in software packages to allow cross-analysis of data from different instruments. The current standard is FCS-2, which adds a number of additional components to the file structure.
Each file collected has a number of keywords, PMT (Photomultiplier Tube) values and gating regions associated with it. Some listmode file structures also contain the instrument setup used to collect the original data. While each instrument collects files of different internal structure, in essence the information collected retains a relatively common format allowing 3rd party software manufacturers to create value added analysis packages.