- BD FACSDiva (Windows) – Full-featured user acquisition and analysis software for the BD FACSAria II. Currently there are two licenses: The first is located on the FACSAria II and the second is available upon request.
- BD CellQuest Pro (Mac) – Full-featured user analysis software with batch processing for the FACSCalibur. A second full featured off-line workstation copy is available upon request.
- TSRI WinMDI (Windows) – Useful free analysis software written in Windows DOS. Does not support batch processing; must save graphs in graphics program such as Powerpoint/Illustrator.
- Treestar FlowJo (Mac) – Full-featured user analysis software with batch processing. Access controlled by USB-dongle (2 available).
- De Novo FacsExpress (Windows) – Full-featured user analysis software with batch processing. Network license at ISB limits use to one user at a time.