Cellquest Software

The software was designed to act as the interface between a computer and the flow cytometer hardware. Its primary functions were:

is a software application developed by Becton Dickinson (BD Biosciences) for the acquisition, analysis, and display of flow cytometry data. For nearly two decades, it was the industry-standard program for BD FACScan, FACSort, FACSCalibur, and FACSCanto instruments.

To use CellQuest data in modern software (FlowJo, FCS Express, R/Bioconductor), export raw .FCS files. CellQuest itself exports statistics: cellquest software

If you are setting up a legacy lab, keep a dedicated Windows XP machine with a serial-to-USB adapter. For analysis, export your .FCS files to FlowJo or R (using flowCore package). But for straightforward, low-throughput experiments, CellQuest still gets the job done.

This is a known issue with Windows 7/10 compatibility. Workaround: Export plots as PICT (Mac) or use Print to PDF instead of direct printing. The software was designed to act as the

| Do This | Avoid This | | :--- | :--- | | Save both .Acq (template) and .FCS (data) files. | Saving only .Acq – you lose all event data. | | Use after moving gates. | Assuming gates auto-update stats. | | Run compensation controls (single-stained beads/cells). | Trying to “guess” compensation values. | | Export final plots as TIFF or PDF. | Printing directly from CellQuest (crash risk). |

Always save both the .Acq template and the .FCS data file. The template lets you reproduce identical analysis settings later. To use CellQuest data in modern software (FlowJo,

| Feature | CellQuest (Legacy) | FACSDiva (Modern) | | :--- | :--- | :--- | | | Primarily FACSCalibur | FACSCanto, LSRFortessa, etc. | | Interface | 2D, menu-heavy | 3D visualization, tabbed interface | | Compensation | Manual slider adjustment | Automated calculation wizards | | OS Support | Mac OS Classic/Early OS X | Windows 10/11, Modern Linux | | Experiment Layout | Manual setup per run | Hierarchy-based experiment templates |