As you probably know, FCS (Flow Cytometry Standard) files are created by flow cytometers. FlowJo can read and analyze FCS files from any cytometer.

Each cytometer will scale your data slightly different during acquisition. The FCS3.0 standard provides for up to 32 bits of data, or a range in the scale of 2^32. Instrument scaling range can vary from 2^18 on FACSDiva equipped instruments to 2^32 on MoFlo Astrios. Many people are used to visualizing data in 4 or 5 decades (a scale of 2^10 or 2^18). However, instruments like the Beckman Coulter Gallios, Life Technologies Attune, BD Accuri C6, and MoFlo Astrios will scale data from 6 to 10 decades. Since FlowJo must scale the data identically to what you see on the machine, we have implemented a great new feature in v10 of FlowJo that will create a specific preference set based on the cytometer on which the data was acquired when loaded into FlowJo.

To learn more about setting up preferences for the display scaling and transformation of the data from your cytometer, click on the Cytometers button in Preferences. For specific information on data scaling visit here. Each preference set can be adjusted based on how you wish to display the data. Linear/logarithmic/biexponential default scaling, scale range, and auto-transform can all be set in these cytometer preferences!

For information on getting FlowJo to match the display of acquisition software, choose your vendor below:


Life Technologies Attune

BD Bioscience

Beckman Coulter







All of these documents are written based on our understanding of the default display of the data on the respective instrument. If your data is not scaled properly or you still have trouble, please contact us (techsupport [at]! We can easily assist you in setting the preferences based on your data. We’ll just need one of your data files so we can help you set the preferences accordingly.