FlowJo version 10 allows you to set up scaling preferences based on the specific cytometer being used.

We have a number of default settings for the various cytometers set.  However, these can be changed or refined. For more information about FlowJo’s display of data for specific cytometers, please see FlowJo and Your Cytometer.

Data is written in two common standards, FCS 2.0 and FCS 3.1 (previously FCS 3.0, Data File Standard for Flow Cytometry, Version FCS 3.1, Normative Reference).  FCS 2.0 data is considered the analog standard and scaling is controlled by the file.  However, with FCS 3.1, the digital standard, scaling and display of data is controlled by the software in which it is analyzed.  All FCS 3.1 data is written as linear, untransformed and uncompensated data.  Hence, the software can control the scaling and transformation upon load.

In older versions of FlowJo, the scaling was limited to number of decades and general transform settings globally.  Hence, scaling did not automatically change based on the cytometer from which the data were acquired.  In version 10, the cytometer preferences are set by reading the cytometer ($CYT) keyword from the files upon load.  Default scaling preferences are then loaded into the preference pane based on the value of the $CYT keyword.  In addition, a preference set is generated for the data from all the different cytometers that have been opened in FlowJo.  This way, a user can load data acquired on a BD instrument running FACSDiva and have it scaled one way (similar to FACSDiva).  They can then load data acquired on a Beckman Coulter Cyan and have it scaled a different way.

Furthermore, with the new cytometer scaling preferences, the user can manipulate the preference sets for each cytometer.  If the default scaling preferences are not exactly correct for your data, the values can be manipulated to scale the data exactly as displayed on the instrument during acquisition.  FlowJo is designed with scaling settings for each cytometer, based on our understanding of the acquisition software, and the way the file is written.  If these default setting do not scale the data properly for your application, please let us know (flowjo@bd.com)!

How to use Cytometer Preferences
Click on the preferences and choose Cytometers.

The list on the left provides all the default cytometers.  Click on any of them to view the default scaling sets.


These sets are only populated when a data file of a particular data type are loaded.  For example, if Attune data has never been loaded into your copy of FlowJo, you will not see this as an option.  Select any of the options on the left and use the options presented to alter the way in which the data is displayed by default in FlowJo v10.

Note: There is not way to “select” which Cytometer an fcs file will use. The fcs files will always use the cytometer settings for whichever cytometer was used to generate the files.

Setting these preferences is only required once.  Please note that if you change the parameter scale or transformation settings, this will take effect in a new workspace.  If you cannot get your parameters to scale correctly, please contact us right away and we can help!