Digital BD cytometers (FACSCanto, FACSLSRII, FACSAria, LSRFortessa, etc.) use FACSDiva software, which produces FCS 3.0 compliant files.
Analog BD cytometers (Calibur and Scan) use the Cell Quest software line, which produce FCS 2.0 compliant files.
FlowJo’s default preferences should display the data the same way as seen on the instrument. You can change these default preference sets in the cytometer specific preferences.
Manual adjustments can also be made after data load by using the T button in the graph window.
Below are examples of data as it appears in FACS Diva and the same data in FlowJo. The log scale is not transformed. Most users now acquire the data on BD instruments with the biexponential transform, which is actually FlowJo’s default display method for BD data.