Cytek uses Cypod software on all of their cytometers, which produces FCS 3.0 compliant files. Cypod files load directly into Flowjo and are scaled identically as Cypod.
One caveat is that Cypod typically does not acquire data with a biexponential transform turned on. Since the data is in the FCS3.0 format, FlowJo plots the data biexponetially transformed by default. We encourage using the biexponetial transformation, as it is a better display type than a simple log transformation. However, it can cause strange artifacts to appear in Cytek data when data is scaled to 1024 or 4 decades (usually on FACScan upgrades). If you would like to turn the biexponential transform off, this can be done in the fcs3.0 scaling preferences or using the T button.
Please contact us with any problems.