Gating
The data generated by flow-cytometers can be plotted in a single dimension, to produce a histogram, or in two-dimensional dot plots or even in three dimensions. The regions on these plots can be sequentially separated, based on fluorescence intensity, by creating a series of subset extractions, termed "gates." Specific gating protocols exist for diagnostic and clinical purposes especially in relation to hematology.
The plots are often made on logarithmic scales. Because different fluorescent dyes' emission spectra overlap, signals at the detectors have to be compensated electronically as well as computationally. Data accumulated using the flow cytometer can be analyzed using software, e.g., WinMDI (only one which is freeware), FCS Express, Flowjo, CytoPaint (aka Paint-A-Gate), VenturiOne, CellQuest Pro, or Cytospec. Once the data are collected, there is no need to stay connected to the flow cytometer. For this reason, analysis is most often performed on a separate computer. This is especially necessary in core facilities where usage of these machines is in high demand.
Read more about this topic: Flow Cytometry, Data Analysis