FlowJo’s Biology Band contains a series of tools for applying mathematical or statistical models to flow data. Some of the tools are intended to be used with specific biological systems.
Biology Band
Cell Cycle
Creates a one-dimensional model of DNA content for the selected population. To use this tool, click on a population at any level of the gating hierarchy and select the Cell Cycle button. The cell cycle window will appear and present a choice of models to use, a variety of data display choices, and constraining tools for difficult to model data. FlowJo will automatically attempt to detect a linear parameter that appears to be a measure of DNA content, and show a histogram of this parameter. The parameter selection is modifiable. An in depth tutorial of how to use this platform is included in the cell cycle tutorial.
Setting Cell Cycle Preferences
Multidimensional Cell Cycle Analysis (CCnD)
Kinetics
A platform for evaluating changes within a data file (tube) over the time of collection. To use this tool, click on a population at any level of the gating hierarchy and select the Kinetics button. The kinetics window will appear and present a graph versus time of some measure of the data. Common choices for the measure are median fluorescence and the fraction of cells exceeding some threshold. The platform allows you to create partitions based on time and display statistics comparing the data within these partitions. An in depth tutorial of how to use this platform is included in the kinetics tutorial.
Exporting Histogram Data and Kinetics Data
Population Comparison
A platform for comparing the differences between two or more files using statistical models. The tools included allow the user to gain insight into which cells are “positive” for any given parameter when compared to a control and whether samples are statistically different. To use this tool, click on a population at any level of the gating hierarchy and select the Population Comparison button. Next drag one or more populations into the platform and drop them into the “Controls” box. FlowJo will merge the control histograms for calculations if more than one is added. Statistics for each individual parameter will be created immediately, and multi-parameter statistics can be created simply by selecting multiple parameters simultaneously. Gates can be created on “positive populations” by right clicking on either an individual parameter or a set of selected parameters and choosing “Create Gates” from the pop-up menu. Statistical comparisons can be created for an entire group by dragging the Population-Comparison node that appears in the workspace to the group, and similarly tables and plots can be created by dragging the icon to the Table Editor and Layout Editor respectively.
Population Comparison Overview
Proliferation Modeling
Perform non-linear curve fitting to map the distribution of an intracellular dye (e.g. CFSE) modeling the generations of cell division in a culture.