The Cytometry band allows users to access additional platforms required for specific analyses.


Compensation will provide an interface to identify single stain controls, set proper gates and create the compensation matrix.  This process is fundamental to accurately analyzing multicolor immunofluorescence flow cytometry data. This button in the workspace allows access the compensation editor interface, where new matrices can be created.
Overview of Compensation
Learn about the compensation editor and compensation processes
The Compensation Interface
Using FlowJo for compensation
Editing a Compensation Matrix
Caveats – Precautions – Instructions
Compensation Protocols and Papers
Helpful resources for practical compensation
The Compensation Matrix File
An explanation of how FlowJo saves your comp matrix

Spectral Plot

Select a node, then use this tool to open up an interactive spectral plot of a single population to use for compensation purposes.

Spectral Population Viewer

Select one or more nodes, then use this tool to compare the spectral signature.

Check Sample Quality

Checking sample quality will examine your fluorescence parameters versus time to examine any aberrations that may have occurred during acquisition.  

Edit Compensation Matrix

Open an interactive editor to change values in the compensation matrix, and see live preview of the effect.

Derive Parameters

Derived parameters allows users to create new parameters to utilize with the data files. Changing ranges of parameters, creating ratios of parameters or converting log/linear can all be done with derived parameters.


How to Derive a New Parameter In FlowJo
Stepwise instructions for generating new parameters
New Parameter Types and Definitions
Log/Lin – Ratio – Time – Add Gain or Offset

Script Editor

The Script Editor is a platform that allows the user to program their own routines into FlowJo using JavaScript without having to worry about compiling a program.