When you modify the matrix, the numbers are converted to give an estimation of the amount (percentage) of spillover into the other parameter. In version 4.5 and after, the matrix can be modified right in FlowJo using the "Edit/Save Matrix" menu option. In very rough terms, the 0.1803 corresponds to approximately 18% spillover (PE-%FITC).Ĭlick here for instructions on modifying the matrix. Thus, 0.1803 is the spillover coefficient between FITC and PE, or the amount of FITC signal in the PE channel for a FITC-stained cell 0.0091 is the amount of the PE signal in the FITC channel for a PE-stained cell. The rows are the spectra of each channel the columns are the contributions of each fluor into the channels. The subsequent lines are the spillover coefficients, corresponding to each of the channels named. The names must match exactly use the names that appear in the $PnN keywords of the FCS file. Channels that are not in this list are not compensated channels in this list that are not in the sample are ignored. The second line has the names of the fluorescence channels that are being compensated. The first line has the title of the compensation matrix. If you save the matrix to a file (using the "Edit/Save Matrix" option), the file looks like this: CompMatrix The detectors, or channels, in the instrument are designed to detect a very specific range of Compensation controls (single stain samples) must now belong to a compensation group inĬompensation has undergone a major redesign for FlowJo Version X! Compensation in flow cytometry is the process of correcting for fluorescence spillover emissions.ĬHAPTER 2 – Creating a FlowJo compensation matrix from single stain controls back to Compensation Workflow Overview Compensation has been reworked for version 10.When the "Compute" button in the compensation matrix dialog window is clicked, FlowJo generates a compensation matrix. In this video, FlowJo Application Scientist Mike Stadnisky introduces you to the newest version of FlowJo with a 24-part run throuįlowJo gives you the ability to compensate your data. This may be necessary in cases where the compensation was inappropriately set during sample collection (although if the sample was over-compensated, then there is no recourse). Also, there may be casesĪccelerate your discovery with the latest features that come with FlowJo v10.6.1: Spectral compensation allows users who collect more channels than they have parameters to get cleaner data if properly done. In spectral flow, light is collected in all detectors for allįlowJo is your biggest fan and strives to be an outstanding source of support. We’re here to help you accelerate routine phenotyping, take your immunology research to the next level, and get you from data to results―one cell at a time.įlowJo applies the compensation matrix generated by acquisition software automatically upon loading data. #Flowjo 10 apply compensation matrix software# If you did not compensate on the machine or use fcs2.0 data, the parameters will not have the comp-prefix. The Compensation Wizard in FlowJo is one of the most frequently used platforms, and by extension potentially the greatest source of confusion on a per-cytometrist basis. #Flowjo 10 apply compensation matrix software#.
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