If you would like the uncompensated always overlaid by default, check this box in the preferences. ![]() Overlay uncompensated – The matrix editor will allow you to overlay your uncompensated data on top of the compensated to view the difference. If you prefer to not see this confirmation box, uncheck the box here in the preferences. Generate the plot or graph you want to copy. These preferences can be very useful since you have the control to set the default values of whatever keyword you wish to automatically assign compensation single stain controls to the compensation group upon loading the files! Matrix EditorĬonfirm Edit – when you click the “Edit” button in the matrix editor, a confirmation box will open asking you to confirm that you wish to edit the matrix. To remove axis labels from copied graphics in Flowjo, you can follow these steps: Open Flowjo and load the FCM data. Some other common keywords are “TUBENAME” and “SampleID”. If you prefer to use a different keyword, you can remove the default $FIL strings using the X icon next to them in this interface and then click the “Add” button to add whatever keywords you would like to use. when resetting the edited FlowJo matrix, remember that it was simply a duplicate of the initial acquisition matrix. Thus, any FCS files put into a workspace that contains the text “comp” or “unstained” in the $FIL, or filename, will be included in the compensation group in your workspace when loaded. To remove the altered compensation matrix from a sample or samples, simply go back to the matrix editor and drag the original (unedited) version of the compensation matrix back on to a sample or group of samples. The default values set are “comp” and “unstained”. Groups act like folders to organize your samples, allows master gating and unique report generation. The interface will open as shown below: Compensation Group Inclusion The Group Inclusion can be used to make files with certain file names get automatically included in the group when they are loaded into FlowJo. Bring up the Compensation Definition dialog window, or Compensation Wizard. Select the Compensation button in the Preferences tool to open the Compensation preferences. ![]() The detectors, or channels, in the instrument are designed to detect a very specific range of emissions. Set a gate for the positive and negative populations for each singly-stained sample. What is compensation FlowJo Compensation has undergone a major redesign for FlowJo Version 10 Compensation in flow cytometry is the process of correcting for fluorescence spillover emissions. $FIL – is the FCS file keyword for the name of the data file written by the cytometer. This is a simple example showing how to do three-color compensation in FlowJo. The “Group Inclusion” can be used to make files with certain file names get automatically included in the group when they are loaded into FlowJo. Select the Compensation button in the Preferences tool to open the Compensation preferences. Set your default preferences for compensation This tool works for matrices created in FlowJo, as the single stain controls are needed to calculate several statistics from to produce each value in the SSM.
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