How can I export the gate assignments for each event?

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How can I export the gate assignments for each event?

Cell-by-cell gate information can be exported for your data through the FCS Express Pipelines feature.

Please use the steps below to learn how to do this.

Step 1. Creating a pipeline

  • Click the Tools tab > Transformations.
  • Click the blue + button and select Pipeline.

  • Rename the pipeline, if desired by clicking the T button.
  • Under Gate Options, keep No Gate as the selection.
  • Under Parameter Options, keep all parameters checkmarked.

Step 2: Add Gate Downsampling pipeline steps

  • Click the blue + button on the right.
  • Hover over the Downsampling category.
  • Select Gate Downsampling.

  • Rename the pipeline step using the gate name. Focus on just one gate in this pipeline step.
  • Select Create new mask parameter(s).
  • For the Downsampling mask name prefix, enter any desired label. This will be part of the column label in the csv.
  • For Save as Classification Values, enter the Gate name.
  • Next to Gate, select the gate of interest from the dropdown menu.

  • The option to Save as a Classification Value will write Include or Exclude to determine whether an event is in that gate.
  • The option to Save as a Numeric (Float) Value will write a number to determine whether a cell is included or excluded from a gate:
    • 0 will be used if that event is excluded from that gate.
    • 1 will be used if that event is included in that gate.

Step 3: Add one pipeline step for each gate

  • Repeat Step 2 for every gate of interest.
  • You'll end up with one pipeline step for each gate.

Step 4 (Optional): Apply the pipeline to a Data Grid

  • Click the Insert tab > Data Grid

  • Click on the blank space of the layout to place the Data Grid
  • Drag and drop the Pipeline onto the Data Grid

  • Within the Data Grid, scroll all the way to the right to view the new Gate Assignment columns
  • Expand the column headers down to view the full column names.

  • The data grid contains one row per event, in the order of acquisition. under a particular column, "Include" indicates that the event in that row is included in the Gate. For example, in the screenshot above, cell 1 is included in Gate 1, Gate 2 and Gate 4. Cell 1 is excluded from Gate 3 and Gate 5.

Step 5: Batch Exporting the gate assignments for each data file

  • Click the Data tab > Save/Merge from Files

 

  • Click Add > Add using Advanced Open Data Dialog
  • Click on the Data List tab
  • Highlight all of the data files
  • Click OK

  • Select Save as Individual Files
  • For Output File Format, select Comma Separated Values Files (csv)
  • For Output Directory, click the Yellow filefolder icon and select where to save the CSV files.
  • For Output File Name, enter a prefix and include the asterisk (*) at the end.
    • The Asterisk (*) represents the full original filename. This helps you keep track of which data file was exported.
  • Under Save Options, select Save compensated/unmixed data using the matrix specified in 'File > Info > Layout Options'.
  • For Save with transformtion, select the pipeline that you created. It is named Gate Downsampling in the example below.
  • Click Save
  • The export process could take several minutes for very large data files (like spectral data).

 

 

Step 5 (alternative): Export the gate assignments for just one data file

  • Complete Step 4.
  • Click on the Data Grid.
  • Click the Data tab > Save from Plot.
  • Click the yellow file folder icon.
  • Select a location for saving the CSV file.
  • Enter a name for the CSV file.
  • For Save as type, select Comma Separated Values Files (*.csv) from the dropdown menu.

 

  • Do not uncheck any of the parameters in the parameter list
  • Click OK

 

 

Step 6: View the gate assignments

  • Navigate to the location where the CSV files were exported.
  • If batch exporting is done, you'll see one CSV file per data file.

 

  • Open one of the CSV files in Excel.
  • The Mask Downsampling columns appear in the right-most columns.
  • A value of 1 means that the event is inside a given gate). A value of 0 means the event is outside a given gate.
  • Please note that there will be separate columns if the gate information is exported as a classification value (Include/Exclude) and a number value (0/1).

  • The events are listed from top to bottom in order of acquisition time.