FCS Express: Tips for MACSquantify users

FCS Express is fully compatible with data acquired using MACSQuantifyâ„¢ software once the data is exported correctly. This page contains instructions for exporting data from the MACSQuantify software for use in FCS Express.

For users with ver.2.3.1129.1 MACSQuantify Software click here

For users with ver.2.2.1031.1 MACSQuantify Software click here

 

Exporting from MACSQuantify version 2.3.1129.1

  1. Open the Options dialog box from the Edit menu.
  2. Under the Software heading, open Export and select FCS.
  3. In the initial dialog box, select Custom from the drop down menu as in figure 1 below.
  4.  

    Figure 1: Custom selection for FCS export.

     

    A second dialog box will open (Figure 2)

  5. Select FCS 3.0 as the Version (figure 2).
  6. Check the Compatible check box in the Options category (figure 2).
  7.  

    Figure 2:  FCS Export formatting for ver2.3 software

     

  8. Select OK.
  9. To batch export .mqd files to .fcs files, highlight all the data files for export.
  10. Right click on the files and select Export sample.
  11. A dialog box will appear to specify an FCS file or CSV file (figure 3).
  12. If a gating strategy was applied to any of the data files, you have the option of creating a separate FCS file each gated population as well. If only an FCS file is required for the original data file, make sure the Skip subpopulations check box is checked (figure 3).
  13. Click OK.
  14. Figure 3:  FCS export dialog box

     

    The FCS files will be located in the same location where the original .mqd data files were opened or added from.

Optional: to program the MACSQuant Analyzer to automatically generate an .fcs file immediately after data acquisition, select Acquire under the Software heading in the Options dialog box and check the box next to Export as FCS (figure 4).

Figure 4: Setting up automatic FCS export in the Acquire Option dialog box

 

 

Your files will now be exported correctly and are ready for use in FCS Express (see below).

 

Exporting from MACSQuantify version 2.2.1031.1

  1. Open the Options dialog box from the Edit menu.
  2. Under the Software heading, open Export and select FCS (figure 5).
  3. Select the FCS3.0 radio button (figure 5).
  4. Check the Compatible check box (figure 5).
  5. Click OK (figure 5).
  6.  

    Figure 5: FCS Export selection in ver2.2 software

     

  7. Follow steps 6-11 as detailed above for 2.3.1129.1 software users for export of .fcs files.

 

Your files will now be exported correctly and are ready for use in FCS Express (see below).

 

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