Export data as FCS or spreadsheet files from whole files and/or gated populations

On occasion, it may be desired to write new FCS files from the Cytobank platform, such as when debarcoding. This workflow is supported in three ways: 

  1. Write new FCS files completely within Cytobank. This feature is known as Split files by populations. 
  2. Write new FCS files to download onto your computer from Cytobank. The files also automatically attach to the source experiment.
  3. Write new text files (spreadsheets) that represent your single cell FCS data to download off of Cytobank. The files also automatically attach to the source experiment.


1) Write new FCS files to a new Experiment within Cytobank (Split files by population)

Navigate to Actions > Clone or click Clone from the Experiment summary page-level navbar.



In the popup window of Create clone of experiment, scroll down to the bottom where it shows Split files by populations and select the populations you would like to export. Or to simply rewrite your files in Cytobank and not remove any events, select the Ungated population. When you select more than one population to export, each population will be written into its own FCS file.  



2, 3) Write new FCS files or spreadsheets of your FCS data to download onto your computer. 

To export FCS files or CSV files from Cytobank, navigate to Actions > Export > Export Events:



Once on the Export Events interface, different settings can be chosen for the export. You can change the settings below to customize the export: 

  • file name 
  • Compensation matrix  
  • Transformation 
  • File format (FCS or Text) 
  • Populations to export 
  • FCS files 
  • Channels (only available for Text file format export)  



After clicking on the green link to Download exported events, status bar will appearThe export may take a few minutes. 



During the export, you can navigate away from the page. You will be notified by email when the export is complete.  If you stay on the page, you will see the message: Export complete! Now you can either click to download the exported zip file or view the files from the Exported files session on the Experiment summary page. 



  • For exporting as FCS, exporting compensated data actually exports the raw data but with a file-internal compensation matrix ($Spillover). The exported file will be in FCS3.1 format. Currently, transformation and channel selection are not available with FCS export. Note that Kaluza Analysis software with the Kaluza Cytobank Plugin allows you to export FCS files with user selected parameters, customized reagent and channel names as well as options to export data with compensation and transformation applied. Please write in to Cytobank support for more information.  
  • When exporting as text, the data can be written in raw format, or with compensation and/or scaling applied, or with channels withheld. All these modifications affect the actual numbers exported. 


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