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 Cytobank, 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 Population", and used to be called "New Experiment from Gated Files".
  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.

 

Each supported workflow begins the same way, by configuring the Working Illustration with which populations/gates you want to pull events from, times which files you want this splitting applied to (remember to update the illustration!). The number of files that result will be equal to the number of populations times the number of files. In the example below, 12 files would result. The Working Illustration only mediates which files and populations are chosen for export. Other applicable settings are chosen later.

 

(begin by configuring your illustration. This step is important because it defines the export parameters)

 

After the illustration is configured, one of the different workflow paths listed above can be taken.

 

1) Write new FCS files to a new Experiment completely within Cytobank (Split Files by Population)

After configuring the Working Illustration per the discussion above, navigate to Actions > Cloning > Split Files by Population

 

(Split Files by Population will write data to a new Cytobank Experiment depending on the configuration of the Working Illustration)

 

To simply rewrite your files in Cytobank and not remove any events, configure the Populations Figure Dimension with only the "ungated" population.

 

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

After configuring the Working Illustration per the discussion above, navigate to Actions > Export > Export Events

 

 

Once on the Export Events interface, different parameters can be chosen for the export.

 

 

  • The resulting file will be available for download and automatically attach itself to the Experiment Summary page of the experiment.
  • For exporting as FCS, exporting compensated data actually exports the raw data but with a file-internal compensation matrix (spill string). Currently, FCS files can't be exported with rewritten raw data according to compensation, scales, or channels. The files can only be split and have a spill string added.
  • 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.

 

 



Have more questions? Submit a request