Cytobank – As the cell flows

Naming and Exporting Files in Diva

July 21, 2011 at 8:20 pm Angela Landrigan 1 comment

Many of our users upload data to Cytobank that were collected on a BD Biosciences flow cytometer using BD FACSDiva™ software. In this post, we will walk you through how to harness the power of naming files in Diva to facilitate analysis on Cytobank and how to export FCS files from Diva for upload to Cytobank.

Detailed naming of sample files in Diva gives you a special advantage unique to Cytobank’s analysis environment. When you upload files to Cytobank, our servers will automatically categorize your files for ease of analysis when you annotate Figure Dimensions. This automated categorization enables you to rapidly generate well-annotated plot layouts and figures. Watch our YouTube video demonstrating this feature!

The Inspector window in Diva is where you name files. Click on the Tube tab, and enter sample information into this field. Before you collect your first sample, take a moment to think ahead about which Figure Dimensions on Cytobank you will use. For example, you may want to enter a donor/individual number, a timepoint label, and a stimulation condition. If you then enable and define these Figure Dimensions, Cytobank will automatically sort your files into the appropriate annotation tags.

Annotate Flow Cytometry Files in Diva (Figure courtesy of J. Irish, CYTO 2011)

When you label fluorescence channels with reagent information in Diva, Cytobank automatically pulls this reagent info from the files, further facilitating your analysis and generation of well-labeled figures. To enter reagent information in Diva, click the Labels tag in the Inspector and type in the reagent names.

Once you are done collecting data from your samples, it is time to export the data as FCS files. To preserve the names you have assigned to your files, it is important that you export your files from Diva as FCS files and NOT as experiments. Exporting an experiment from Diva will generate FCS files with numbered filenames. We are working on a way to import Diva experiments into Cytobank (and convert the numbered filenames), but until then, exporting your files as FCS files is the easiest way to import files from Diva and work with them in Cytobank.

Exporting FCS Files (from BD FACSDiva v6 manual)

Select the experiments or tubes to export, then click File → Export → FCS files. Choose a file destination, and click Save. Your files are now ready for upload and analysis on Cytobank!

- Angela

Entry filed under: Cytobank, Flow Cytometry. Tags: annotation, BD, channels, Diva, FACSDiva, FCS files, figure dimensions, Inspector window, reagent names, tube name.