On occasion, it may be convenient to write new FCS files from the Cytobank platform, such as when debarcoding samples, modifying the file-internal compensation or to create smaller files containing only events from a specific population. This workflow is supported in three ways:
- Write new FCS files within the Cytobank platform. This feature is known as Split files by populations.
- Write new FCS files to download to your computer from the Cytobank platform. This feature is known as Export events as FCS files.
- Write new text files (spreadsheets) that represent your single cell FCS data to download off the Cytobank platform. This feature is known as Export events as TXT files.
Write new FCS files to a new experiment within the Cytobank platform: Split files by population
To write new FCS files into a new clone experiment, navigate to the Actions menu in the blue navigation bar and select Clone or click Clone from the Experiment summary page-level navbar.
In the Create clone of experiment dialogue, scroll down to the bottom where it shows Split files by populations (SFBP) and click on Select populations... to select the populations you would like to export. When you select more than one population to export, each population will be written into its own FCS file. For instance, if you select two original FCS files and three populations, six new FCS files will be created in the clone experiment. To simply rewrite your files in the Cytobank platform including all events, select the Ungated population.
Please note that if your experiment includes gating groups, only the FCS files associated with the gating group from which populations are selected will be used by the SFBP tool to generate new FCS files. If you only select populations from the B cell gating group, only the FCS files associated with the B cell gating group will be SFBP and cloned. Read more about the experiment cloning settings in this article.
Once you have selected the populations, the dialogue will update informing you of the number of new FCS files that will be generated. Click on Submit clone to complete the process.
Write new FCS files or spreadsheets of your FCS data to download onto your computer
To export FCS files or CSV files from a Cytobank experiment, navigate to the Actions menu and select Export Events.
On the Export events dialogue, different settings can be chosen for the export. You can change the settings below to customize the export:
- Filename.
- Transformation: raw values or transformed based on experiment scale settings, only available for Text format export.
- File format: FCS3.1 or Text.
- Include/exclude header with FCS filename: only available for Text format export.
- Gating group: only if the experiment includes some gating groups. Note that only one gating group can be selected at a time.
- Populations to export.
- FCS files to export.
- Channels: only available for Text format export.
Note that the exported events in FCS or TXT format will be compensated according to the experiment-wide compensation selected at the time of the export. If you selected to export events as FCS, the new files will contain a file-internal compensation matrix in the $Spillover keyword.
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 to Cytobank support for more information.
After clicking on the green Submit export button a status bar will appear. The 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.
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For Research Use Only. Not for use in diagnostic procedures.