Overview of working with panels and channels

This Article has multiple sections. Click the links in the index below to jump between sections.

  1. Background
  2. Navigate to the panel setup page
  3. Create new panels and move files between panels
  4. Control panel visibility
  5. Rename a channel name within a panel
  6. Delete a panel


The term  Channel refers to the cytometer channel on which your data were collected. FCS files contain channel information in two parts: detector name (referred to as Channel Name) and marker/reagent name.


(Channel information in two parts: machine detector name and experiment-specific reagent or marker. The former is also termed short channel name. The latter is also termed long channel name)

The detector name is associated with the machine and generally not changed from experiment to experiment. The marker name is entered by the operator of the machine on a per-use basis, and generally indicates what biological target is being studied on the channel in question. Other terms sometimes used for these two channel parts are short channel name and long channel name, respectively.

The collection of channels and the markers being studied on them form a panel. In the Cytobank platform, a panel is visualized in a table similar to the image above. In addition, panel is a term that describes an organizational structure for files. Files reside in a panel, and all the files within a panel need to have the same collection of channels and reagent names. If this condition isn't met, a panel/channel conflict will result. If there is a panel/channel conflict, see this article on resolving panel/channel conflicts.

Navigating to the Panel Setup Page

From within any Cytobankexperiment, navigate to  Sample Tags menu and select Assign panels.


 (Navigating to the panel setup page)

Create new panels and move files between panels

A panel is an organizational structure for FCS files (aka samples). All samples within a panel must have the same collection of channels and reagent names, otherwise, a panel/channel conflict will arise.

Samples can be moved into a new or already existing panel by selecting the samples within a panel and then clicking on the move button. Afterwards, select the desired destination. Note that files can also be moved to an existing panel by clicking on the panel itself.


(Move file(s) to a new panel or existing panel)

Control panel visibility

By default, all panels in an experiment will be visible and all files within those panels will be available for analysis. At least one panel must be visible. You can hide panels by unchecking the box near the name of a specific panel.

When a panel is invisible it will appear greyed out and all FCS files belonging to it won’t be available for analysis.


(Configure which panels are available for analysis in the experiment. Left: panels 1 and 2 are visible and available for analysis. Right: only panel 1 is available for analysis and panel 2 is greyed out)

Rename a Channel Within a Panel

The reagent name (also known as long channel name or marker name) can be changed in the Cytobank platform by clicking the text cell and editing it. When finished, press enter on the keyboard or click somewhere outside the cell. The renaming will apply to all samples within the panel.

The short channel name (aka instrument channel name or detector name) cannot be edited in the Cytobank platform.



(Rename a channel in Cytobank)

Delete a panel
Deletion of a panel happens automatically as a consequence of moving all the samples out of a panel.

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