Overview of working with panels and channels

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

Visit this other article for instructions on resolving panel/channel conflicts.

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

 

Background

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

 

(Channels 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 Cytobank, 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.

 

Navigating to the Panel Setup Page

From within any Cytobank Experiment, navigate to Sample Tags > Set Up Channels and Panels.

 

panel-channel-setup.png

(navigating to the panel setup page)

 

 

Moving Samples into New or Existing 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.

panel-channel-move-between-panels.png

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

 

Rename a Channel Within a Panel

The reagent name (also known as long channel name or marker name) can be changed in Cytobank 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 Cytobank.

 

rename_channel.gif

(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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