Scale types and equations in Cytobank

Cytobank offers three ways in which to transform / scale your data:

  1. Raw / Linear - the data are displayed exactly as they appear in the file.
  2. Log - each data point is displayed as Log10(raw_value). Raw_value is the data value from the FCS file.
  3. Arcsinh - each data point is displayed as arcsinh(raw_value / scale_argument). Raw_value is the data value from the FCS file and scale_argument is set within the scale settings of the experiment.

Cytobank will automatically set scale equation for most channels to Arcsinh for data produced by most modern cytometers, according to metadata found in the FCS file. Older cytometers that produce data without negative values may be set to Log. FCS files without certain metadata may default to linear scales and need manual scaling after import to Cytobank.

Scale settings can be customized by using the the scale editor in any Cytobank Experiment:



For more reading on data display, check out our blog post on making beautiful plots!

Cytobank does not explicitly support biexponential, Hyperlog, or Logicle scaling. However, highly similar results can be gotten from the generic arcsinh equation, as all of these scaling methods are variations on the same theme.

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