Write .fcs files for flow cytometry

Adapted from https://github.com/ZELLMECHANIK-DRESDEN/fcswrite

cytoflow.utility.fcswrite.write_fcs(filename, chn_names, chn_ranges, data, compat_chn_names=True, compat_percent=True, compat_negative=True, compat_copy=True, verbose=0, **kws)[source]

Write numpy data to an .fcs file (FCS3.0 file format)

  • filename (str) – Path to the output .fcs file
  • chn_names (list of str, length C) – Names of the output channels
  • chn_ranges (dictionary) – Keys: channel names. Values: ranges
  • data (2d ndarray of shape (N,C)) – The numpy array data to store as .fcs file format.
  • compat_chn_names (bool) – Compatibility mode for 3rd party flow analysis software: The characters ” “, “?”, and “_” are removed in the output channel names.
  • compat_percent (bool) – Compatibliity mode for 3rd party flow analysis software: If a column in data contains values only between 0 and 1, they are multiplied by 100.
  • compat_negative (bool) – Compatibliity mode for 3rd party flow analysis software: Flip the sign of data if its mean is smaller than zero.
  • compat_copy (bool) – Do not override the input array data when modified in compatibility mode.
  • kwargs (Str) – Additional keyword arguments are written as keyword/value pairs in the TEXT segment of the FCS file.


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