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Extract Flow Cytometry data from FCS files version 3+.

Project description

Extract metadata and data from FCS (3.0, 3.1) files.

Data extraction supports file formats:
  • Mode: List (L)
  • Datatypes: I, F, D
Implemented parameter data set options:
  • raw
  • channel values
  • scale values (log10, gain)
  • channel and scale combined into one data set
  • fluorescence compensation
  • log10 scaled fluorescence compensation
Metadata extraction features:
  • support for non-compliant files
  • merge or separate csv files
  • rolling mean for any keyword with a numeric value
  • append new fcs files to previously generated metadata csv file
Interactive dashboard plots using the xfcsdashboard add-on module.


Using pip:

pip install xfcs

Without pip:

python install

Command Line Usage

See USAGE for expanded details.

To see a list of available commands and arguments, run ‘’xfcs data –help’’ or ‘’xfcs metadata –help’‘

extract data: xfcs data [options]
extract metadata: xfcs metadata [options]


  • Python 3.5 or greater
  • numpy
  • pandas


xfcs is released under the BSD 2-clause license. See LICENSE for details.

Project details

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Files for xfcs, version 1.1.6
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