FCS (.fcs, .lmd)

Background & Context

    • FCS molecular biology format.
    • Standard format for storing and exchanging flow cytometry data.
    • Mixed ASCII/binary format.
    • Stores signal intensities for cell events as an array.
    • Metainformation about the data acquisition is stored in the file.

Import & Export

  • Import["file.fcs"] returns an array representing the cellular events stored in the file.
  • Export["file.fcs",{paramnames,events}] exports a list of parameter names and an array of events to the FCS format.
  • Export["file.fcs",{paramnames,paramreagents,events}] exports a list of parameter names, a list of parameter reagents, and an array of events to the FCS format.
  • Import["file.fcs",elem] imports the specified element from an FCS file.
  • Import["file.fcs",{{elem1,elem2,…}}] imports multiple elements.
  • The import format can be specified with Import["file","FCS"] or Import["file",{"FCS",elem,…}].
  • Export["file.fcs",{expr1,expr2,…},{{elem1,elem2,…}}] treats each expri as specifying the corresponding elemi.
  • Export["file.fcs",expr,opt1->val1,…] exports expr with the specified option elements taken to have the specified values.
  • Export["file.fcs",{elem1->expr1,elem2->expr2,…},"Rules"] uses rules to specify the elements to be exported.
  • See the following reference pages for full general information:
  • Import, Exportimport from or export to a file
    CloudImport, CloudExportimport from or export to a cloud object
    ImportString, ExportStringimport from or export to a string
    ImportByteArray, ExportByteArrayimport from or export to a byte array

Import Elements

  • General Import elements:
  • "Elements" list of elements and options available in this file
    "Summary"summary of the file
    "Rules"list of rules for all available elements
  • File metadata:
  • "Header"raw file header given as a list of rules
  • Data representation elements:
  • "Events"cellular events as an array
    "ParameterName"parameter names as a list of rules (import) or a list (export)
    "ParameterReagent"parameter reagents as a list of rules (import) or a list (export)
  • Additional data elements:
  • "Data"cellular events as an array
    "LabeledData"list of rules for data stored in the file
  • Import uses the "Events" element by default for the FCS format.
  • Export requires at least a list of parameter names and an array of events.
  • Export can optionally take a list of parameter reagents. All other optional keys must be specified via the "OptionalKeys" option.

Options

  • Advanced Export options:
  • "DataType"Automaticdata type used to encode events
    "OptionalKeys"{}optional keys to include in the header, as a list of rules
  • The Wolfram Language attempts to identify the most compact format in which the events can be encoded. Automatic data type identification may be overridden via the "DataType" option.
  • Valid settings for "DataType" are:
  • "UnsignedInteger8"8-bit unsigned integer
    "UnsignedInteger16"16-bit unsigned integer
    "UnsignedInteger24"24-bit unsigned integer
    "UnsignedInteger32"32-bit unsigned integer
    "Real32"IEEE single-precision real number
    "Real64"IEEE double-precision real number
  • The Wolfram Language will automatically overwrite certain protected keys (such as "$BEGINDATA" and "$BYTEORD") that are specified in "OptionalKeys". Thus, if you are re-exporting an imported FCS file, you may directly set "OptionalKeys" to the value of the "Header" element from the imported FCS file. Parameter reagents ("$PnS" keys) will be removed from "OptionalKeys" only if parameter reagents are provided in the main Export expression.

Examples

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Basic Examples  (7)

Read the file header from a sample FCS file:

Read the parameter names and reagents:

Read events and display the first several in a table:

Export an array of event values with parameter names:

Specify a data type to use when exporting:

Export an array of event values with parameter names and parameter reagents:

Export a version of a data file with the same header, but with a small subset of the events:

Scope  (6)

Plot the untransformed events in a density histogram:

Plot the events with axes transformed by ArcSinh as a shaded contour plot:

Use FindClusters to automatically detect similar groups of cells:

Create a grid of 25 of the possible biaxial plots:

Perform polygon gating of cell populations:

The FCS standard does not support negative integers:

Alternatively, export negative integers as reals: