Keywords are paired combinations of a category and a value that pertain to the cytometric data contained in a workspace.
Keyword values can either be imparted to the FCS data file at the time of collection, or added post-acquisition in FlowJo. In either case they are accessible through FlowJo, and are useful for organizing data. FCS is an acronym for Flow Cytometry Standard. It is essentially the set of rules that cytometer manufacturers follow when creating their data output format, and it includes a required set of keywords that must be written to the header portion of an FCS file.
This page contains a list of the special keywords defined as part of the FCS 3.1 Standard, along with a brief description of the corresponding keyword value, as many of the categories do not have particularly descriptive names. The description of the FCS format on the International Society for the Advancement of Cytometry’s (ISAC) webpage, and the actual standard in PDF form are available at, respectively:
Cytometer manufacturers can add additional proprietary keywords to the files that come from their machines in addition to the required keywords. These can be distinguished in that the required keywords all start with a $. Additional keywords can be created from within FlowJo and saved with your workspace (though they will not save with your FCS file(s) as we do not modify your raw data, ever). Click here for more information on adding keywords to the workspace.
Keywords can be used in a Value Series. For information about how FlowJo handles FCS files, go here.
Scientists can use their own keyword identifiers, but they may not start with $, unless it is defined in the specification document.
Required Keywords | |
| $BEGINANALYSIS | Byte-offset to the beginning of the ANALYSIS segment. |
| $BEGINDATA | Byte-offset to the beginning of the DATA segment. |
| $BEGINSTEXT | Byte-offset to the beginning of a supplemental TEXT segment. |
| $BYTEORD | Byte order for data acquisition computer. |
| $DATATYPE | Type of data in DATA segment (ASCII, integer, floating point). |
| $ENDANALYSIS | Byte-offset to the end of the ANALYSIS segment. |
| $ENDDATA | Byte-offset to the end of the DATA segment. |
| $ENDSTEXT | Byte-offset to the end of a supplemental TEXT segment. |
| $MODE | Data mode (list mode, histogram). |
| $NEXTDATA | Byte offset to next data set in the file. |
| $PAR | Number of parameters in an event. |
| $PnB | Number of bits reserved for parameter number n. |
| $PnE | Amplification type for parameter n. |
| $PnR | Range for parameter number n. |
| $TOT | Total number of events in the data set. |
Optional Keywords | |
| $ABRT | Events lost due to data acquisition electronic coincidence. |
| $BTIM | Clock time at beginning of data acquisition. |
| $CELLS | Description of objects measured. |
| $COM | Comment. |
| $COMP | Fluorescence compensation matrix. |
| $CSMODE | Cell subset mode, number of subsets to which an object may belong. |
| $CSVBITS | Number of bits used to encode a cell subset identifier. |
| $CSVnFLAG | The bit set as a flag for subset n. |
| $CYT | Type of flow cytometer. |
| $CYTSN | Flow cytometer serial number. |
| $DATE | Date of data set acquisition. |
| $ETIM | Clock time at end of data acquisition. |
| $EXP | Name of investigator initiating the experiment. |
| $FIL | Name of the data file containing the data set. |
| $GATE | Number of gating parameters. |
| $GATING | Specifies region combinations used for gating. |
| $GnE | Amplification type for gating parameter number n. |
| $GnF | Optical filter used for gating parameter number n. |
| $GnN | Name of gating parameter number n. |
| $GnP | Percent of emitted light collected by gating parameter n. |
| $GnR | Range of gating parameter n. |
| $GnN | Name used for gating parameter n. |
| $GnT | Detector type for gating parameter n. |
| $GnV | Detector voltage for gating parameter n. |
| $INST | Institution at which data acquired. |
| $LOST | Number of events lost due to computer busy. |
| $OP | Name of flow cytometry operator. |
| $Pkn | Peak channel number of univariate histogram for parameter n. |
| $PKNn | Count in peak channel of univariate histogram for parameter n. |
| $PnF | Name of optical filter for parameter n. |
| $PnG | Amplifier gain used for acquisition of parameter n. |
| $PnL | Excitation wavelength for parameter n. |
| $PnN | Short name for parameter n. |
| $PnO | Excitation power for parameter n. |
| $PnP | Percent of emitted light collected by parameter n. |
| $PnS | Name used for parameter n. |
| $PnT | Detector type for parameter n. |
| $PnV | Detector voltage for parameter n. |
| $PROJ | Name of the experiment project. |
| $RnI | Gating region for parameter number n. |
| $RnW | Window settings for gating region n. |
| $SMNO | Specimen (tube or well) label. |
| $SRC | Source of the specimen (patient name, cell types). |
| $SYS | Type of computer and its operating system. |
| $TIMESTEP | Time step for time parameter. |
| $TR | Trigger parameter and its threshold. |
| $UNICODE | UNICODE code page for string type keyword values. |