About

This application performs conversion between files conforming to the Data File Standard for Flow Cytometry (FCS) and the Network Common Data Form (NetCDF); Conventions for List Mode Binary Data File.

The application is available as a command line application as well as a wizard-based graphical user interface. The graphical user interface starts automatically when no arguments are specified for the fcs2netcdf.jar (ConverterApp class)

Run the converter GUI from the Web

  1. If you dont already have it installed, install Java 1.6. This will also install WebStart and the Java Plug-In.
  2. Launch List Mode Data Converter with Java WebStart.

Run it as a command line application

Download (below) and use it as follows: 

USAGE: java -jar fcs2netcdf.jar // starts the graphical user interface
       java -jar fcs2netcdf.jar -to [FCS | netCDF] -i inputFile -o outputFile [options...]
       java -jar fcs2netcdf.jar -h
       java -jar fcs2netcdf.jar -v

 -d N    : Dataset number.
           * For FCS -> netCDF conversion only.
           * Can be used to select a dataset from a multidataset FCS file.
           * The first dataset has the number 0 (default).
 -h      : Provides help/usage only (no conversion is performed).
 -i FILE : Input file (mandatory).
 -id VAL : Internal file identifier (optional).
           * For FCS -> netCDF conversion only.
           * Should be globally unique and in the form of an URI.
           * Will be automatically generated if not provided.
 -o FILE : Output file (mandatory).
 -p N    : Floating point precision for parameters converted from FCS log scale 
           or from netCDF files.
           * Use "-p 32" for a single precision floating point (default).
           * Use "-p 64" for a double precision floating point.
 -q      : Quiet mode. Suppresses screen output.
 -r      : Rewrite existing file.
 -to VAL : Conversion type (mandatory).
           * Use "-to FCS" for a conversion from netCDF to FCS.
           * Use "-to netCDF" for a conversion from FCS to netCDF.
 -v      : Provides version info only (no conversion is performed).
 -z VAL  : Time zone for time parameter conversion.
           * For FCS -> netCDF conversion only.
           * Use [+|-]dd:00, where dd is between 00 and 12.
           * Default value is "+00:00".

Download

Get the binary package from the download section.

Alternativelly

Download the fcs2netcdf.jar as well as required third party libraries.

Required Third Party Libraries

Extract the following zip file and keep it in the lib subfolder of the folder with the fcs2netcdf.jar. The libraries included in the zip are the following:

Sources

Download the source codes from the download section. Alternativelly, the latest sources may be obtained from the SVN repository.

Documentation

Follow this link to view the javadoc documentation or obtain the latest javadoc from the SVN repository. Alternativelly, the documentation can be downloaded in the download section.

Last update: February 19th, 2008