Analytical Cytometry Standard
NetCDF Conventions for List Mode Data Component
The Flow Cytometry Standard (FCS) specification has been adopted for the common representation of flow cytometry data, and this standard is supported by all analytical instrument and third party software suppliers. It includes data, metadata and analysis components within the same file. However, metadata and analysis components, if included at all, are not recorded in a standardized fashion or in sufficient detail for use by independent parties. We are proposing to address these shortcomings via series of related data standard proposals. Different components describing analytical cytometry experiments would be stored reusing standard formats such as XML or RDF, and all the components would be bundled together into an Analytical Cytometry Standard (ACS) container. This document demonstrates how the Network Common Data Form (NetCDF) data format could be used to capture the most important component of FCS files: the recordings of the fluorescent or light-scattering properties of hundred of thousands of individual particles. NetCDF is a set of freely available software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Many groups, including NASA and the Los Alamos National Laboratory, have adopted NetCDF as a standard way to represent some forms of scientific data. Conventions have been developed on how to use NetCDF to store data for climate and weather forecast, aviation research, geographic information systems, ocean and atmosphere research and descriptions of molecular dynamics simulations. This document introduces the NetCDF format and describes how to use NetCDF to store list mode data files.
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The latest proposal (v071011) on how to use NetCDF to store binary list mode data.
Example NetCDF test files that have been used to for computation as shown in table 1 of the proposal above. These files may also be used as a demonstration of how NetCDF may be used to store cytometry list mode data. Please note that the data within these files have been artificially generated for testing purposes only.