Gating-ML - ISAC Candidate Recommendation

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Analytical Cytometry Standard (ACS) - Gating-ML Component

ISAC Candidate Recommendation for representing gating descriptions in flow cytometry

Introduction

Gating in flow cytometry is a well known and highly important process for selecting populations of interests by defining the characteristics of particles for further data acquisition or analysis. It may also be used for sorting purposes, e.g., for distinguishing among multiple heterogonous populations in a single sample.

The Gating-ML specification represents a proposal on how to form unambiguous XML-based gate definitions that may be used independently as well as included as one of the components of ACS. Such a description of gates can facilitate the interchange and validation of data between different software packages with the potential of significant increase of hardware and software interoperability. The specification supports rectangular gates in n dimensions (i.e., from one-dimensional range gates up to n-dimensional hyper-rectangular regions), polygon gates in two (and more) dimensions, ellipsoid gates in n dimensions, decision tree structures, and Boolean collections of any of the types of gates. Gates can be uniquely identified and may be ordered into a hierarchical structure to describe a gating strategy. Gates may be applied on parameters as in list mode data files (e.g., FCS files) or on transformed parameters as described by any explicit parameter transformation. Therefore, since version 1.5, parameter transformation and compensation description are included as part of the Gating-ML specification.

Document Status

Gating-ML has undergone several revisions since the first public release in February 2006. At this point, the International Society for Analytical Cytology (ISAC) Data Standards Task Force (ISAC DSTF) is satisfied that the specification serves its purpose, and has released it as a Candidate Recommendation to the ISAC membership and other interested parties. At this stage, third party implementations are encouraged and feedback from the community, especially implementors is welcome. While the specification may slightly change further in the future, significant features and design aspects will likely remain unchanged.

The content of the Gating-ML specification

This specification consists of the following parts:

• A PDF document providing a detailed description of the "Gating-ML" XML.
• The XML schemas (currently Gating-ML.v1.5.xsd, Transformations.v1.5.xsd, and DataTypes.v1.5.xsd), defining syntax of Gating-ML compliant files and usable to validate Gating-ML XML documents.
• Set of examples of Gating-ML XML files.
• User documentation on the XML schema (HTML and UML format).
• Set of informative Gating-ML software compliance tests.

Download

All the components of the specification are available for download in our download section at sourceforge.net.

The latest version of the text of the specification can also be downloaded from http://flowcyt.sourceforge.net/gating/latest.pdf.

The latest full version can also be downloaded from http://flowcyt.sourceforge.net/gating/latest.full.zip. (This does not include the compliance tests, which are only available in our download section at sourceforge.net.

Last update: June 10th, 2008