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Open Access Highly Accessed Data Note

Flow cytometry data standards

Josef Spidlen1, Parisa Shooshtari12, Tobias R Kollmann3 and Ryan R Brinkman14*

Author affiliations

1 Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada

2 Department of Computer Science, University of British Columbia, Vancouver, BC, Canada

3 Division of Infectious & Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC Canada

4 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada

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Citation and License

BMC Research Notes 2011, 4:50  doi:10.1186/1756-0500-4-50

Published: 7 March 2011

Abstract

Background

Flow cytometry is a widely used analytical technique for examining microscopic particles, such as cells. The Flow Cytometry Standard (FCS) was developed in 1984 for storing flow data and it is supported by all instrument and third party software vendors. However, FCS does not capture the full scope of flow cytometry (FCM)-related data and metadata, and data standards have recently been developed to address this shortcoming.

Findings

The Data Standards Task Force (DSTF) of the International Society for the Advancement of Cytometry (ISAC) has developed several data standards to complement the raw data encoded in FCS files. Efforts started with the Minimum Information about a Flow Cytometry Experiment, a minimal data reporting standard of details necessary to include when publishing FCM experiments to facilitate third party understanding. MIFlowCyt is now being recommended to authors by publishers as part of manuscript submission, and manuscripts are being checked by reviewers and editors for compliance. Gating-ML was then introduced to capture gating descriptions - an essential part of FCM data analysis describing the selection of cell populations of interest. The Classification Results File Format was developed to accommodate results of the gating process, mostly within the context of automated clustering. Additionally, the Archival Cytometry Standard bundles data with all the other components describing experiments. Here, we introduce these recent standards and provide the very first example of how they can be used to report FCM data including analysis and results in a standardized, computationally exchangeable form.

Conclusions

Reporting standards and open file formats are essential for scientific collaboration and independent validation. The recently developed FCM data standards are now being incorporated into third party software tools and data repositories, which will ultimately facilitate understanding and data reuse.