Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Mar 7;4:50.
doi: 10.1186/1756-0500-4-50.

Flow Cytometry Data Standards

Free PMC article

Flow Cytometry Data Standards

Josef Spidlen et al. BMC Res Notes. .
Free PMC article


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.


Figure 1
Figure 1
Analytical pipeline captured in the provided ACS example file. The Figure shows an overview of the analytical pipeline captured in the ACS example file. The work flow is demonstrated by solid line arrows. Data files are preprocessed and manually gated for monocytes, dendritic cells (DCs, including myeloid and plasmacytoid subpopulations - mDCs and pDCs) and B cells, as well as additional novel populations whose roles in the immune response still need to be further investigated. The gating hierarchy (stored in Gating-ML files) is indicated by dashed line arrows. In parallel to this effort, the preprocessed FCS data files are fed to a clustering and cluster matching algorithm, which identifies monocytes, dendritic cells, B cells and additional subpopulations independently of the manual gating. The results of the automated and manual gating process are compared in order to determine the suitability of this automated analysis approach.

Similar articles

See all similar articles

Cited by 5 articles


    1. Murphy RF, Chused TM. A proposal for a flow cytometric data file standard. Cytometry Part A. 1984;5(5):553–555. doi: 10.1002/cyto.990050521. - DOI - PubMed
    1. Spidlen J, Moore W, Parks D, Goldberg M, Bray C, Bierre P, Gorombey P, Hyun B, Hubbard M, Lange S, Lefebvre R, Leif RR, Novo D, Ostruszka L, Treister A, Wood J, Murphy RF, Roederer M, Sudar D, Zigon R, Brinkman RR. Data File Standard for Flow Cytometry, Version FCS 3.1. Cytometry Part A. 2010;77:97–100. - PMC - PubMed
    1. Lee JA, Spidlen J, Boyce K, Cai J, Crosbie N, Dalphin M, Furlong J, Gasparetto M, Goldberg M, Goralczyk EM, Hyun B, Jansen K, Kollmann T, Kong M, Leif R, McWeeney S, Moloshok TD, Moore W, Nolan G, Nolan J, Nikolich-Zugich J, Parrish D, Purcell B, Qian Y, Selvaraj B, Smith C, Tchuvatkina O, Wertheimer A, Wilkinson P, Wilson C, Wood J, Zigon R, Scheuermann RH, Brinkman RR. MIFlowCyt: The minimum information about a flow cytometry experiment. Cytometry Part A. 2008;73A(10):926–930. doi: 10.1002/cyto.a.20623. - DOI - PMC - PubMed
    1. W3C. Extensible Markup Language. accessed January 2011.
    1. Spidlen J, Leif RC, Moore W, Roederer M, Brinkman RR. Gating-ML: XML-based Gating Descriptions in Flow Cytometry. Cytometry Part A. 2008;73(12):1151–1157. doi: 10.1002/cyto.a.20637. - DOI - PMC - PubMed

LinkOut - more resources