Online resources

Cytometry Literature

• Journals and Articles
  • Cytometry Part A: a leading journal that publishes research articles and advancements in the field of cytometry, including innovative techniques and applications in flow cytometry.
  • OMIPs (Optimized Multicolor Immunophenotyping Panels) published in Cytometry Part A are standardized sets of reagents and protocols designed to ensure reliable and reproducible results, primarily for specific immunophenotyping applications.
  • Current Protocols in Cytometry: a reference guide that provides detailed, peer-reviewed protocols for conducting and optimizing flow cytometry experiments.
• Flow cytometry data repositories
  • FlowRepository contains FCS file datasets made accessible as part of MIFlowCyt reporting.

Publishing Flow Cytometry data

• Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) guidelines
  • MIFlowCyt is a standardized framework that ensures the comprehensive and consistent reporting of flow cytometry experiments, enhancing reproducibility and data sharing.
  • See Lee et al., 2008 Cytometry A
• Data presentation is a critical aspect to accurately reflect flow cytometry data
  • See this webinar for a good overview of how to present flow cytometry data.

E-Learning Platforms

• Online Courses on Flow Cytometry
  • BD's online flow cytometry course
• Webinars and Video Tutorials for Cytometry
  • iBiology has two excellent videos giving an overview of flow cytometry and imaging cytometry
    • Overview of flow cytometry 
    • Imaging cytometry 
  • Francis Crick Flow Cytometry Training 2020 
  • UChicago Flow
• Useful blogs
  • Oliver Burton’s Colibri Cytometry page has an excellent blog discussing many of the latest issues and literature in flow cytometry
  • The blog at Cheeky Scientist contains many good articles covering a wide range of cytometry topics
  • The blog from the Cytometry and Antibody Technology facility at the University of Chicago highlights the latest literature and many technical aspects of flow cytometry
• Podcasts
  • ChUG
  • Flow Stars

Spectral Flow Cytometry Resources

• Cytek Biosciences
• Thermo Fisher Scientific (Including Assays and Reagents)
• BioLegend (Including Spectral Analyser Information)
• Understanding high dimensional data
  • The rise of spectral cytometry has led to a large increase in the number of markers used in studies.
  • Overview of high dimensional flow cytometry
    • An excellent review article: Liechti et al., An updated guide for the perplexed: cytometry in the high-dimensional era. Nature Immunology. 2021
    • The current limits of panel design: Konecny et al., OMIP-102: 50-color phenotyping of the human immune system with in-depth assessment of T cells and dendritic cells . Cytometry A. 2024
    • Dimensionality reduction
      • Dimensionality reduction is crucial for flow cytometry as it simplifies the complex multi-dimensional data, enabling clearer visualization and interpretation of cellular characteristics and populations. Two of the most common algorithms are tSNE and UMAP, implemented in common flow cytometry analysis softwares.
        • tSNE
        • UMAP
  • Clustering algorithms
    • Cell clustering is vital for flow cytometry as it facilitates the identification and categorization of distinct cell populations within large, high-dimensional datasets.
    • One of the most commonly used clustering algorithms is FlowSOM.

Tissue Cytometry

• Tissue cytometry involves the measurement of cells in their tissue context, enabled at EXCC by our MACSima platform.
• An excellent showcase of this technology is found in Kinkhabwala et al., MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors. Sci Rep. 2022 Feb 3;12(1):1911. doi: 10.1038/s41598-022-05841-4.  

At EXCC, we can offer help with various data analysis pipelines. Email us at cytometry@exeter.ac.uk for more information.

Commercial software

• FlowJo
  • FlowJo is used for wide range of cytometry analysis.
  • See FlowJo University for help
  • Contact cytometry@exeter.ac.uk to arrange access to a seat.
• FCS Express
  • FCS Express is a powerful choice of software for routine analysis while the use of pipelines streamline high dimensional flow cytometry analysis.
  • See videos here for tutorials
  • Contact cytometry@exeter.ac.uk for information on how to use our shared licence.

Programming libraries

• Programmatic approaches allow advanced and automated cytometry analysis pipelines.
  • FlowCore in R
  • FlowKit in Python

Spectral Analysis Tools

• Fluorescence Spectral Viewers: help optimize panel design by visualizing and managing fluorochrome spectra overlap.
• • Biolegend spectral viewer
  • Cytek spectral viewer: recommended for users of the Aurora 
  • Fluorescent protein database 

Panel Building Tools

• Many companies can offer recommendations on panels, including Biolegend, BD and Cytek.
  • Contact cytometry@exeter.ac.uk for rep details.
• Websites with good panel builders include:
  • FluoroFinder
  • Bio-Rad
  • Biolegend
  • Thermofisher

Reagent and Equipment Suppliers

Contact cytometry@exeter.ac.uk for rep details for the following companies:

• BioLegend
• BD Biosciences
• Thermo Fisher Scientific
• Cytek Biosciences
• Beckman Coulter
• Abcam
• Proteintech
• Miltenyi

Flow cytometry societies

• International Society for the Advancement of Cytometry - a professional organisation for cytometrists. ISAC hosts conferences, and provides resources, data standards, and online education.
• Royal Microscopical Society - supports research and teaching in microscopy, imaging and cytometry. 

Forums

• The r/flowcytometry community on reddit is highly active
• The Flow Cytometry Discord is fairly active and gives a venue to discuss technical cytometry issues.

Mailing lists

• The Purdue mailing list is the most wide reaching communication tool for cytometrists, including  job adverts, the latest conferences and technical cytometry questions
  • Contact cytometry@exeter.ac.uk to be added.