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番茄视频 Centre for Cytomics

Education

Cytometry: A Philosophy of Single-Cell Understanding

Cytometry includes a collection of tools for probing biology at the level of single cells. Cytometry enables researchers to uncover cellular heterogeneity, trace dynamic responses, and identify rare or transitional states that drive health and disease. At the 番茄视频 Centre for Cytomics, we embrace cytometry as a philosophy of precision, depth, and discovery. 

How Flow Cytometry Works

Flow cytometry operates by directing cells in a fluid stream through lasers, where each cell is individually illuminated and analysed in real time. Fluorescently labelled antibodies or dyes are used to detect specific proteins, cellular structures, or functional states. As each cell passes through the laser, detectors capture information on light scatter (revealing size and internal complexity) and fluorescence emission (indicating the presence and quantity of labelled targets). This high-throughput method allows researchers to measure multiple parameters from thousands of cells per second, making it ideal for both routine immunophenotyping and complex, multiparameter investigations.

What Is Cytomics?

Cytomics is the integration of cytometry with other omics disciplines, such as proteomics, transcriptomics, and metabolomics, to create a more comprehensive understanding of cellular systems. By linking phenotypic data from cytometry with molecular data from other platforms, cytomics enables deep, systems-level insights into cellular function and behaviour. At the 番茄视频 Centre for Cytomics, we foster collaboration across these domains to drive innovation in integrative single-cell biology.

Education at EXCC

We offer education, training, and support to help researchers navigate and harness the power of single-cell analysis. We run a basic flow cytometry course every 2 months, and offer hands-on training for our analysers. We are also involved in educational efforts across the cytometry community, and this year we are launching the GW4 Cytometry Computing Workshop.

Below, we have compiled a set of resources for understanding cytomics.

Cytometry Literature

  • Journals and Articles
    • : a leading journal that publishes research articles and advancements in the field of cytometry, including innovative techniques and applications in flow cytometry.
    • published in Cytometry Part A are standardized sets of reagents and protocols designed to ensure reliable and reproducible results, primarily for specific immunophenotyping applications.
    • : a reference guide that provides detailed, peer-reviewed protocols for conducting and optimizing flow cytometry experiments.
  • Flow cytometry data repositories
    • 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
  • Data presentation is a critical aspect to accurately reflect flow cytometry data
    • for a good overview of how to present flow cytometry data.

 

 

E-Learning Platforms

  • Online Courses on Flow Cytometry
  • Webinars and Video Tutorials for Cytometry
    • iBiology has two excellent videos giving an overview of flow cytometry and imaging cytometry
  • Useful blogs
    • has an excellent blog discussing many of the latest issues and literature in flow cytometry
    • The contains many good articles covering a wide range of cytometry topics
    • The at the University of Chicago highlights the latest literature and many technical aspects of flow cytometry
  • Podcasts

 

Spectral Flow Cytometry Resources

  • 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:
      • The current limits of panel design:
      • 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.
    • 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.

 

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:  

At EXCC, we can offer help with various data analysis pipelines. Email us at for more information.

Commercial software

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

Programming libraries

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

Spectral Analysis Tools

  • Fluorescence Spectral Viewers: help optimize panel design by visualizing and managing fluorochrome spectra overlap.
    • : recommended for users of the Aurora 

Panel Building Tools

  • Many companies can offer recommendations on panels, including Biolegend, BD and Cytek.
    • Contact  for rep details.
  • Websites with good panel builders include:

Reagent and Equipment Suppliers

Contact for rep details for the following companies:

Flow cytometry societies

  • - a professional organisation for cytometrists. ISAC hosts conferences, and provides resources, data standards, and online education.
  • - supports research and teaching in microscopy, imaging and cytometry. 

Forums

  • The community on reddit is highly active
  • The is fairly active and gives a venue to discuss technical cytometry issues.

Mailing lists

  • The is the most wide reaching communication tool for cytometrists, including  job adverts, the latest conferences and technical cytometry questions
    • Contact to be added.