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 Exeter 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 Exeter 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
- 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
- Webinars and Video Tutorials for Cytometry
- iBiology has two excellent videos giving an overview of flow cytometry and 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
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: KonecnyOMIP-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.
- 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
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:
Reagent and Equipment Suppliers
Contact cytometry@exeter.ac.uk for rep details for the following companies:
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.
