Flow Cytometry-Introduction, Principle, Using Procedure, Uses, and Keynotes


Flow cytometry is a powerful laboratory technique used in the fields of biology, medicine, and immunology to analyze and quantify various physical and chemical characteristics of cells and particles. It allows for the rapid and simultaneous measurement of multiple properties of individual cells as they flow in a fluid stream through a specialized instrument called a flow cytometer. Here’s an introduction to flow cytometry:

Principle of Flow Cytometry: At its core, flow cytometry relies on the principles of fluidics, optics, and fluorescence. The main steps of flow cytometry include:

  1. Sample Preparation: Cells or particles of interest are suspended in a liquid medium and labeled with fluorescent markers, often called fluorochromes. These markers can target specific cellular components, such as DNA, proteins, or cell surface receptors.
  2. Flowing the Sample: The prepared sample is injected into a flow cytometer, where it is forced through a narrow, focused stream of fluid (sheath fluid). This stream ensures that particles pass through the laser beam in single file.
  3. Laser Excitation: As cells or particles flow through the instrument, they pass through one or more laser beams. These lasers emit light at specific wavelengths that excite the fluorochromes bound to the cells. Each fluorochrome emits light at a different, characteristic wavelength when excited.
  4. Light Scatter and Fluorescence Detection: The flow cytometer measures two types of signals:
    • Forward Scatter (FSC): This measures the size of the cell or particle. Larger objects scatter more light and produce higher FSC signals.
    • Side Scatter (SSC): This measures the granularity or complexity of the cell. Structures within the cell, such as organelles, scatter light and produce higher SSC signals.
    • Fluorescence Emission: The fluorochromes emit light at specific wavelengths, which is captured by detectors. Multiple detectors are used to capture emissions from different fluorochromes.
  5. Data Analysis: The collected data is processed and analyzed by specialized software. The software can generate histograms, scatterplots, and other graphical representations of the data. Researchers can use these representations to identify and quantify different cell populations, measure expression levels of specific proteins, and more.

Applications of Flow Cytometry: It is a versatile tool with a wide range of applications, including:

  • Immunophenotyping: Identifying and characterizing immune cell populations.
  • Cell Cycle Analysis: Determining the stages of the cell cycle in proliferating cells.
  • Apoptosis Detection: Measuring programmed cell death.
  • Cell Sorting: Physically separating cells of interest based on their characteristics.
  • DNA Content Analysis: Determining ploidy and DNA content.
  • Intracellular Protein Analysis: Studying protein expression within cells.
  • Microbiology: Counting and characterizing bacteria and other microorganisms


The principle of flow cytometry is based on the simultaneous measurement of multiple physical and chemical properties of individual particles, typically cells, as they flow in a fluid stream through a specialized instrument called a flow cytometer. The main principles underlying flow cytometry include:

1. Fluidics:

  • Sample Preparation: Cells or particles of interest are suspended in a liquid medium and introduced into the flow cytometer as a single-cell suspension.
  • Hydrodynamic Focusing: The sample stream is directed into a narrow, focused core within a sheath fluid. This ensures that particles flow single file through the laser beam, enhancing measurement accuracy.

2. Light Interactions:

  • Laser Excitation: As cells or particles pass through the instrument, they intersect one or more laser beams. These lasers emit light at specific wavelengths, depending on their type (e.g., argon, helium-neon, or solid-state lasers).
  • Scattering of Light: When the laser beam interacts with a particle, two types of light scatter occur:
    • Forward Scatter (FSC): This measures the intensity of light scattered in the forward direction. It is proportional to the size of the particle.
    • Side Scatter (SSC): This measures the intensity of light scattered at an angle to the incident beam. It reflects the granularity and internal complexity of the particle. Structures within the particle, such as organelles, influence SSC.

3. Fluorescence Detection:

  • Fluorochrome Labeling: Cells or particles are often labeled with fluorescent markers called fluorochromes. These markers can target specific cellular components (e.g., DNA, proteins, or cell surface receptors) and emit fluorescence when excited by laser light.
  • Fluorescence Emission: Each fluorochrome emits light at specific wavelengths when excited by the laser. Multiple detectors capture these emissions, allowing the measurement of multiple parameters simultaneously.

4. Data Analysis:

  • Data Collection: The flow cytometer continuously records the FSC, SSC, and fluorescence signals as particles flow through the laser beams.
  • Data Processing: Specialized software processes the collected data, generating histograms, scatterplots, and other graphical representations.
  • Analysis: Researchers can identify and quantify different cell populations, measure protein expression levels, assess cell cycle stages, detect apoptosis, and more using the analyzed data.

Using Procedure

The procedure for using flow cytometry involves several steps, from sample preparation to data analysis. Here’s a general overview of the process:

1. Sample Preparation:

  • Obtain the biological sample (e.g., cells, tissues, or particles) and prepare it for analysis.
  • Ensure the sample is in a single-cell suspension. If necessary, dissociate tissues or cells and filter to remove clumps.
  • Label the cells or particles with fluorescent markers (fluorochromes) that target specific cellular components or proteins of interest.

2. Calibration and Setup:

  • Calibrate the flow cytometer using control beads or particles of known size and fluorescence intensity. This ensures accurate measurements.
  • Set up the instrument parameters, including laser wavelengths, photomultiplier tube (PMT) voltages, and compensation settings for multiple fluorochromes.

3. Instrument Start-Up:

  • Turn on the flow cytometer and allow it to stabilize.
  • Verify that the sheath fluid and waste containers are properly connected and that the flow cell is clean and free of air bubbles.

4. Sample Acquisition:

  • Load the sample into the flow cytometer. Ensure proper mixing and stability during acquisition.
  • Adjust the flow rate to optimize the event rate (number of analyzed particles per second) for accurate data collection. Avoid oversaturation.
  • Start data acquisition.

5. Laser Excitation and Light Scattering:

  • The sample flows through the laser beams in single file.
  • Lasers excite the fluorochromes, causing them to emit fluorescence.
  • Light scattering, including forward scatter (FSC) and side scatter (SSC), provides information about the size and granularity of the particles.

6. Fluorescence Detection:

  • Detectors capture the emitted fluorescence from the labeled cells or particles.
  • Each fluorochrome is detected at a specific wavelength, allowing for simultaneous measurement of multiple parameters.

7. Data Collection:

  • The flow cytometer records data for each analyzed particle, including FSC, SSC, and fluorescence intensity for each fluorochrome.
  • Data are typically collected in list mode, recording information about each particle individually.

8. Data Analysis:

  • Export the acquired data to analysis software (e.g., FlowJo, FCS Express, or BD FACSDiva).
  • Perform data gating, which involves defining populations of interest based on scatter and fluorescence characteristics.
  • Analyze populations for specific parameters, such as protein expression levels, cell cycle stages, or apoptosis.

9. Data Presentation:

  • Generate graphical representations of the data, including histograms, scatterplots, and density plots.
  • Prepare figures or reports for publication or further analysis.

10. Clean-Up: – After analysis, clean and maintain the flow cytometer according to the manufacturer’s instructions. – Dispose of samples and waste appropriately.


Flow cytometry is a versatile laboratory technique widely used in various fields of science and medicine due to its ability to provide quantitative and qualitative information about cells and particles at the single-cell level. Some of the primary uses of it include:

1. Immunophenotyping:

  • Cell Surface Marker Analysis: It is used to identify and quantify cell populations based on the expression of specific cell surface markers. This is crucial in immunology for characterizing immune cells, such as T cells, B cells, and various subsets.

2. Cell Cycle Analysis:

  • Flow cytometry helps researchers determine the phases of the cell cycle (G0/G1, S, G2/M) by measuring DNA content. This is essential for studying cell proliferation and identifying cells in different phases of growth.

3. Apoptosis Detection:

  • It can detect apoptotic cells based on changes in cell morphology, membrane integrity, and the presence of phosphatidylserine on the cell surface. It’s valuable for assessing programmed cell death.

4. Intracellular Protein Analysis:

  • Researchers use flow cytometry to measure intracellular protein expression. Cells are fixed, permeabilized, and stained with fluorochrome-labeled antibodies to assess protein levels.

5. Cell Viability and Cell Counting:

  • It can assess cell viability by using fluorescent dyes that indicate membrane integrity. It’s also used for precise cell counting and determining cell concentrations.

6. Cell Sorting:

  • Flow cytometers equipped with cell sorters can physically separate cells based on their characteristics. This is essential for isolating specific cell populations for further study.

7. Functional Assays:

  • Flow cytometry is used to assess the functional characteristics of cells, such as measuring calcium flux, reactive oxygen species production, and cytokine secretion.

8. Microbiology and Virology:

  • It can be used to analyze microorganisms, including bacteria and viruses. It’s employed in identifying and counting microbial populations.

9. Hematology:

  • In clinical settings, flow cytometry aids in diagnosing blood disorders, including leukemia and lymphoma, by analyzing blood cell populations and identifying abnormal cells.

10. Drug Screening and Pharmacology:

  • It is used to evaluate the effects of drugs on cell viability, proliferation, and signaling pathways. It’s crucial for drug development and toxicity testing.

11. Cancer Research:

  • Flow cytometry helps researchers study cancer cells, assess tumor heterogeneity, and investigate markers associated with cancer progression.

12. Marine Biology:

  • It is used in marine biology to analyze phytoplankton populations and study marine microorganisms.

13. Stem Cell Research:

  • Flow cytometry is employed to identify and isolate stem cell populations based on specific surface markers.

14. Environmental Science:

  • It is used in environmental studies to analyze particles in water, study microbial communities, and assess the health of ecosystems.

15. Quality Control in Biotechnology and Pharmaceuticals:

  • It plays a role in quality control processes for biopharmaceuticals, ensuring product consistency and purity.


Flow cytometry is a powerful analytical technique used in various fields, including immunology, cell biology, clinical diagnostics, and microbiology. Here are some keynotes on flow cytometry:

1. Single-Cell Analysis: It enables the analysis of individual cells within heterogeneous populations, providing detailed insights into cellular characteristics.

2. Multiparametric Analysis: Flow cytometers can measure multiple parameters simultaneously, including cell size, granularity, and fluorescence signals from various markers. This allows for comprehensive cell profiling.

3. Immunophenotyping: Flow cytometry is widely used to identify and quantify immune cell populations based on cell surface marker expression. It’s crucial for immunological research and clinical immunophenotyping.

4. DNA Content Analysis: It assesses the DNA content of cells, enabling cell cycle analysis and the detection of aneuploidy or abnormal DNA content.

5. Apoptosis Detection: The technique is valuable for detecting apoptotic cells by assessing changes in cell membrane integrity, mitochondrial function, or phosphatidylserine exposure.

6. Cell Sorting: Flow cytometers equipped with cell sorters can physically separate cells based on their characteristics, facilitating the isolation of specific cell populations.

7. Clinical Diagnostics: It is used in clinical laboratories for blood cell counting, immunophenotyping of leukemia and lymphoma, and assessing immune system function.

8. Microbiology and Virology: It aids in microbial analysis, such as bacteria and viruses, allowing for identification, counting, and characterization.

9. Drug Development: Flow cytometry plays a critical role in drug screening, toxicity testing, and studying the effects of drugs on cell function.

10. Marine Biology: Researchers use flow cytometry to study phytoplankton populations, marine microorganisms, and the health of aquatic ecosystems.

11. Stem Cell Research: It is instrumental in identifying and isolating stem cell populations based on specific surface markers.

12. Quality Control: It is employed in biotechnology and pharmaceutical industries for quality control of biopharmaceutical products, ensuring consistency and purity.

13. Research Tools: Flow cytometry is a fundamental tool for basic and translational research, providing essential data for scientific discoveries and advancements.

14. Data Analysis: Specialized software is used to analyze flow cytometry data, allowing researchers to define cell populations, measure marker expression, and generate graphical representations.

15. Continuous Advancements: Ongoing technological innovations continue to expand the capabilities of flow cytometry, making it an ever-evolving and essential technique in modern science.

Further Readings

“Flow Cytometry: Principles and Applications” by Alice Longobardi Givan: This comprehensive book covers the fundamental principles of flow cytometry, including instrumentation, data analysis, and various applications in biology and medicine.

2. “Flow Cytometry: A Basic Introduction” by Michael G. Ormerod: This introductory text provides a clear and concise overview of flow cytometry, making it a great starting point for beginners.

3. “Practical Flow Cytometry” by Howard M. Shapiro: This widely used textbook offers practical insights into flow cytometry techniques, data analysis, and applications, making it suitable for both novice and experienced users.

4. Online Courses: Many universities and organizations offer online courses and tutorials on flow cytometry. Check platforms like Coursera, edX, or your local academic institutions for available courses.

5. Flow Cytometry Journals: Journals like “Cytometry Part A” and “Cytometry Part B: Clinical Cytometry” regularly publish research articles and reviews related to flow cytometry.

6. Manufacturers’ Resources: Companies that produce flow cytometry instruments, such as BD Biosciences, Beckman Coulter, and Sony Biotechnology, often provide educational resources, webinars, and application notes on their websites.

7. Flow Cytometry Associations: Organizations like the International Society for Advancement of Cytometry (ISAC) offer resources, webinars, and conferences focused on flow cytometry.

8. Research Papers: To explore the latest advancements and applications of flow cytometry, consider reading research papers in scientific journals. Websites like PubMed can help you find relevant articles.

9. Flow Cytometry Core Facilities: If you have access to a flow cytometry core facility at an academic institution or research center, their staff may provide training and resources for users.

10. Hands-on Training: If possible, attend workshops or training sessions offered by flow cytometry experts and facilities. Practical experience is invaluable in mastering this technique.

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