Cell Counting

Learn how to count cells using a variety of methods, techniques, and technologies




Cell Counting Methods and Techniques

Cell counting is fundamental and critical to numerous biological experiments. Assays such as drug compound toxicity, cell proliferation, and inhibition of cell division rely on the assessment of the number or density of cells in a well.

Assessing proliferation, cytotoxicity, or confluency using cell counting can be quickly accomplished with either brightfield or fluorescent imaging using automated imaging system, a cell counter and an analysis software.

  • Image Cytometry

    Image cytometry is a cell counting technique that combines low magnification microscopy with imaging and analysis tools. Image cytometry is useful for providing information on a broad range of cellular characteristics on a large population of cells in a single assay. Image cytometry can be used on unlabeled or fluorescently labeled cells and can be performed multiple times on a population to provide information about cellular dynamics over time.

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    Automated Cell Counter

    Cell counting with an automated imaging system can greatly speed up cell quantification while reducing manual labor and human errors. There are a variety of cell counting methods, such as label-free cell counting under transmitted light or detection of nuclear dye with fluorescent imaging.

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  • How to Detect Cytotoxicity in Cells

    Cytotoxicity is often measured in response to an experimental treatment or potential drug. Having a way to easily screen cytotoxicity in treated cells is critical to identifying new therapeutic treatments or understanding cellular signaling pathways that affect cell health. Common indicators of cytotoxicity include the ATP level in a cell population and integrity of cellular membranes, both of which can be measured using a variety of microplate-based assays.

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    How to Assess Cell Viability

    Cell viability can be assessed by examining parameters such as cell membrane integrity or the activity of cellular enzymes. On a microplate readers, these parameters can be detected using fluorescent reagents. For example, a red cell-impermeant, DNA-binding dye only stains dead or dying cells whose membranes are compromised, while a green live-cell dye only fluoresces when metabolic enzymes are active.

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  • How to Measure Cell Migration

    Cell migration, the movement of cells from one location to another, is a critical component of both normal and abnormal biological processes. The migration of unlabeled or fluorescently labeled cells from one area of a microplate well to another can be monitored using a cellular imaging system. Automated analysis software calculates the amount of cell migration in each well.

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    How to Calculate Transfection Efficiency

    Measuring transfection efficiency provides researchers with an early indication of their gene editing yield before using the modified cells for targeted assays. High quality images can be acquired with both the Transmitted Light and with a fluorescence channel indicating transfection of the cell. Image analysis software identifies and counts every cell plus scores them as GFP-positive or not. Afterwards, a transfection efficiency may be calculated from the ratio.

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  • How to Count Cells with Fluorescent Markers

    Image and analyze compound effects based on cells staining positive for different fluorescent markers. The consistent and statistically relevant quantitative analysis allows for the testing of multiple compounds at differing concentrations. Read the application note to learn more about the difference between cell counting using fluorescent or transmitted light imaging.

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    How to Count Cells with Transmitted Light

    Transmitted light segmentation (analysis) algorithms increase the accuracy of counting diverse cell types and are typically used to image unstained live or fixed cells. In addition to the standard cell counting methods for detecting fluorescent nuclei or cell bodies. Watch the video to learn how you can set up parameters to run transmitted light cell scoring.

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  • Cell Cycle Analysis

    Transition of a cell through the cell cycle can be monitored using fluorescently labeled cell cycle proteins that are cyclically expressed and degraded. FUCCI technology is based on the overexpression the cell cycle-dependent proteins geminin and Cdt1, respectively fused to a green fluorophore and a red fluorophore. Cdt1 levels peak in G1 phase, so cells in G1 appear green; geminin levels rise in late S, G2 and M phase, so cells in these phases appear red.

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Resources of Cell Counting

Videos and Demos

Transmitted light cell scoring on the ImageXpress Pico

Related Products & Services of Cell Counting

Automated cell counters, like the SpectraMax® i3x Multi-Mode Microplate Reader with SpectraMax MiniMax cytometer or the ImageXpress® Pico Automated Cell Imaging System, can assess proliferation, cytotoxicity, or confluency with either brightfield or fluorescent imaging.


SpectraMax i3x Multi-Mode Microplate Reader with SpectraMax MiniMax cytometer enables quick imaging and analysis of cells and gives you a front-row view of phenotypic changes that accompany cytotoxicity, cell proliferation, and protein expression. Our StainFree Cell counting Technology now includes fluorescent green and red detection channels and additional brightfield analysis features.


ImageXpress Pico Automated Cell Imaging System is an automated cell counter using transmitted light or fluorescent imaging to capture data-rich outputs such as nuclear size, total and average cell area, and intensity. In addition to the standard cell counting methods for detecting fluorescent nuclei or cell bodies, the software includes three additional protocols for counting cells in transmitted light based on cell size and shape.


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