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Cell Imaging & Analysis

Acquire and analyze quantitative data for cell-based model applications

Cell imaging: Acquisition and analysis

Researchers have several options in methods for imaging cells, from phase-contrast microscopy that shows intact cells to fluorescent imaging of single molecules or organelles. Cellular analysis is performed to evaluate and measure the current state of cells, such as cell integrity, toxicity, and viability and various other research applications. An integral part of cellular analysis is data collection, analysis, and export into a meaningful and useful format.

Cellular analysis workflow

Protocols for culturing, plating, and maintaining cells will vary between different cell models however, the steps below outline a general workflow for cell-based imaging assays from upstream media prep through downstream experimental analysis using a high-content imaging system and cellular analysis software.




  1. Plate cells into labware of choice (chamber slides, dishes, microplates)
  2. Treat cells – Perform cell treatments with desired compounds if part of the assay workflow
  3. Stain for markers – If required, label cells with the desired fluorophores (fluorescent dyes, fluorescent protein – peptide fusions, etc.
  4. Acquire cell image – Place the plate into the cell imaging system and start acquiring your live cell images
  5. Analyze cell image – Use cellular imaging analysis software to run quantitative analysis of live cell images

Accelerate your screening with high-content and automated imaging

This technical webinar will focus on high-content screening applications such as those involved in viral research, neurite outgrowth studies, and organoid models. The information provided will apply to researchers currently working with cell-based assays and doing live-cell imaging, and those looking to automate and/or increase their current imaging workflow.

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Types of cellular imaging methods

Whether the demand is for a high-content and high-throughput or a simple-to-use system, our cellular imaging solutions can accommodate acquisition and analysis that suits the needs of a screening or research lab. Here, we’ve briefly described several methods in cellular imaging:

  • Phase-contrast microscopy shows intact cells
  • Fluorescent imaging can show single molecules or organelles
  • Brightfield microscopy is useful for visualizing whole cells rapidly
  • Confocal microscopy is preferred for high-quality images and 3D reconstruction of cells
  • 4D live-cell imaging combines confocal with time-lapse microscopy
  • Automated microscopy employs software and hardware features which ensure robust focus in every field-of-view combined with sophisticated image analysis software to generate repeatable and subjective quantitative data


Common cell-based assays and applications

Here, we’ve highlighted several cell-based assay topics from 3D cell cultures to stem cell research as well as applications for cardiomyocytes and toxicity screening.

  • 3D Cell Models

    3d Cell Models

    3D cell cultures offer the advantage of closely recapitulating aspects of human tissues including the architecture, cell organization, cell-cell and cell-matrix interactions, and more physiologically-relevant diffusion characteristics. Utilization of 3D cellular assays adds value to research and screening campaigns, spanning the translational gap between 2D cell cultures and whole-animal models. By reproducing important parameters of the in vivo environment, 3D models can provide unique insight into the behavior of stem cells and developing tissues in vitro.

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    Cancer Research

    Cancer Research

    Cancer researchers need tools that enable them to more easily study the complex and often poorly understood interactions between cancerous cells and their environment, and to identify points of therapeutic intervention. Learn about instrumentation and software that facilitate cancer research using, in many cases, biologically relevant 3D cellular models like spheroids, organoids, and organ-on-a-chip systems that simulate the in vivo environment of a tumor or organ.

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  • Cardiomyocytes


    Stem cells differentiated into cardiomyocytes are used to screen early for potential toxicological effects of drugs, thus helping to avoid investment in development of drugs which will fail in clinical trials due to cardiac toxicity.

    Cell Counting

    Cell Counting

    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.

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  • Cell Migration Assay

    Cell Migration Assay

    The movement or migration of cells is often measured in vitro to elucidate the mechanisms of various physiological activities such as wound healing or cancer cell metastasis. Cell migration assays may be conducted in a controlled environment using live cell timelapse imaging.

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    Cell Painting

    Cell Painting

    Cell Painting is a high-content, multiplexed image-based assay used for cytological profiling. In a Cell Painting assay, up to six fluorescent dyes are used to label different components of the cell including the nucleus, the endoplasmic reticulum, mitochondria, cytoskeleton, the Golgi apparatus, and RNA. The goal is to “paint” as much of the cell as possible to capture a representative image of the whole cell.

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  • COVID-19 and Infectious Disease Research

    COVID-19 and Infectious Disease Research

    Here we've addressed common applications in infectious disease research including cell line development, binding affinity, viral neutralization, viral titer and more with a focused effort on understanding the SARS-CoV-2 virus in order to develop potential therapies for COVID-19 including vaccines, therapeutics and diagnostics.

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    eBook: Cellular Imaging Insights

    Cellular imaging Insights

    Elucidating complex cellular pathways within 2D and 3D cellular structures in response to chemical stimulation or stress is the goal of many researchers. The capacity to which scientists have access to and can adopt emerging cellular imaging and analysis technology fuels their level of understanding.

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  • Live Cell Imaging

    Live Cell Imaging

    Live cell imaging is the study of cellular structure and function in living cells via microscopy. It enables the visualization and quantitation of dynamic cellular processes in real time. Live cell imaging encompasses a broad range of topics and biological applications—whether it is performing long-term kinetic assays or fluorescently labeling live cells.

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    Neurite Outgrowth / Neurite Tracing

    Neurite Outgrowth

    Neurons create connections via extensions of their cellular body called processes. This biological phenomenon is referred to as neurite outgrowth. Understanding the signaling mechanisms driving neurite outgrowth provides valuable insight into neurotoxic responses, compound screening, and for interpreting factors influencing neural regeneration. Using the ImageXpress Micro system in combination with MetaXpress Image Analysis Software automated neurite outgrowth imaging and analysis is possible for slide or microplate-based cellular assays.

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  • Stem Cell Research

    Stem Cell Research

    Pluripotent stem cells can be used for studies in developmental biology or differentiated as a source for organ-specific cells and used for live or fixed cell-based assays on slides or in multi-well plates. The ImageXpress system has utility in all parts of the stem cell researcher’s workflow, from tracking differentiation, to quality control, to measuring functionality of specific cell types.

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    Toxicity Screening

    Toxicity Screening

    Screening for off-target or toxic effects is very important during the development of new drugs and for the extension of the therapeutic potential of existing molecules. ImageXpress systems are fully integrated hardware and software platforms for automated acquisition and analysis of images for high-throughput cell-based cytotoxicity testing. Configured with optional environmental control, living cell responses or kinetic reactions can be monitored in real time for several days.

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Resources of Cellular Imaging

Videos & Webinars

Transitioning high-content assays to 3D: Scientific opportunities and imaging challenges

Gain deeper insights into cellular 3D structures with water immersion objectives

Accelerate your screening with high-content and automated imaging

ImageXpress Pico Automated Imaging

ImageXpress Pico Automated Imaging System Virtual Tour

 ImageXpress Micro Confocal Virtual Tour

ImageXpress Micro Confocal Virtual Tour

ImageXpress Nano High Content

ImageXpress Nano High-Content Imaging System Virtual Tour

Image analysis on ImageXpress Micro Confocal using MetaXpress

Basic workflow from image acquisition to analysis on the ImageXpress Micro Confocal using MetaXpress

Automated Imaging and You – Quantitative microscopy for every lab, Powerful data for all

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