3D Cell Culture & Analysis


In recent years 3D organotypic culture models and multicellular tumor spheroids have gained popularity as tools for research, drug discovery and toxicity studies. Several studies have shown the benefit of such models over 2D culture, and 3D cell cultures, microtissues, and organoids are increasingly being used to bridge the gap between 2D cell cultures and in vivo animal models.

3D cell models are more physiologically relevant than biochemical assays and 2D cell cultures, as they more closely represent the microenvironments, cell-to-cell interactions, and biological processes that occur in vivo. 3D cell models show a higher degree of morphological and functional differentiation – again, similar to in vivo cell characteristics.

PerkinElmer provides a portfolio of products for the preparation, imaging and analysis of 3D cell cultures with our best-in-class solutions, to help life science researchers begin to generate more physiologically relevant data that can power better-informed decisions.


Grow 3D cell culture with speciality microplates

Prepare 3D cell models with GrowDex hydrogels and speciality microplates.

GrowDex hydrogels enable reproducible, scalable and convenient animal-free 3D cell culture applications. GrowDex mimics the extracellular matrix and supports cell growth and differentiation, and can be used for 3D cell culture of spheroids and organoids, in personalized medicine, regenerative medicine, organ-on-a-chip models and more.

CellCarrier Spheroid ULA microplates enable the use of three-dimensional (3D) cell culture models for cell-based microplate assays. The unique Ultra-Low Attachment (ULA) surface promotes the formation of consistently round spheroids. The optically-clear, round bottom wells produces high-quality imaging results.

3D InSight™ Human Liver Microtissues from InSphero labeled imaged on the Operetta CLS system
3D InSight™ Human Liver Microtissues from InSphero labeled imaged on the Operetta CLS system

Detect with sensitive detection and high-content imaging solutions

Detect with sensitive detection and high-content imaging solutions

Our multimode microplate readers and high-content analysis systems, plus innovative reagents, provide you with highly sensitive solutions for 3D cell culture imaging and detection.

Due to their size, 3D cell models and tissues pose characteristic challenges to any imaging system but benefit greatly from confocal imaging, as provided by both our Operetta® CLS and Opera Phenix® Plus high-content imaging systems.

As 3D samples are thick compared to the focal depth of the lens, spinning disk confocal systems perform better when the pinhole distance has been increased to minimize pinhole crosstalk, as is the case for the Opera Phenix Plus HCS system.

As 3D tissues are grown in aqueous media, the image quality is greatly improved when using water immersion lenses, which are available on both the Operetta CLS and Opera Phenix Plus systems.

During assay development, or prior to high-content imaging, with the EnSight multimode plate reader you can monitor the growth and health of your 3D cell cultures by measuring size, shape, and more using image cytometry. You can also combine imaging with other technologies such as AlphaLISA® to detect secreted proteins.

ATPlite 3D and ATPlite 1step 3D reagent kits for cell viability and proliferation provide a simple, robust protocol for ATP-content endpoint measurements of 3D spheroids.


Analyze with powerful and intuitive informatics solutions to uncover new insights

Our scientific software and informatics solutions give you the tools to optimize imaging of 3D cell models and then aggregate, search, mine, and visualize critical data - and turn it into actionable insights.

  • Turn data into understanding with the intuitive Harmony imaging and analysis software for the Opera Phenix Plus and Operetta CLS systems. You can accelerate 3D image acquisition and analysis, better understand spatial relationships, discover new perspectives not visible in 2D and measure volume and morphology in 3D. Optional PreciScan™ intelligent acquisition lets you pre-scan to locate your sample in the well for significantly reduced acquisition and analysis times.
  • Quickly process, analyze, share, and store the vast volumes of data generated by high-content screening and cellular imaging and get answers sooner with Signals Image Artist image analysis and management platform.
Products & Services (11)
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1-11 of 11 Products & Services

  • Operetta CLS high-content analysis system

    Operetta CLS High-Content Analysis System

    Uncover deep biological understanding in your everyday assays and innovative applications using the Operetta CLS high-content analysis system. Featuring a unique combination of technologies, the system delivers all the speed, sensitivity and resolution you need to reveal fine sub-cellular details. And with our simple, powerful Harmony 4.5 software, Operetta CLS lets you find even subtle phenotypic changes.
  • EnSight Multimode Plate Reader

    EnSight Multimode Plate Reader

    The EnSight® multimode plate reader offers HTS Alpha, Ultra-sensitive Luminescence and fast well-imaging technologies alongside conventional multimode detection technologies. Imaging & online data analysis is fast: a 384-well plate can be imaged in less than 5 mins. The system’s modular design, combined with workflow-based Kaleido data acquisition & analysis software, gives a truly versatile plate reader that gets users productive quickly.
  • GrowDase


    GrowDase enzyme breaks down GrowDex® hydrogel to form a solution in an easy one- step efficient cell recovery process. 3D cell structures such as spheroids, organoid or biopsies are retained with no impact on cell viability or functionality. Liberated cells can be used in gene or protein expression studies or for future experiments.

    Price Range : 136.00 USD - 179.00 USD
  • GrowDex


    GrowDex®-A is a ready to use, transparent hydrogel that has been specifically developed to bind different biotinylated molecules, whose presence may enhance cell culture conditions for specific 3D applications. GrowDex-A consists of avidin conjugated nanofibrillar cellulose which can be customized by binding different biotinylated molecules e.g. proteins or peptides, to create a cell specific matrix.  Ambient handling and shear thinning properties of GrowDex-A enable easy dispensing and use in automated systems.

    Price Range : 218.00 USD - 565.00 USD
  • GrowDex-T Hydrogel - 2.5 ml


    GrowDex®-T is an animal-free ready to use hydrogel that has been specifically developed to offer superior imaging properties, but without compromising on any of the advantages of the original hydrogel GrowDex. GrowDex-T can be mixed directly with cells and culture media, no gelation or cross-linking step required. Ambient handling and shear thinning properties of GrowDex-T enable easy dispensing and use in automated systems.

    Price Range : 193.00 USD - 506.00 USD
  • GrowDex


    GrowDex® is an animal-free hydrogel that enables complete control over the culture environment for cells.

    GrowDex can be used in a wide range of cell-based assays such as microscopic imaging or metabolic activity measurement. GrowDex has been validated on various cell models and applications including primary hepatocytes, patient derived cells, 3D organoid formation, hepatocyte toxicity, stem cell proliferation and differentiation, tumour cell migration and invasion, neurite outgrowth and network formation.

    Price Range : 155.00 USD - 373.00 USD
  • ATPlite 3D Kit

    ATPlite 3D, 300 assay point kit

    ATP-monitoring luminescence assay for quantitative evaluation of proliferation and cytotoxicity of mammalian cells cultured in 3D spheroids.
    List Price : 183.00 USD
  • ATPlite 1-step 3D kit

    ATPlite 1step 3D, 10 mL kit

    ATP-monitoring luminescence assay for quantitative evaluation of proliferation and cytotoxicity of mammalian cells cultured in 3D spheroids. The 1-step format only requires one addition step, and can be used for continuous processing.
    List Price : 93.00 USD
  • CellCarrier Spheroid ULA 96-well Microplates

    Round bottom, clear 96-well polystyrene microplates coated with Ultra Low Attachment (ULA) surface for 3D culture of mammalian cells. This ULA coating in round-bottom wells facilitates formation of round spheroids after incubating seeded cells.
    Price Range : 299.00 USD - 1254.00 USD
  • Harmony Software 1

    Harmony High-Content Imaging and Analysis Software

    Easily quantify complex cellular phenotypes with Harmony® high-content analysis software. Harmony software is designed for PerkinElmer high-content screening systems.
  • PreciScan_Software

    PreciScan Intelligent Acquisition

    Harness the power of intelligent image acquisition with PreciScan for more efficient high-content imaging and analysis. This optional plug-in for Harmony high-content analysis software enables you to more accurately target your object of interest for significantly reduced acquisition and analysis times, particularly valuable for 3D microtissue and rare event studies.
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