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Cleared spheroid of a co-culture of HCT-116-GFP (colon cancer) / NIH-3T3-RFP (fibroblasts) cells stained with Hoechst for nuclei.
Sample courtesy of InSphero AG. Schlieren, Switzerland Sample courtesy of InSphero AG. Schlieren, Switzerland
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Organoids Research

Streamline organoid analysis and spheroid screening with high-content 3D imaging solutions for faster research outcomes

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Overcome 3D Cell Culture Imaging Challenges with Advanced Organoid Solutions Traditional imaging approaches struggle with the complex 3D architecture of organoids and spheroids, limiting throughput and compromising data quality in drug discovery workflows. ZEISS advanced imaging systems solve these challenges by delivering high-resolution 3D visualization, gentle live-cell monitoring, and automated high-content screening capabilities that accelerate your research from disease modeling to therapeutic development. Transform your organoid workflows with imaging solutions designed specifically for the unique demands of 3D cell culture research.
  • High-Resolution 3D Cell Culture Imaging

    Visualize complex organoid and spheroid structures with exceptional detail, enabling precise analysis of cell organization, lumen formation, and tissue morphology critical for disease modeling and drug discovery applications.

  •
    Gentle Live-Cell Monitoring for Dynamic Studies

    Track growth, differentiation, morphogenesis, and drug responses in real-time without phototoxicity, preserving organoid viability for extended time-lapse studies essential for therapeutic development.

  •
    Automated High-Throughput 3D Analysis

    Scale your organoid screening workflows with automated image acquisition and quantitative analysis, accelerating drug discovery timelines and reducing manual intervention for consistent, reproducible results.

Comprehensive 3D Imaging Solutions for Organoid Screening & Analysis

ZEISS arivis Pro Software

Analysis tools tailored for organoid research, including segmentation, quantification, and tracking of cellular dynamics

ZEISS Celldiscoverer 7

High-resolution imaging and advanced analysis capabilities that enable detailed exploration of organoid development, cellular interactions, and functional studies in real-time

ZEISS LSM Lightfield 4D

Accelerate 3D Imaging and Screening of Colorectal Cancer Models for Enhanced Drug Response Analysis and Cellular Interactions

ZEISS Lightsheet 7

Explore the complexities of neuronal morphology in 3D

ZEISS LSM 990

Acquire multiple images simultaneously, reducing acquisition time and preserving sample integrity

ZEISS arivis software has allowed us to extract crucial insights from our high-content imaging experiments, leading to better-informed decisions in drug discovery and development.

Marta da Silva, PhD Senior Scientist, Charles River Laboratories

Related Applications for Organoid Research

Recommended Products for Organoid Research

  • Instant Volumetric High-Speed Imaging of Living Organisms

    LSM Lightfield 4D

    ZEISS Lightfield 4D significantly enhances organoid research by enabling rapid 3D imaging of organoids at a rate of several per second, which dramatically increases throughput for screening large sample sets.

    Explore the LSM Lightfield 4D

    Product features

    • Capture intricate structural details of organoids, enabling in-depth studies of cellular architecture and interactions within complex biological systems
    • Support a wide range of applications in cancer research, from understanding tumor behavior to investigating immune cell interactions, driving advancements in treatment strategies
    • Enhanced drug response studies
    • Detailed structural analysis

  • Adaptable Automation for Advanced Workflows

    ZEISS Celldiscoverer 7

    ZEISS Celldiscoverer 7 is designed for high-throughput, automated imaging, which significantly enhances productivity in organoid research. Researchers can set up experiments to image multiple organoid samples without manual intervention, saving time and reducing the potential for human error.

    Explore the Celldiscoverer 7

    Product Features

    • High resolution imaging
    • Live cell imaging, enabling researchers to monitor dynamic processes within organoids over time
    • Advanced environmental control features, such as temperature, CO2, and humidity

  • Light-Sheet Multiview Imaging of Living and Cleared Specimens

    ZEISS Lightsheet 7

    ZEISS Lightsheet 7 offers advanced light-sheet fluorescence microscopy, providing high-speed, high-resolution imaging with minimal phototoxicity, making it ideal for live organoid studies. Its large field of view and multicolor imaging capabilities enable detailed visualization of complex cellular interactions and structures within organoids.

    Explore the Lightsheet 7

    Product features

    • Large fields of view
    • Label and visualize multiple targets within the same organoid sample
    • High speed spatial resolution
    • 3D imaging and reconstruction
    • Reduced background noise

  • Fast Optical Sectioning of Developing Organisms and Tissue Microstructures

    Lattice SIM 3

    Lattice SIM 3 provides super-resolution imaging capabilities, allowing researchers to achieve resolutions beyond the diffraction limit of light. This is crucial for organoid research, where understanding the fine details of cellular structures and interactions is essential for elucidating biological functions.

    Explore the Lattice SIM 3

    Product Features

    • Fast imaging speed
    • High-sensitivity detectors that enhance the signal-to-noise ratio.
    • Multicolor imaging
    • Versatile sample compatibility

  • Long-Term Volumetric Imaging of Living Cells

    ZEISS Lattice Lightsheet 7

    ZEISS Lattice Lightsheet 7 provides advanced lattice light-sheet microscopy, offering high-speed, high-resolution imaging with minimal phototoxicity, making it ideal for live organoid studies. Its capabilities for 3D imaging and reconstruction, along with multicolor imaging, enable detailed visualization of complex cellular interactions and structures within organoids.

    Explore the Lattice Lightsheet 7

    Product features

    • Compatible with a wide range of sample types
    • Environmental control features, such as temperature and CO2 regulation
    • Hghly efficient illumination with minimal phototoxicity and photobleaching
    • Accompanying software provides intuitive tools for image acquisition, processing, and analysis

  • Your Powerful Scientific Imaging Software

    ZEISS arivis Pro

    ZEISS arivis Pro is a powerful image analysis software that significantly supports organoid and spheroid research by providing advanced tools for quantitative analysis and visualization of complex biological structures. Its capabilities include automated segmentation, tracking, and measurement of organoid and spheroid features, enabling researchers to extract meaningful data on growth, morphology, and cellular interactions.

    Get a Quote or Buy Now

    Product features

    • Automated segmentation, tracking, and measurement of organoid features
    • Multichannel imaging data, allowing researchers to analyze multiple fluorescent markers simultaneously.
    • 3D visualization
    • High-throughput analysis
    Explore arivis Software
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  • High-performance Digital Slide Scanning Tailored to Your Application Needs

    ZEISS Axioscan 7
    Buy or Try the Stemi 508

    Whether your focus is spatial biology at scale, life science research, clinical applications or geology, the Axioscan 7 slide scanning microscope brings you advanced automation capabilities and exceptional image quality.

    Get a Quote or Buy Now
    Explore the Axioscan 7

  • Examine and Assess your Living Cells Quickly and Easily

    ZEISS Primovert
    Buy or Try the Primovert

    ZEISS Primovert is a compact and ergonomic inverted microscope designed for cell and tissue culture, offering high-quality long working distance phase contrast optics. Its user-friendly design and efficient LED illumination make it ideal for routine laboratory work and educational purposes.

    Get a Quote or Buy Now
    Explore the Primovert

  • Your Smart Microscope for Biomedical Routine and Research

    ZEISS Axioscope 5
    Buy or Try the Axioscope 5

    While working with Axioscope 5 all you have to do is focus and press Snap. You're done. This allows you to fully concentrate on analyzing and documenting your samples. You'll work more efficiently, save time and produce high contrast images with best image quality. What's more: this even works without any PC involved.

    Get a Quote or Buy Now
    Explore the Axioscope 5
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Configure your Axioscan 7 for Spatial Biology

Workflow automation for spatial biology at scale

The new Axioscan 7 Spatial Biology Configuration is designed to maximize efficiency, accuracy, and reproducibility for multiplex immunofluorescence (mIF) and high-throughput spatial biology workflows.

Configure your Axioscan 7 for Spatial Biology

Organoids Research FAQs

  • Organoids often exceed 200-500μm in thickness, making traditional confocal imaging challenging due to light scattering and phototoxicity concerns. ZEISS Lightsheet 7 and Lattice Lightsheet 7 systems provide gentle, rapid volume imaging with minimal photodamage, enabling extended time-lapse studies. The lightsheet approach illuminates only the focal plane being imaged, dramatically reducing photobleaching while maintaining exceptional image quality throughout the entire organoid volume.

  • ZEISS microscopes such as Celldiscoverer 7 and LSM 980 with Airyscan offer environmental control (CO₂, humidity, temperature) and sensitive detectors to ensure high-quality imaging with minimal phototoxicity, enabling researchers to monitor development and response to treatment in real time.

  • This requires balancing resolution with field of view - a common challenge in organoid research. The ZEISS LSM 990 Lightfield 4D provides enhanced sensitivity for deep confocal imaging, while Lattice SIM 3 offers super-resolution capabilities when subcellular detail is critical. For comprehensive workflows, arivis Pro enables seamless integration of multi-scale datasets, allowing you to correlate molecular-level events with tissue-scale organization patterns.

  • Core facilities need versatile platforms that can support everything from basic morphology to advanced live-cell imaging. ZEISS systems offer modular configurations - the LSM 990 can be equipped for routine organoid imaging and upgraded for specialized applications, while the Celldiscoverer 7 serves both screening and detailed analysis needs. arivis Pro provides consistent analysis workflows across different imaging modalities, reducing training overhead and ensuring reproducible results regardless of which system users choose..
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