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5 µm section of a formalin fixed paraffin-embedded mouse small intestine swiss roll. Section was stained with a 14 CODEX antibody panel designed to visualize intestinal stem and enteroendocrine cells (Lysozyme in red, villin in green, MHCII in gray, vimentin in cyan, Ki67 in magenta, and Olfm4 in yellow). Blue signals correspond to DAPI nuclear staining. Acquisition was done with a ZEISS Axio Observer microscope and processing with the Akoya CODEX Processor.
Courtesy of D. Bejarano, Life and Medical Sciences Institute (LIMES) of the University of Bonn, Germany Courtesy of D. Bejarano, Life and Medical Sciences Institute (LIMES) of the University of Bonn, Germany
Use Case

Tissue Imaging

Break through traditional imaging barriers with ZEISS solutions that combine deep penetration, minimal photodamage, and automated workflows for consistent results.

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Unlock Advanced Tissue Imaging Solutions ZEISS microscopy solutions empower researchers to image complex tissues and whole organs with exceptional clarity, speed, and scale. From deep 3D imaging of cleared samples to high-resolution multiplexed analysis and advanced spectral unmixing, ZEISS systems address key challenges in tissue microscopy—minimizing photodamage, enabling accurate marker separation, and delivering scalable data analysis. Whether you're studying development, disease, or spatial biology, ZEISS delivers the precision and performance to push your research further.

Enhancing Tissue Analysis

ZEISS arivis Pro

Precise 3D Visualization, Structural Interpretation, and Scalable Analysis of High-Resolution Datasets

ZEISS LSM 990 Spectral Multiplex

Spectral Unmixing and High Detector Coverage

ZEISS Lightsheet 7

Whole Organ Imaging in Cleared Tissue Microscopy

ZEISS Axioscan 7 Spatial Biology

Reproducible Multiplex Spatial Profiling at Scale

ZEISS LATTICE SIM + ELYRA 7

Super-Resolution, 3D Imaging, and Tissue Compatibility

  • Preserve structural detail without photodamage

    Fast, gentle 3D imaging of optically cleared tissues—such as whole brains, lungs, or kidneys.

    ZEISS Lightsheet 7 Applications
  • Enhanced sensitivity and resolution

    Visualize and separate up to 5+ markers—even in autofluorescent or challenging samples—supporting spatial biology, immunophenotyping, and detailed cellular mapping.

    ZEISS Spatial Biology Imaging Systems
  • Scalable analysis tools for large tissue datasets

    AI-driven segmentation, batch processing, and cloud collaboration to streamline analysis and insight generation.

    ZEISS Advanced Image Analysis
Courtesy of Ultivue, Inc.

New Dimensions in Tissue Imaging

ZEISS Spatial Biology Systems

From high-speed, high-resolution imaging and non-destructive 3D visualization, to real-time analysis, discover advanced microscopy techniques that capture both intricate and dynamic details of plant specimens.

  • Using ZEISS Axioscan, we can image whole tissue sections with up to 7 fluorophores. Combined with powerful software, this allows us to assess spatial phenotyping of tumor microenvironments and is now applied to a wide range of projects.

    Dr. Caroline Bouzin Facility Manager, 2IP Imaging Platform at the Institute of Experimental and Clinical Research at the UCLouvain, Brussels, Belgium

  • We would like to exploit the high dimensionality of multiplex tissue microscopy to study the diversity of myeloid cells in multiple tissues and identify non-described tissue-specific populations. There is so much we still don’t understand and we see great potential in leveraging such findings to eventually lead to new and better targeted treatments for multiple health conditions.

    Dr. David Bejarano Postdoctoral Researcher, Schlitzer Lab at the Life and Medical Sciences Institute (LIMES), University of Bonn, Germany

  • The light sheet microscope shows us extremely complex neural networks without spending hours trying to piece the images back together.

    Dr. Kent Willis University of Alabama at Birgminham, USA

Related Applications for Tissue Imaging

Recommended Products for Tissue Imaging

  • Scalable Multiplex Imaging for Routine Applications

    ZEISS Axioscan 7 Spatial Biology

    Load ZEISS Axioscan 7 spatial biology with 100 samples and scan them all in less than a day with unprecedented speed, fully automated and supported by AI-enabled tissue detection and high dynamic range imaging.

    Get a Quote or Buy Now

    Product features

    • Automated high-speed scanning
    • Digitize your slides with consistent quality across a variety of imaging modes
    • Reliable 24/7 operation
    Explore the Axioscan 7

  • Multi-Fluorescence Imaging for In-Depth Understanding of Spatial Biology

    ZEISS LSM 990 Spectral Multiplex

    LSM 990 Spectral Multiplex excels in the spectral separation of fluorescent labels. Optimize your advanced spectral multiplexing experiments with numerous protein markers and clear separation of fluorescence signals while reliably eliminating autofluorescence.

    Explore the LSM 990

    Product Features

    • Efficient spectral multiplexing
    • User-friendly experiment design
    • Workflow automation beyond imaging

  • Light-Sheet Multiview Imaging of Living and Cleared Specimens

    ZEISS Lightsheet 7

    ZEISS Lightsheet 7 is purpose-built for fast, gentle 3D imaging of large, optically cleared tissue samples and whole organs with subcellular resolution—ideal for researchers studying tissue architecture, organ development, and disease mechanisms at scale.

    Explore the Lightsheet 7

    Product features

    • Whole organ imaging
    • Tissue clearing workflows
    • Neural and vascular network mapping
    • Tumor invasion and metastasis visualization

  • Fast Optical Sectioning of Developing Organisms and Tissue Microstructures

    ZEISS Lattice SIM 3

    ZEISS Lattice SIM 3 is specifically designed to meet the imaging requirements of multicellular organisms and tissue sections. This system exploits the full potential of the SIM Apotome technology: fast optical sectioning at superior quality, large fields of view with access to smaller regions of interest, near-isotropic resolution, and the gentlest super-resolution imaging possible.

    Explore the Lattice SIM 3

    Product features

    • Capture entire model organisms and tissue sections
    • Acquire super-resolution images as fast and gentle as widefield images
    • Go from a large-field overview to the super-resolution details

  • Inverted Microscope Platform with AI Assisted Experiment Startup

    ZEISS Axio Observer

    ZEISS Axio Observer is your inverse platform for demanding multimodal imaging of living and fixed specimens. Combine Axio Observer with a wealth of technologies and refine it to support your experiments precisely.

    Explore the Axio Observer

    Product Features

    • Flexibility from widefield to super-resolution imaging
    • Unique guidance through your experiments
    • Efficient imaging thanks to a high degree of automation

  • 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.

    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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From Complexity to Clarity

Workflow Automation for Spatial Biology at Scale

ZEISS solutions for spatial biology facilitate the seamless integration of spatial profiling into your workflows, ensuring efficient and consistent multiplexed spatial profiling at scale.

Configure your Axioscan 7 Spatial Biology

ZEISS Lab Essentials

  • Your Greenough Stereo Microscope with 8:1 Zoom

    ZEISS Stemi 508
    Buy or Try the Stemi 508

    With the 8:1 zoom you bring up smallest details. Stemi 508 offers an ergonomic viewing angle of 35° - stay relaxed even after hours of work.

    Get a Quote or Buy Now

  • Your Smart Microscope for Biomedical Routine and Research

    ZEISS Axioscope 5
    Buy or Try the Axioscope 5

    Acquire four fluorescence channels with just one click. Camera settings such as white balanced are done automatically.

    Get a Quote or Buy Now

  • Examine and Assess your Living Cells Quickly and Easily

    ZEISS Primovert
    Buy or Try the Primovert

    Examine unstained cells in phase contrast and GFP-labeled cells in fluorescence contrast quickly and efficiently.

    Get a Quote or Buy Now
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Tissue Imaging FAQs

  • ZEISS Axioscan 7 creates high-resolution digital maps that can be registered with spatial omics data, while arivis Pro provides powerful tools for overlaying and analyzing multi-modal datasets. This combination enables seamless correlation between morphology and molecular profiles.

  • Yes. ZEISS LSM 990 with Airyscan and Spectral Multiplexing provides high-resolution imaging of multiple fluorescent markers, even in autofluorescent tissues. LSM 990 Spectral Multiplex covers a wavelength range from 380-900 nm and can separate 10 or more labels simultaneously.

  • The ZEISS Axioscan 7 is designed for high-throughput whole slide scanning in both brightfield and fluorescence. It's ideal for digitizing tissue libraries, supporting spatial omics workflows, and integrating with analysis platforms..

  • Yes. ZEISS Lattice Lightsheet 7 and Lightfield 4D systems allow for fast, long-term 4D imaging under physiological conditions with minimal phototoxicity. These are ideal for developmental biology, immune cell tracking, and organoid dynamics.

  • ZEISS arivis Pro and arivis Cloud provide scalable 3D/4D analysis for large datasets. You can segment, track, and quantify features like glomeruli, neurons, or vasculature—even across full organs or whole-slide images.

  • Lattice SIM 3 provides 120nm lateral resolution with structured illumination that works effectively in tissue samples. Unlike other super-resolution techniques, it maintains compatibility with standard fluorophores and provides excellent performance in scattering tissue environments.
Comprehensive Solutions and Capabilities

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Explore applications to discover tailored solutions for your unique laboratory needs and elevate your research capabilities.