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5 μm FFPE section of mouse kidney simultaneously stained with 6 IF markers plus DAPI. Imaged on Axioscan 7 spatial biology for spatial omics applications
ZEISS Spatial Biology Solutions

Spatial Biology Imaging

From Complexity to Clarity: Workflow Automation at Scale

Unlock clarity in complexity and accelerate your spatial biology research. ZEISS solutions for spatial biology seamlessly integrate multiplexed tissue imaging and analysis into your workflows, enabling scalable, reproducible, and high-throughput spatial profiling. By visualizing cellular interactions in their native tissue context, our technologies empower researchers to gain deeper insights into disease mechanisms and transform the way pathology and translational science are approached.

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  • Seamless sample to report experience
  • Automated Whole Slide Imaging for consistent results
  • Advanced analysis software for insightful data interpretation
5 μm frozen section of mouse spleen simultaneously stained with 7 markers plus DAPI. Imaged on Axioscan 7 spatial biology for spatial transcriptomics analysis.
Inflammation and autoimmunity

Uncovering pathways and cell-types in inflammatory processes

Immuno-Oncology

Evaluating immunotherapy effectiveness and tumor immune interactions
Infectious Disease and vaccines

Mapping immune responses to pathogens and vaccine efficacy
Other applications

● Cardiovascular diseases
● Transplant, GVHD
● Regenerative medicine
● Gastrointestinal Diseases
Metabolic diseases

Investigating tissue-specific metabolic pathways and immune cell infiltration in conditions like diabetes and obesity
Neurology

Exploring immune-neural interactions and their role in neurological disorders
Automated multiplex immunofluorescence imaging of up to eight biomarkers across 100 slides per run—ideal for high-throughput clinical research and drug development.

Unlock the Power of Spatial Biology

Are you working in translational research, immuno-oncology, or a service lab seeking a high-throughput tissue imaging workflow that ensures accuracy and reproducibility across large cohorts?
The ZEISS tissue multiplexing workflow for biopharma, academic medical centers, and CROs scales spatial biology to routine histopathology settings. By integrating automated slide scanning, multiplex staining, and streamlined analysis, laboratories can generate rich biomarker data with high consistency and reproducibility across studies.


Standardized and automated methods ensure consistency across multi-site clinical studies and longitudinal projects. The workflow also streamlines analysis and reporting through integrated software, enabling researchers to evaluate multiple biomarkers simultaneously and translate data into actionable biological and clinical insights.

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See ZEISS Technology in Action

Request a demo tailored to your needs—whether virtual or in-person at the ZEISS Microscopy Customer Center.

Choose the experience that works best for you!

Schedule a Demo

End-to-End Spatial Biology Workflow Starter

A Seamless Sample to Report Experience
Diagram explaining the end-to-end spatial biology workflow starter bundle ​
Staining Ultivue 4-Plex T-Act Kit​
Image of Ultivue 4-Plex T-Act Kit​

Pre-optimized panel with verified reagent performance and superior staining protocol for best speed and ease-of-use​.
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Imaging Axioscan 7 spatial biology

Optimized configuration with best performance for routine spatial biology proteomics workflows​
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Imaging SlideStream annual license​
Screenshot of SlideStream, intuitive workflow manager software for scan and analysis automation

Streamlined, fully automated image acquisition experience, with seamless integration for Ultivue scan protocols and automated image transfer to mindpeak platform.​
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Analysis Mindpeak starter license​

- Includes access and Spatial Biology research platform, Image Viewer, Image Storage and Data Analysis Platform​

- AI-Powered Image Analysis Algorithms​

- 6 months , 0.5Tb , 25 images can be analyzed​
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Our Streamlined Spatial Biology Workflow

With our ZEISS Spatial Biology offering, we simplify high-throughput multiplex IF imaging and analysis making it robust, scalable, and accessible. Our seamless tissue multiplexing workflow aims to empower routine histopathology labs, including those with no prior spatial biology expertise, to generate comprehensive, reproducible biomarker data across large sample cohorts.​ By combining automation, optimized imaging, and AI-powered analysis, we pave the way for the translational adoption of spatial proteomics and the transition to clinical practice.​
  • Reagents

    Staining

    Ready-to-use and validated portfolio of reagents.
    Fluorescently labeled antibody reagents used for staining samples

    Our solution is compatible with a broad range of multiplex immunofluorescence reagents, giving users the flexibility to work with their preferred chemistries.​

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    Compatible assays:

    • Chromogenic protocols, e.g. H&E, IHC, mIHC
    • Fluorescence protocols, e.g. Ultivue in-situ-plex, Kromnigon StreptaClick Color/Precision
  • ZEISS Axioscan 7 Spatial Biology

    Imaging

    ZEISS optics built for routine spatial biology applications.
    High performance high-through slide scanner for fluorescence imaging

    Load the scanner with 100 samples and scan them in less than a day with unprecedented speed, fully automated and supported by AI-enabled tissue detection and high dynamic range imaging. Analyze up to eight biomarkers at the same time and generate highly reproducible data you can rely on. We offer complementary service solutions to integrate streamlined workflow solutions into pre-existing LIMS and IMS systems.​

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    Product features

    • Superior sensitivity, high dynamic range and fast multiplex IF imaging
    • High consistency via fluorescence intensity normalization for superior shading quality and image reproducibility across time and devices
    • Up to eight spectrally separated channels
    • Enhanced barcode recognition, AI-driven mIF tissue detection, and pre-defined scan profiles optimized for robust mIF and BF imaging​
    Explore the Axioscan 7
  • SlideStream

    Automation

    Intuitive workflow manager software

    Streamlined amd simplified user Interface optimized for routine user. The new assay manager allows for easy set-up of new imaging and analysis routines without the need for expert microscopy knowledge.

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    Product features

    • Automated based on slide barcodes and slide information
    • 1-click to effortlessly scan and analyze 100 slides
    • Service for laboratory information management system (LMS) integration
    • Customizable workflow and interfaces
    • Integration to Mindpeak AI-powered image analysis cloud platform
  • Mindpeak analysis

    Analysis

    Sample to report without the fuss.
    Mindpeak. AI-powered data analysis and image management platform

    Generate actionable insights from your images, using our new spatial biology platform for fast, scalable, and effortless multiplexed IF image data analysis.​

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    Product features

    • Cloud native 1-click automated tissue image analysis with maximum ease-of-use for user-independency​
    • Browser access to images and analysis - anywhere, anytime
    • Standardized reports with user defined phenotypes and QC-functions for image and result quality​
Explore all ZEISS Biopharma offerings

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

Compatibility with Leading Reagents

The system supports both DNA-barcoded multiplex immunofluorescence (mIF) and Tyramide Signal Amplification (TSA)-based chemistries. Researchers can also deploy a wide variety of fluorophores – spanning industry standards like OPAL™ dyes as well as next-generation TSA dyes from Spatomics – to achieve robust, high-resolution imaging in 8-plex assays and beyond. Compatible reagent solution leaders include:

  • InSituPlex

    Ultivue by Vizgen

  • SignalStar® mIHC

    Cell Signaling Technology

  • StreptaClick® TSA panels

    Kromnigon

Reagents - Tailored for Tissue Multiplex Staining

The starter bundle explicitly includes an OmniVUE™ reagents kit for “T-Act” biomarker analysis from Ultivue, including co-optimized StarVUE™ AI-analysis. At the heart of Ultivue are two technology platforms:​

SlideStream Inuitive Workflow Manager Software

Simplify the process of scanning, analyzing, and managing high-volume microscopy slides

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    ZEISS' SlideStream Assay Management Software, transforms multiplex imaging into a compatible, scalable, and reproducible spatial biology workflow.

  • ZEISS' spatial biology bundle has transformed the way we generate spatial phenotypic data for our clinical research.

    Prof. Christoph Kuppe, MD, PhD University Clinic RWTH Aachen

  • ZEISS is addressing a key bottleneck in whole-tissue scanning through their workflow and we are benefitting from the efficiency gain.

    Christopher Mills Senior Scientist, Concept Life Sciences (CRO in United Kingdom)

Elevate your multiplexing IF and IHC workflows with ZEISS Axioscan 7 for Spatial Biology combined with the power of Mindpeak, leaders in the field of digital pathology. Our new Spatial Biology analytics platform enables effortless transition to cloud-based image analysis—giving researchers remote access to their images, project organization tools, and automated AI-driven workflows. Powered by Mindpeak’s foundation AI models for advanced image analysis, the system delivers robust results and standardized reporting, without the need for expertise and efforts to adjust or develop algorithms, while still offering the flexibilities to analyze a growing set of common biomarkers used in oncology and immuno-oncology including customizable phenotype definitions for precision in biomedical assays.​

FAQs: Axioscan 7 Spatial Biology

FAQs: SlideStream Workflow Manager

  • No prior microscopy experience is required. The software and scanner are designed for ease of use, with an intuitive interface and automated workflows that enable any operator to run the system efficiently, with minimal or no training.

  • The Axioscan 7 connects to the LIMS by scanning QR codes or barcodes printed on the slide labels. The scanner reads the slides unique ID from the code on the sample, retrieves the required additional information from the LIMS, which will be used to automatically populate the SlideStream interface with the relevant details, streamlining the workflow and reducing the need to manually re-enter pre-existing data.

FAQs: Image Management System and data analysis platform

  • For optimal performance, we recommend using the latest version of Google Chrome, a stable internet connection with at least 10 Mbps bandwidth, and a computer running a current, up-to-date operating system. These requirements ensure smooth and responsive operation of the platform.

  • Yes, local deployment is possible. For customers handling large image volumes or requiring local data storage, Mindpeak offers hybrid deployment options. In this setup, data is stored on the customer’s server while processing is performed on Mindpeak’s secure cloud infrastructure, helping reduce storage costs while maintaining greater control over sensitive data.

  • Storage limitations are defined by the IT infrastructure of customers as defined in their purchased packages. Additional storage capacities can always be acquired ad hoc in alignment with customer needs and budget requirements.

  • We partner exclusively with ISO 27001-certified cloud providers, such as AWS and Hetzner, to ensure enterprise-grade data protection. All data is encrypted both at rest and in transit, and regular security audits are performed to safeguard your sensitive research. These measures ensure your data remains secure, private, and fully under your control.

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