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 Systems

From Complexity to Clarity: Workflow Automation at Scale

Turn complexity into clarity and enhance your research capabilities. ZEISS solutions for spatial biology facilitate the seamless integration of spatial profiling into your workflows, ensuring efficient and consistent multiplexed spatial profiling at scale. We accelerate research to better insights and transform the understanding of cellular systems to revolutionize pathology.

  • Seamless sample to report experience
  • Automated Whole Slide Imaging for consistent results
  • Advanced analysis software for insightful data interpretation

Workflow demos for biotech & pharma

Select the demo that suits your needs

  • Virtual demo: Personalized insights into ZEISS technology
  • Demo at ZMCC: Visit ZEISS Microscopy Customer Center (ZMCC)
  • Select your experience: Choose the demo that fits your schedule

Unlock the Power of Spatial Biology

Workflow Automation for Spatial Biology at Scale

  • Automated Spatial Biology at Scale

    ZEISS delivers automated mIF workflows to streamline biomarker discovery across large sample cohorts.

    ZEISS has introduced a powerful spatial biology solution centered on the Axioscan 7, enabling automated multiplex immunofluorescence imaging of up to eight biomarkers across 100 slides per run—ideal for high-throughput clinical research and drug development.

End-to-End Spatial Biology Workflow Starter

A Seamless Sample to Report Exprience

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​.

Imaging Axioscan 7 spatial biology

Optimized configuration with best performance for routine spatial biology proteomics workflows​

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.​

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​

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.

  • The seamless integration of reagents, Axioscan 7, SlideStream, and Mindpeak analytics offers an incredibly user-friendly and fully automated workflow. It has transformed the way we generate spatial phenotypic data; fast, reproducible, and scalable for our clinical research.

    Prof. Christoph Kuppe, MD, PhD University Clinic RWTH Aachen
  • A key bottleneck in any spatial biology project is whole-slide tissue scanning, which can lead to unplanned reviews and repeat imaging, making it difficult to predict delivery timelines and associated costs. ZEISS is addressing this challenge with an efficient and reproducible automated workflow that truly benefits CROs offering this service. I’m thrilled to be collaborating with ZEISS in advancing scanning technology and delivering superior outcomes for our clients.

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

Where Spatial Biology Matters

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
ZEISS spatial biology enables multiplex imaging to study tissue inflammation and autoimmune disease mechanisms with high precision and throughput.

Uncovering pathways and cell-types in inflammatory processes

Immuno-Oncology
ZEISS spatial biology solutions enable high-throughput, multiplex imaging to advance biomarker discovery in immuno-oncology research.

Evaluating immunotherapy effectiveness and tumor immune interactions

Infectious Disease and vaccines
ZEISS spatial biology solutions empower immunology research with high-resolution, multiplex imaging for deep immune profiling and tissue analysis.

Mapping immune responses to pathogens and vaccine efficacy

Other applications
ZEISS spatial biology supports multiplex imaging to advance tissue regeneration research with detailed cellular and molecular insights.

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

Metabolic diseases
ZEISS spatial biology tools support multiplex imaging and analysis to uncover tissue-level insights in metabolic disease research.

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

Neurology
ZEISS spatial biology solutions enable detailed multiplex imaging to explore neural tissue architecture and biomarkers in neurology research.

Exploring immune-neural interactions and their role in neurological disorders

Drug Development

  • Icon describing target validation

    Target Validation

    Confirms expression & spatial relevance of the target

  • Icon describing mechanism of action studies

    Mechanism of Action Studies

    Confirms how drugs work & their impact on tissue microenvironments

  • Icon describing drug efficacy & pharmacodynamics (PD) studies

    Drug Efficacy & Pharmacodynamics (PD) Studies

    Evaluates treatment effects at the tissue level

  • Icon describing toxicology & safety studies

    Toxicology & Safety Studies

    Detects off-target effects and potential toxicity risks

  • Icon describing predictive biomarkers for patient stratification

    Predictive Biomarkers for Patient Stratification

    Enables personalized medicine & companion diagnostics

  • Icon describing clinical trial monitoring & response assessment

    Clinical Trial Monitoring & Response Assessment

    Tracks drug efficacy & resistance mechanisms over time

  • project overview
  • project image overview ims
  • Image viewer with quality accepted
  • marker display and results qc
  • phenotypes
  • phenotypes zoom in
  • Screenshot of a Mindpeak landing page with a ZEISS projects overview
    Screenshot of a Mindpeak landing page with a ZEISS projects overview
  • Screenshot of a Mindpeak project image overview named mIF Tumor Screen
    Screenshot of a Mindpeak project image overview named mIF Tumor Screen
  • Screenshot of an image viewer in Mindpeak, showing image quality accepted
    Screenshot of an image viewer in Mindpeak, showing image quality accepted
  • Screenshot of an image viewer in Mindpeak, showing the marker display and the results
    Screenshot of an image viewer in Mindpeak, showing the marker display and the results
  • Screenshot of an image viewer in Mindpeak, showing phenotypes
    Screenshot of an image viewer in Mindpeak, showing phenotypes
  • Screenshot of an image viewer in Mindpeak, with phenotypes zoomed in
    Screenshot of an image viewer in Mindpeak, with phenotypes zoomed in

Mindpeak Cloud-Based Analysis Solutions for Highest Precision in Biomedical Research1

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.​

Reagents - Tailored for Tissue Multiplex Staining1

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:​

InSituPlex®
Massively parallel single-molecule amplification

  • Highly configurable multiplexed biomarker detection​
  • Pre-optimized, clinical-grade assay performance​
  • Fast and gentle high-throughput workflow

STARVUE™
Deep learning enabling faster image-to-insight​

  • Biomarker morphology and signal intensity-driven cell classification​
  • Highly scalable and adaptable image processing​
  • Enables precise accurate results faster at a lower cost

The integration of Ultivue’s assay solutions into the new ZEISS End-to-End workflow offering, put you on the fast track to generate accurate, reliable and reproducible data.

FAQs

Axioscan 7 Spatial Biology

  • The Axioscan 7 spatial biology can separate 8 fluorescence channels, currently supported by Kromnigon SpectraClick reagents. A typical panel could consist of 7 target markers plus DAPI. Supported fluorophores include DAPI, CFP, GFP, DsRed, Cy3, Cy5, Cy7 and fluorophores with similar spectral properties. Single round staining and single shot imaging can be done for 8-channels. For going to higher marker numbers (e.g. 14, 28, etc.) cyclic staining and imaging can be performed.

  • The physical slide capacity of the system is 100 slides (25 trays, 4 slides each). The system can image over 100 slides per day thanks to the high level of automation and high scan speed. 10 mm2 tissue area can be scanned in 3 to ~10 minutes pure scan time for 5- or 8-Plex respectively.

  • Yes. A single run can include up to 100 slides, each potentially containing multiple tissue sections or cores. Pre-configured scan profiles for mIF and chromogenic assay stained tissue can be selected per sample, allowing users to load and run diverse experiments in one batch, in a single automated workflow.

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.

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.

Contact Us

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