How many markers/targets can be detected using the 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.

Are the channels spectrally separated, or is spectral unmixing required? Is post-processing necessary?

The system supports a broad set of recommended reagents and fluorophores that align with the built-in filter sets. When using an optimized assay with balanced signal intensities between neighboring channels, channel crosstalk is minimal, typically around 4%. If needed, integrated spectral unmixing can be applied as an automated post-processing step, further refining signal clarity without additional user effort.

What is the speed and throughput of the Axioscan 7 spatial biology?

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.

Can I upgrade my Axioscan Z.1 or Axioscan7 to the Axioscan 7 spatial biology?

If you're using an Axioscan 7, an upgrade to the Spatial Biology configuration is possible. An upgrade path from Axioscan Z.1 is not available. For more details on how we can support your transition, please contact your local ZEISS sales and support team.

Are the antibody staining steps performed on the instrument?

No, antibody staining is performed off-instrument. Depending on the assay system, the entire panel can be stained at once or in multiple rounds, either manually or using an automated stainer, prior to scanning with the Axioscan 7 Spatial Biology system.

Can I run multiple samples, assay types, and panels in the same run?

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.

What is the recommended tissue thickness for scanning on the Axioscan 7 spatial biology?

We recommend a tissue thickness of 2–10 μm for optimal scanning. However, for thicker sections, the system supports Z-stack imaging to capture multiple focal planes, ensuring high-quality data acquisition. The recommended thickness for having optimal results with the data analysis algorithm is 2-5 μm.

Does the user need prior microscopy experience or special training to operate the software and Axioscan 7 spatial biology?

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.

How can an operator use the scanner without prior training?

The system includes a library of pre-optimized scan profiles for assays from supported reagent providers, stored in its database. By integrating with the user's LIMS or lab book system, the Axioscan automatically retrieves sample information, including assay type, and applies the appropriate scan profile eliminating the need for manual setup or extensive training.

Can I create and run custom assays easily in SlideStream?

Yes. SlideStream includes a simplified feature for setting up custom assays, allowing users to quickly define scan and analysis settings without complex configurations. This enables flexible adaptation to new assays while keeping the workflow efficient and user-friendly.

What happens if I do not have any LIMS or digital lab book system? Can I still easily operate the system?

Yes, you can import a simple CSV file containing sample names and assay type information, which can be uploaded to the system for seamless operation. Alternatively, you can manually enter sample details directly in the software interface and select the appropriate assay to start the scan.

How is the connection between LIMS and the Axioscan 7 enabled?

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.

What are the minimum technical requirements to use the system?

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.

How is data transferred from the scanner to the Image Management System (IMS)?

Through the SlideStream workflow, images are automatically uploaded to the customer-specific cloud server instance as soon as scanning is complete. Once uploaded, they are immediately accessible for review in the mIF IMS. An active internet connection is required for the scanner to enable this seamless data transfer.

Can I use the Mindpeak IMS and AI without a browser?

No, the IMS is browser-based and requires a browser to access its interface. However, it is possible to install a local, non-cloud deployment option that still uses the browser but operates entirely within the customer’s network. In this setup, our dockerized AI models are installed on-premises, ensuring that image and result data remain fully contained within the local infrastructure. Please contact us to discuss further details on the process.

Can I use Mindpeak’s IMS and AI workflow as a standalone platform without SlideStream?

Currently, a standalone version without ZEISS SlideStream is not available. However, we’re actively exploring this option. In the meantime, we offer customized integrations with existing IMS platforms. These can range from shallow integrations, launching results in a separate Mindpeak IMS browser window—to deep integrations where results are directly embedded into third-party IMS viewers. Our experience from partnering with 16 IMS providers, including Paige, Sectra, Philips, and Proscia, supports seamless integration into mIF workflows.

Can mindpeak be deployed locally on a customer’s server?

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.

How does the algorithm identify cells?

Cells are detected by the foundation model based on the nuclear counterstain input, e.g. DAPI and each individual marker channel. In contrast to non-AI based methods, the cell detection is based on the visible morphology of the cells, making those solutions very robust. Foundational AI models are based on 10.000s of images and millions of data points across many different markers and tissue types and allow the detection of similar markers without further training.

What is the storage limit of mindpeak IMS?

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.

What are the internet speed and web browser requirements?

We recommend an internet connection of 100 Mbit/s or higher, with 1 Gbit/s ideal for smoother performance, especially when working with large images or in multi-user environments. For the best experience, use Google Chrome (version 120 or higher).

What level of security is provided for storing data on the cloud? How can I trust that my data remains private?

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.

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.

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

Unlock the Power of Spatial Biology

Spatial biology enables detailed analysis of cell presence, abundance, spatial distribution, and cell-to-cell interactions within the native tissue microenvironment. By leveraging multiplex immunofluorescence (mIF) staining with multiple biomarkers, it goes beyond traditional methods, allowing simultaneous visualization and quantification of numerous proteins within a single tissue section.

This powerful approach provides in-depth insights into complex biological processes, such as immune cell infiltration in tumors, pathogen-host interactions, inflammatory responses, metabolic dysregulation, and neuroimmune communication. Spatial biology is driving innovation across fields like immuno-oncology, infectious disease research, neurology, metabolic and cardiovascular health, and regenerative medicine, paving the way for more precise and predictive diagnostics.

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

Enabling Efficient, Reproducible Multiplex Spatial Profiling at Scale

Are you a translational, immuno-oncology researcher or service laboratory looking for a comprehensive solution that enables you to work at high throughput while ensuring accurate and reproducible data? The ZEISS tissue multiplexing workflow for biopharma, Academic Medical Centers and CROs enables routine histopathology laboratories with no prior experience of spatial biology methods to deliver rich biomarker data with high consistency across large cohorts.

Benefit from the efficiency of this tissue multiplexing workflow in your large cohorts, even under tight deadlines. Standardized methods allow you to conduct multi-site clinical trials with consistency over time, ensuring reproducible and consistent results. In addition, our solution streamlines data analysis and reporting, making it easier to evaluate multiple parameters and gain actionable insights.

End-to-End Spatial Biology Workflow Starter Bundle

Seamless Sample to Report Experience

Staining 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

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.

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Spatial Biology Imaging Systems

Unlock the Power of Spatial Biology

Enabling Efficient, Reproducible Multiplex Spatial Profiling at Scale

End-to-End Spatial Biology Workflow Starter Bundle

Reagents - Tailored for Tissue Multiplex Staining¹

Transform Your Research Today

Get a Consultation

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Download White Paper

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Spatial Biology Imaging Systems

Unlock the Power of Spatial Biology

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Enabling Efficient, Reproducible Multiplex Spatial Profiling at Scale

End-to-End Spatial Biology Workflow Starter Bundle ​

Reagents - Tailored for Tissue Multiplex Staining1

Transform Your Research Today

Get a Consultation

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Download White Paper

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Download the Product Flyer

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End-to-End Spatial Biology Workflow Starter Bundle

Reagents - Tailored for Tissue Multiplex Staining¹