Spatial biology simplified

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 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.

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.

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.

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.

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.

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. 

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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).

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.

• https://d1.awsstatic.com/certifications/iso_27001_global_certification.pdf
• https://www.hetzner.com/assets/downloads/FOX-Zertifikat.pdf