CellScape™ PSP
Knowledge Base

The CellScape PSP platform is an advanced spatial biology system designed for high-plex, quantitative spatial phenotyping at single-cell and subcellular resolution within formalin-fixed paraffin-embedded (FFPE) or fresh frozen (FF) samples. It integrates the highest-resolution spatial imaging, automated fluidics, and flexible assay chemistry to facilitate comprehensive spatial proteomics studies.

The CellScape PSP platform is ideal for studies requiring spatially resolved protein data with best-in-class resolution, including research in oncology, immunology, neuroscience, and infectious disease. Researchers use the CellScape PSP platform to analyze tissue architecture, cellular interactions, and disease microenvironments with subcellular precision. Its unmatched flexibility and modularity are well suited for custom assay development, and its straightforward and simple workflow make it highly valuable for biomarker validation following discovery studies.

The CellScape™ PSP platform is compatible with tissue samples from any species and supports both fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) formats. It uses a standard 75 mm x 25 mm glass microscope slide (frosted or unfrosted), making it easy to incorporate into existing workflows. With the Whole Slide Imaging Chamber (WSIC) technology, each slide is converted into a microfluidic device—enabling uniform reagent delivery and high-plex staining across the entire tissue section.

The CellScape PSP platform facilitates whole-slide imaging with an available imaging area of up to 710mm², facilitating the use of large tissue sections, tissue arrays, and tissue mircoarrays (TMAs).

Yes, the CellScape PSP platform supports whole-slide imaging.

Thanks to the gentle EpicIF workflow and filtered photobleaching, we’ve seen minimal issues with reduced marker detection in later staining rounds. To address any concerns about steric hindrance or epitope instability, we recommend placing “high-risk” markers in the earliest cycles.

The CellScape PSP platform can automate the sequential staining and imaging of up to four slides in a single run.

Yes, the CellScape PSP is offered through Canopy Multiomics Services. This service allows customers to outsource the entire workflow, including sample submission and prep, automated staining, high-plex imaging, and cell phenotyping. For more details or to initiate a project, you can visit our dedicated CellScape platform services page.

From sample input to data output, Bruker Spatial Biology offers world-class customer support to our customers. Our technical and customer support teams are trained to provide local and remote support from project conception to completion.

The CellScape PSP platform is designed and manufactured by Bruker Corporation, and it is distributed globally via Bruker Spatial Biology.

Yes, contact your local representative here to generate quantitative spatial phenotyping data from the CellScape platform via our Technology Access Program (TAP).

The CellScape PSP platform can stain up to four conjugated antibodies in a single cycle.

The CellScape PSP platform’s automated fluidics unit comes with 15 reservoirs, which hold cocktails of up to four antibodies each. This allows users to stain and analyze up to 60 markers in a single automated run.

If needed, users can swap out reservoirs to stain additional markers on the same sample. The platform also allows users to map defined reservoir groups to individual samples, facilitating the automated execution of distinct assay panels within a single run on the CellScape platform.

Yes, the CellScape PSP platform supports whole-slide imaging.

Yes, you can use your own antibodies with the CellScape PSP platform. The system is designed with flexibility in mind, allowing researchers to incorporate custom antibody panels tailored to their specific scientific questions. It supports the use of any commercially available, or custom-made antibody that has been directly conjugated to an organic fluorophore compatible with EpicIF technology, enabling users to readily adapt existing reagents or validated clones for use in multiplexed spatial experiments. This open approach eliminates the need for proprietary reagents and simplifies panel development, making it easier to maintain experimental continuity and take advantage of trusted antibody sources.

The CellScape PSP platform employs a straightforward workflow for antibody validation and multiplex assay design. If you’re familiar with techniques used in immunohistochemistry (IHC-P or IHC-IF), you’re likely familiar with ours! To validate your own antibodies for use on the CellScape PSP platform, it’s important to follow a systematic approach to ensure specificity, sensitivity, and reproducibility within your spatial assays. Our team has developed an optimized process to do this, which can be found in our Design and Validation Process Tech Note.

Yes, validated antibody panels are available for use with the CellScape PSP platform through our VistaPlex™ Multiplexing Assay Kits. These ready-to-use panels are designed to streamline the development of high-quality spatial proteomics assays by providing rigorously validated antibodies and optimized protocols. Each VistaPlex panel undergoes a thorough multi-step validation process that includes assessments of specificity, sensitivity, reproducibility, and suitability across a range of tissue types and experimental conditions. These panels are modular and can be used as-is or supplemented with additional user-validated antibodies, making them a flexible and reliable foundation for building customized spatial proteomics experiments on the CellScape platform.

The CellScape PSP platform is compatible with a wide range of organic fluorophores, offering flexibility in assay design and enabling high-plex spatial proteomics using the EpicIF™ imaging workflow. The system’s high dynamic range (HDR) imaging and enhanced photobleaching capabilities allow for clear, multiplexed detection of multiple biomarkers with minimal spectral overlap. The CellScape platform is optimized for use with most commercially available fluorophores across the visible spectrum, including commonly used dyes such as series, among others. For additional information about fluorophore compatibility, see the CellScape PSP platform User Manual.

The CellScape PSP platform supports multiple protein detection modalities, providing researchers with the flexibility to tailor spatial proteomic assays to a wide range of experimental needs. At its core, the platform leverages cyclic direct immunofluorescence that enables iterative staining, imaging, and photobleaching of fluorescently labeled antibodies. This method allows for high-plex detection of protein biomarkers on a single tissue section while preserving spatial context. In situ proximity ligation assays for interactome detection is also supported on the CellScape platform, deepening the understanding of the interplay between proteins in their native environment.

Yes, the CellScape platform can simultaneously detect both protein and RNA analytes on the same sample. Learn more about our RNA-FISH compatible mIF assay design in a recent AACR poster.

The CellScape PSP platform employs EpicIF (Enhanced Photobleaching in Cyclic Immunofluorescence) technology to remove fluorescence signals between imaging cycles. This process utilizes a proprietary reagent, the EpicIF solution, in conjunction with visible light to eliminate fluorescence signal gently and effectively from a wide range of organic fluorophores. The method is designed to preserve tissue integrity and epitope stability, allowing for multiple rounds of staining and imaging without compromising sample quality. Integrated into the platform’s automated fluidics system, EpicIF technology streamlines the workflow, enabling high-plex spatial proteomics experiments with expanded flexibility in antibody and fluorophore selection.

The CellScape PSP sample preparation workflow is straightforward, especially to researchers familiar with immunohistochemistry (IHC-P or IHC-Fr). It supports both fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tissues. For FF samples, 7 µm cryosections are mounted on slides, fixed using cold acetone and ethanol, and rinsed with wash buffer. FFPE samples are sectioned at 5 µm, deparaffinized through graded solvents, and undergo antigen retrieval at 95°C before a final buffer wash.

Prepared slides are assembled into Whole-Slide Imaging Chambers (WSICs) using the CellScape Slide Assembly Tool. Antibody working solutions are diluted, centrifuged, and optionally filtered. The CellScape system is then initialized, fluidics are primed, and samples are loaded for imaging. For more information about sample preparation, see the CellScape PSP platform User Manual.

The correct storage conditions for CellScape PSP reagents can be found throughout the CellScape PSP platform User Manual, particularly within the materials and reagent sections of each protocol. These conditions include room temperature, 4˚C, -20˚C and -80˚C. Always refer to the specific reagent’s section within the manual for temperature guidelines and handling best practices.

The CellScape PSP platform generates quantitative spatial proteomics data with best-in-class resolution from tissue sections using cyclic multiplexed immunofluorescence imaging. Each experiment produces multichannel whole-slide images capturing the spatial distribution and expression levels of protein biomarkers at single-cell and subcellular resolution. This includes fluorescence intensity data per marker, cell segmentation maps, and positional information for each cell across the tissue architecture.

Data outputs are saved in OME-TIFF format, compatible with a wide range of third-party image analysis tools. When using the EpicIF^™ workflow, the system also collects repeated imaging cycles from the same tissue section, enabling deep phenotyping through high-plex protein detection. The result is a rich dataset that supports detailed analyses of cell types, states, interactions, and spatial organization within the tissue microenvironment.

The CellScape PSP platform outputs image data in the OME-TIFF format, enabling compatibility with a variety of third-party image analysis and quantification tools. Image acquisition, assay design, and instrument automation are facilitated via the CellScape Navigator software, while downstream image analysis can be performed using a variety of open-source and commercial platforms.

Common image analysis tools for tasks such as image visualization and quantification include QuPath, HALO by Indica Labs, and Visiopharm. For advanced cell segmentation, deep learning-based pipelines such as StarDist, DeepCell, and Cellpose are often used, and these tools can identify cell boundaries, classify cell types, and quantify protein expression per cell across spatial coordinates.

Users can also analyze CellScape data using custom image analysis pipelines and open-access libraries available in R, MATLAB, and Python (e.g., Scanpy, Squidpy, Seurat) to conduct multidimensional data exploration, supervised and unsupervised clustering, neighborhood analysis, and other spatial analyses. The open data format and high-resolution output from the CellScape platform make it easy to tailor analysis workflows to specific research needs.

Yes, data from the CellScape PSP platform can be integrated with transcriptomic or genomic data to support multiomic analyses. The platform generates spatially resolved, high-plex protein expression data at single-cell resolution, which can complement transcriptomic datasets—such as bulk RNA-seq, single-cell RNA-seq, or spatial transcriptomics—by providing protein-level validation and insight into post-transcriptional regulation and cell signaling.

Because the CellScape platform outputs data in standard formats like OME-TIFF and provides quantitative fluorescence intensity measurements, these datasets can be aligned with other omics layers using computational tools and shared spatial coordinates. This allows researchers to map transcriptomic signatures to spatially defined cell phenotypes, investigate correlations between RNA and protein expression, or explore how genomic alterations influence the proteomic landscape within the tissue microenvironment.

Integration typically involves bioinformatics platforms which support multiomic data harmonization and spatial analysis. This cross-modal capability makes CellScape PSP a powerful tool for building comprehensive, spatially contextualized biological models.

Data produced from the CellScape PSP platform enables researchers to answer a wide range of spatial biology questions. With best-in-class resolution, users can identify and map diverse cell types and states based on protein expression and co-expression of various biomarkers, revealing how these populations are distinct and distributed across tissue compartments. The platform allows detailed analysis of spatial relationships, such as where specific cells reside relative to anatomical landmarks or how immune cells are positioned around tumor cells as well as their relative infiltration state. With its unmatched flexibility, researchers can also explore direct or inferred cell–cell interactions, uncovering potential communication between neighboring cell types. Additionally, CellScape PSP supports profiling of the tissue microenvironment, helping to characterize the cellular composition and heterogeneity of complex structures like tumors or inflamed tissues. The system also enables the detection of spatial gradients and zonation patterns—important for understanding processes like immune infiltration or tissue remodeling—and facilitates comparison of spatial architecture across disease states, treatment conditions, or time points. Altogether, CellScape PSP provides a powerful means to study not just what cells are present, but where and how they function within their native spatial context.

For additional analysis support, please contact your FAS at support.spatial@bruker.com.

We also offer outsourced data analysis as part of our Canopy Multiomics Service offering.