The CellScape™ PSP Platform Knowledge Base

CellScape PSP Assays and Applications

SEE ALSO: CellScape PSP - Home CellScape PSP System CellScape PSP - Data Analysis

This Knowledge Base serves as a technical resource specifically to answer common questions and assist with troubleshooting; NanoU is the primary source for manuals, guides, and other documentation for CellScape PSP systems and products.

For additional assistance, email support.spatial@bruker.com.

Throughput is affected by numerous variables, such as number of total markers, markers per cycle, tissue type, and total scan area.

For researchers looking to increase throughput while maintaining single-cell resolution, see the below table for throughput examples using our FalconFAST™ Imaging mode, assuming an average of 4 markers per cycle, and an antibody incubation time of 1 hour for FFPE or 15 minutes for fresh frozen tissue:

 

Sample type Total markers Total scan area (mm2) Throughput
FFPE 25 81 12 hours
FFPE 50 81 23 hours
FFPE 25 200 16 hours
FFPE 50 200 29 hours
Fresh frozen 25 81 6 hours
Fresh frozen 50 81 11 hours
Fresh frozen 25 200 9 hours
Fresh frozen 50 200 17 hours

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, 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.

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 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.

Throughput is affected by numerous variables, such as number of total markers, markers per cycle, tissue type, and total scan area.

For researchers looking to increase throughput while maintaining single-cell resolution, see the below table for throughput examples using our FalconFAST™ Imaging mode, assuming an average of 4 markers per cycle, and an antibody incubation time of 1 hour for FFPE or 15 minutes for fresh frozen tissue:

 

Safety Data Sheets (SDSs) can be requested from support.spatial@bruker.com as needed.

Waste should be disposed of according to your facility’s waste disposal procedures.

Some customer-provided reagents, such as ethanol, xylene, and formalin may also be considered hazardous and should be stored and disposed of according to your facility’s procedures.

Always be sure to read, understand and maintain SDSs for all chemicals and reagents according to your facility’s requirements.

Yes, you can add additional antibodies to a sample that has already gone through the full CellScape PSP staining and imaging workflow. After an experiment, samples are typically stored within the assembled Whole-Slide Imaging Chamber (WSIC) filled with CellScape Storage Buffer at 4°C. Before restaining, inspect the chamber for complete adhesion and minimal air bubbles, and confirm that the sample remains properly aligned. Additional staining cycles can then be added using the same EpicIF™ workflow: apply new antibody working solutions, allow appropriate incubation, wash, image, and photobleach as needed. For best performance, reprocessing should be done within a reasonable timeframe after initial imaging and under proper storage conditions. Learn more in our blog post:  Data-driven Assay Expansion: Re-examine Multiplex Immunofluorescence Slides Based on Initial Staining Results

A typical run for a 40-plex panel on 100mm2 of FFPE tissue takes 31 hours. This is reduced to 18 hours when using our FalconFAST imaging mode.

Consumable Shelf-life from date of manufacture
EpicIF solution 1 year
Storage buffer 1 year
Wash buffer-500mL 2 years
Wash buffer-1L 2 years
Wash buffer-10x500mL 2 years
Whole slide imaging chamber 2 years