PhenoCycler-Fusion System

The spatial architecture of tissue samples can strongly influence disease pathology, progression and treatment response. Several studies have outlined the importance of studying the spatial context of tumor samples to predict treatment response. The PhenoCycler-Fusion (CODEX) System performs comprehensive spatial phenotyping across whole slides to detect protein in situ at single-cell resolution. The system is part of an integrated spatial biology workflow including single-step tissue staining, image acquisition and on-board processing. It can analyze 50+ proteins with standard antibodies from a pre-designed or custom panel.

The PhenoImager Fusion microscope can function as a standalone ultrafast slide scanner ideal for standard throughput and high-plex spatial phenotyping applications. It has fluorescence and brightfield capabilities and can separate up to 7 colors with a resolution up to 0.25 um/pixel.

PhenoCycler Fusion













  • A comprehensive end-to-end solution containing the fluidics platform, assay reagents, and bioinformatics
  • Scalable and capable of imaging 6 biomarkers at high throughput to more than 50+ biomarkers per run
  • Isolates autofluorescence from tissue samples for more accurate and quantifiable imaging
  • Preserves the sample for downstream Region Of Interest (ROI) analysis and H&E staining

Tissue Types

  • Mouse Fresh Frozen
  • Human Fresh Frozen
  • Human FFPE
  • TMAs (tumor microarrays)

Sample Preparation and workflow:

Sections can be placed on standard, positively charged histology slides. Tissues must fit within the imageable area below.

PhenoCycler Fusion System 2





PhenoCycler Staining Workflow (50+ antibodies):

PhenoCycler Fusion System 3














PhenoCycler staining uses antibodies attached to a unique oligonucleotide barcode. All antibodies are stained in a single cocktail, and the automated system then adds 3 complementary reporters at a time with a fluorophore which specifically detects each unique antibody. The signals are revealed, imaged, and gently removed, and the process repeats until all the markers are imaged.

Akoya Resources

Technical resources: Tissue processing best practices, Tissue Staining procedure, molecular barcoding workflow, etc –

PCF Screened Antibody Database:

Explore interactive datasets:


Using the PhenoCycler-Fusion 2.0:

The first step is to contact the facility at and briefly describe the project. Next, we will schedule a meeting to discuss your needs, clarify the sample type, number, and antibody panel needed, and ask you to submit an order request on FBS.