CosMx™ Human 6K Discovery Panel

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Make the Leap to Single-Cell Spatial and Unlock Unprecedented Biology with 6000 Genes

Are you developing a single-cell atlas, identifying functional cell states, defining ligand-receptor interactome, characterizing tissue microenvironment phenotypes or doing biomarker discovery? If so, the CosMx™ 6K Discovery panel enables you to spatially analyze virtually the entire reactome at the single cell level and achieve breakthrough results.

Circular 'wheel' logo for CosMx 6K Human Discovery Panel

How it Works

Accelerate your single cell spatial transcriptomics with this fully validated, 6K plex RNA panel, with simple sample preparation, an easy-to-use and reliable spatial multiomics platform and streamlined data analysis.


Measure 6000 RNA targets

Profile the most significant genes across every biological pathway​ + over 400 ligand-receptor pairs. View gene list »


Best-in-class cell segmentation algorithms for spatial single cell analysis

Using a nuclear stain plus 4 protein markers for cell segmentation.


Confidence in data quality

Negative control targets.


Customize with up to 200 additional RNA targets


Cell Atlasing
Ligand-Receptor Interaction
Cell Typing
Biomarker Discovery
Cell Atlasing

Semi-supervised cell typing using Allen Human M1 Atlas

nb_clus #1 (motorClus20_custom_qc_2)

Novel clusters: Astro_2, L2.Neuron_1, Oligo_2, Oligo_3, e, pia.mater

Ligand-Receptor Interaction

Discovery of spatially co-expressed ligands in diverse types of cells in FFPE liver cancer

Cell Typing

Ligands Co-localization Identify Rare Cell Type in Human Brain: Sst Chodl neurons

Unsupervised clustering is performed on the correlation matrix of ligands’ neighborhood expression profiles to identify clusters of co-localized ligands. One ligand cluster consists of 3 ligands, SST, NPY, CORT, and shows strong correlation in their neighborhood expression profiles. The co-expression of those 3 ligands identify a rare cell type, Sst Chodl interneurons, in the dataset.

The igraph network built from the ligands’ correlation matrix, colored by the identified ligand clusters, showing how the same-cell ligand cascade identifies very rare cortical interneurons with long-range projections.
A depiction of the location of transcripts overlaid on top of morphology images with legends shown on the right. The heatmap shows the ensembled neighborhood expression for the chosen ligand cluster in space.

Biomarker Discovery

Plex does matter.

The utilization of the CosMx 6K Discovery Panel enables a more comprehensive analysis of Differential Expression and significantly enhances the potential for biomarker discovery. As shown across the two volcano plots, the CosMx 6K Discovery Panel identifies a larger number of statistically significant and biologically meaningful genes associated with Kidney cancer as compared to the CosMx Universal Cell Characterization (1K) Panel.

Why use CosMx 6K Discovery Panel over scRNA-seq?

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AACR 2024: Reveal spatial signatures of TME and oncogenic pathways using 6K plex single-cell spatial molecular imaging on FFPE tissue

Ultra High-Plex Single-Cell Spatial Multiomic Imaging of Human Brain Sections – AGBT 2024

A Universal 6,000-plex RNA Panel to Construct Comprehensive Single-Cell Spatial Atlases Across Multiple FFPE Human Tissues – AGBT 2024

Path to the holy grail of spatial biology: Spatial single-cell whole transcriptomes using 6000-plex spatial molecular imaging on FFPE tissue – AACR 2023

High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging

Resolving the spatial distribution of RNA and protein in tissues at subcellular resolution is a challenge in the field of spatial biology. We describe spatial molecular imaging, a system that measures RNAs and proteins in intact biological samples at subcellular resolution by performing multiple cycles of nucleic acid hybridization of fluorescent molecular barcodes.