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GeoMx®
Morphology Markers

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What are morphology markers?

Morphology explores the relationship between biological structures. Morphology markers help reveal the structural architecture of tissue and identify regions of interest (ROI).

With GeoMx DSP, fluorescently labeled antibodies and/or RNA probes can be used to inform the presence of anatomical structures, cell types, and compartments, which helps with the selection and segmentation of ROIs into distinct biological compartments for further high-plex digital profiling.

How it Works

 

GeoMx DSP’s fluorescent imaging system utilizes LEDs with filter sets centered on standard FITC, Cy3, Texas Red, and Cy5 channels. Users can stain FFPE, fresh frozen, or fixed frozen tissues with morphology markers to label tissue compartments and cell types and select regions of interest (ROI) based on the tissue biology. Using the integrated segmentation algorithm in DSP software, ROIs then may be automatically divided into discrete biological compartments or areas of illumination (AOI) for precise profiling and to answer specific biological questions.

Morphology Marker Information

NanoString Morphology Marker Kits
NanoString Qualified & Verified Markers
NanoString TAP Morphology Markers
Community Verified Morphology Markers
Third Party Morphology Markers
NanoString Morphology Marker Kits

NanoString Morphology Marker Kits

These morphology markers are commonly used to profile tumor and immune compartments or neuronal populations. These fluorescent dye-conjugated antibodies are validated for a diverse array of tissues and GeoMx assays across mouse and human tissues. These kits are utilized with a SYTO 13 nucleic acid stain kit. The Morphology Kit configuration files are used to auto-populate key target information on the GeoMx scan setup step and can be downloaded here.

NanoString Qualified & Verified Markers

NanoString Qualified & Verified Morphology Markers

These markers are obtained from our partners including Abcam, Biolegend, and other vendors, and tested in GeoMx assays following the “Qualified” and “Verified” approaches. Qualified marker tests showed the expected staining pattern typically in a single tissue. Verified markers had gone through more extensive testing on multiple tissues, when possible, and were used for GeoMx ROI segmentation. Moreover, target specific positive tissue staining as verified by an experienced pathologist.

NanoString TAP Morphology Markers

NanoString TAP Morphology Markers

The Technology Access Program (TAP) allows users to run small trial projects. Through this work, the program has developed a long list of morphology markers observed to work well with specific tissues under specific conditions. A list of successfully utilized antibodies, RNAscope probes, and the tested tissues has been compiled to help users with their research projects: TAP tested morphology markers

Community Verified Morphology Markers

Community Verified Morphology Markers

The NanoString user community works with a wide range of morphology markers and tissue types. We are compiling a list of pre-screened markers that worked well with specific tissues by our customers. We encourage our users to share markers that have successfully been used in a GeoMx experiment. Let the research community know by submitting your verified morphology markers via this Community Verified Morphology Markers Form

Third Party Morphology Markers

Third-Party Morphology Markers​

For RNA morphology targets, you can learn about our joint workflow solution with our partner Advanced Cell Diagnostics (ACD) and how to select qualified RNAscope probe combinations: ACD and NanoString Partnership

For antibody morphology markers, it is recommended to begin with those already validated for IF/IHC assays by our antibody partners, Abcam or Biolegend, or another provider. Once selected, it is important that they are tested using the specific staining protocols used for GeoMx. Please refer to Morphology Marker Guidelines for further details.​

Target datasheets Cell/structure Marked Species / sample type Fluorophore Vendor
Acta2 Fibroblasts, smooth muscle, cell motility Mouse Frozen AF488 ThermoFisher
Aqp1 Water-specific channel Mouse FFPE AF647 Abcam
Epcam Tumors; epithelial tissue Mouse FFPE AF488 Abcam
Epcam Tumors; epithelial tissue Mouse Frozen AF647 Abcam
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen AF647 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen AF594 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF532 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF488 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF647 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF647 BioLegend
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen AF647 BioLegend
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen DL594 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen AF532 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen AF532 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen AF647 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF647 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF594 Novus
Iba1 Glial cells Mouse FFPE AF647 CST
Iba1 Glial cells Mouse Frozen AF647 CST
Laminin (Pan-Laminin) Basement membrane; extracellular matrix Mouse FFPE AF532 Novus
Laminin (Pan-Laminin) Basement membrane; extracellular matrix Mouse FFPE AF488 Novus
Map2 Microtubules Mouse FFPE AF647 Abcam
Map2 Microtubules Mouse FFPE AF488 Abcam
Mbp Myelin Basic Protein, all neurons Mouse FFPE AF647 BioLegend
Mbp Myelin Basic Protein, all neurons Mouse Frozen AF647 CST
Mbp Myelin Basic Protein, all neurons Mouse Frozen AF594 CST
Myh11 Smooth muscle Mouse FFPE AF647 Abcam
Nefh Intermediate filaments, neurons Mouse FFPE AF594 Novus
Nefh Intermediate filaments, neurons Mouse Frozen AF594 Novus
Tdp43 Aggregates in ALS Mouse FFPE AF647 Abcam
Tubb3 Microtubules; Neurons Mouse FFPE AF647 Abcam
Tubb3 Microtubules; Neurons Mouse FFPE AF647 BioLegend
AQP1 Water-specific channel Human FFPE AF647 Abcam
APP / β Amyloid Alzheimer’s diseased brain plaques Human FFPE AF647 Novus
CD103 / ITGAE Intra-epithelial lymphocytes Human FFPE AF647 Abcam
CD20 B cells Human FFPE AF647 Novus
CD20 B cells Human FFPE AF647 Abcam
CD20 B cells Human FFPE AF488 Abcam
CD4 Most thymocytes Human FFPE AF647 Abcam
CD57 / B3GAT1 NK cells, CD8+ T cells, neural cells, striated muscle Human FFPE AF594 BioLegend
CD68 Macrophages Human FFPE AF488 Novus
CD68 Macrophages Human FFPE AF647 BioLegend
CD68 Macrophages Human FFPE AF594 Novus
CD8a Cytotoxic T lymphocytes Human FFPE AF594 BioLegend
COL1A1 / Collagen I Extracellular matrix Human FFPE AF647 Abcam
ELA2 / Neutrophil Elastase Neutrophils Human FFPE AF594 Novus
ELA2 / Neutrophil Elastase Neutrophils Human FFPE AF488 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human FFPE AF594 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human FFPE AF488 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human Frozen DL594 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human Frozen AF532 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human Frozen AF532 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human Frozen AF647 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human Frozen AF647 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human FFPE AF594 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human Frozen AF488 Novus
HLA-G Trophoblasts, thymic epithelial cells, tumors Human FFPE AF488 Santa Cruz
IBA1 Glial cells Human FFPE AF647 CST
IBA1 Glial cells Human Frozen AF647 CST
KRT7 (Cytokeratin) Epithelial cells Human FFPE AF647 Abcam
KRT8/18 (Cytokeratin) Epithelial cells Human FFPE AF594 Novus
Laminin (Pan-Laminin) Basement membrane Human FFPE AF594 Novus
MAP2 Microtubules Human FFPE AF488 Abcam
MBP Myelin Basic Protein, all neurons Human FFPE AF647 BioLegend
MBP Myelin Basic Protein, all neurons Human Frozen AF647 CST
NEFH Intermediate filaments, neurons Human FFPE AF647 Novus
NEFH Intermediate filaments, neurons Human FFPE AF594 Novus
NEFH Intermediate filaments, neurons Human FFPE AF594 Novus
OCLN Tight junctions Human FFPE AF594 Novus
PD-1 Activated T and B cells Human FFPE AF647 Abcam
Tau Neurons; Alzheimer’s diseased brain plaques Human FFPE AF647 Abcam
Tau – Phospho (T181) Neurons; Alzheimer’s diseased brain plaques Human FFPE AF594 BioLegend
Tau – Phospho (T181) Neurons; Alzheimer’s diseased brain plaques Human FFPE AF488 BioLegend
Tau – Phospho (S404) Neurons; Alzheimer’s diseased brain plaques Human FFPE AF488 CST
Tau – Phospho (T205) Neurons; Alzheimer’s diseased brain plaques Human FFPE AF488 CST
TUBB3 Microtubules in the central and peripheral nervous system Human FFPE AF647 Abcam
APP / β Amyloid Alzheimer’s diseased brain plaques Human FFPE AF647 CST
APP / β Amyloid Alzheimer’s diseased brain plaques Human FFPE AF594 CST
APP / β Amyloid Alzheimer’s diseased brain plaques Human FFPE AF488 CST
CD163 M2 macrophages and monocytes Human FFPE AF647 Abcam
CD20 B cells Human FFPE AF594 Novus
CD3 T lymphocytes Human FFPE AF647 Novus
CD3 T lymphocytes Human FFPE AF594 Novus
CD3 T lymphocytes Human FFPE AF532 Novus
CD3 T lymphocytes Human FFPE AF488 Novus
CD31 Endothelial cells Human FFPE AF647 Abcam
CD31 Endothelial cells Human FFPE AF488 Abcam
CD68 Macrophages Human FFPE AF647 Santa Cruz
CD68 Macrophages Human FFPE AF647 Novus
CD68 Macrophages Human FFPE AF532 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human FFPE AF647 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF532 Novus
HLA-G Trophoblasts, thymic epithelial cells, tumors Human FFPE AF647 Santa Cruz
IBA1 Glial cells Human FFPE AF594 CST
KRT (Pan-Cytokeratin) Epithelial cells Human FFPE AF594 Novus
KRT (Pan-Cytokeratin) Epithelial cells Human FFPE AF488 Novus
Laminin (Pan-Laminin) Basement membrane Human FFPE AF647 Novus
MBP Myelin Basic Protein, all neurons Human FFPE AF647 CST
MBP Myelin Basic Protein, all neurons Human FFPE AF488 CST
OCLN Tight junctions Human FFPE AF647 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF532 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE DL594 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse FFPE AF488 Novus
Iba1 Glial cells Mouse FFPE AF594 CST
Iba1 Glial cells Mouse FFPE AF488 CST
Mbp Myelin Basic Protein, all neurons Mouse FFPE AF647 CST
AQP4 Water-specific channel Human FFPE AF488 Abcam
CD11c Dendritic cells (antigen presenting) Human FFPE AF488 Abcam
CD68 Macrophages Human Frozen AF488 Novus
CD138 Cytoskeleton-interstitial matrix; Plasma cells, several tumors Human FFPE AF488 BioLegend
EPCAM Epithelial cells, tumors Human FFPE AF647 Abcam
Epcam Epithelial cells, tumors Mouse Frozen AF488 Abcam
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human FFPE AF488 BioLegend
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen AF594 BioLegend
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human FFPE AF647 BioLegend
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human Frozen AF647 BioLegend
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human FFPE AF647 Novus
GFAP Glial Fibrillary Acidic Protein in Mature Astrocytes Human Frozen AF488 Novus
Gfap Glial Fibrillary Acidic Protein in Mature Astrocytes Mouse Frozen AF488 Novus
IBA1 Glial cells Human FFPE AF488 CST
KRT (Pan-Cytokeratin) Epithelial cells Human Frozen AF594 Novus
Laminin (Pan-Laminin) Basement membrane Mouse Frozen AF594 Novus
Lgr5 Overexpressed in cancers of the ovary, colon, and liver Mouse FFPE AF594 Novus
MAP2 Microtubules Human Frozen AF647 Abcam
Mbp Myelin Basic Protein, all neurons Mouse FFPE AF488 CST
MBP Myelin Basic Protein, all neurons Human FFPE AF594 CST
Mbp Myelin Basic Protein, all neurons Human Frozen AF594 CST
Mbp Myelin Basic Protein, all neurons Mouse FFPE AF488 BioLegend
Mbp Myelin Basic Protein, all neurons Mouse Frozen AF647 BioLegend
MOG Myelin sheath Human FFPE AF647 Abcam
MUC1 Epithelial cancers; secretory epithelium Human FFPE AF594 Novus
MUC1 Epithelial cancers; secretory epithelium Human FFPE AF647 Novus
Nefh Intermediate filaments, neurons Mouse Frozen AF488 Novus
Nefh Intermediate filaments, neurons Mouse Frozen AF532 Novus
Nefh Intermediate filaments, neurons Mouse Frozen AF647 Novus
PD-1 Activated T and B cells Human FFPE AF647 Abcam
PD-L1 T and B cells, many tumor cells Human FFPE AF647 Abcam
Tau – Phospho (T181) Neurons; Alzheimer’s diseased brain plaques Mouse Frozen AF488 BioLegend
Tau – Phospho (T181) Neurons; Alzheimer’s diseased brain plaques Mouse Frozen AF594 BioLegend
Tdp43 Aggregates in ALS Mouse Frozen AF594 Abcam
TDP43 Aggregates in ALS Human FFPE AF647 Abcam
Tdp43 Aggregates in ALS Mouse Frozen AF647 Abcam
Tubb3 Microtubules in the central and peripheral nervous system Mouse Frozen AF647 BioLegend
VIM Intermediate filaments of mesenchymal origin; sarcomas Human FFPE AF488 Abcam
VIM Intermediate filaments of mesenchymal origin; sarcomas Human FFPE AF594 Abcam
VIM Intermediate filaments of mesenchymal origin; sarcomas Human Frozen AF594 Abcam
Vim Intermediate filaments of mesenchymal origin; sarcomas Mouse Frozen AF647 Abcam

*For detailed clone information, download the complete list here.

Related Resources

NanoU Course: How To Use Morphology Markers with the GeoMx DSP
Whitepaper Morphology Marker Guidelines
Blog The Importance of Segmentation in Spatial Biology
Whitepaper Molecularly Guided Highly Multiplexed Spatial Profiling with RNAscope and GeoMx Assays – Whitepaper
Brochure GeoMx Digital Spatial Profiler Product Brochure