Neuroscience and neurology applications

Neuroscience Showcase

Build Comprehensive Whole Brain Atlas with the MERSCOPE® Platform

Accurately characterizing every individual cell within the brain is challenging due to the low expression of many functionally important genes. MERSCOPE’s high sensitivity, effective multiplexing capacity, and sub-celluar resolution enable users to build a comprehensive whole brain atlas.

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MERFISH Mouse Brain Atlas

To demonstrate the power of the MERSCOPE® Platform, we generated the MERFISH Mouse Brain Receptor Map that includes canonical cell type markers, nonsensory G-Protein coupled receptors (GPCRs), and Receptor Tyrosine Kinases (RTKs). We designed this specific gene panel because nonsensory GPCRs mediate signaling and may play vital roles behind brain aging and neurodegenerative disorders. However, GPCRs are notoriously difficult to analyze. Thus, the ability to completely spatially profile GPCR expression across the brain with cellular context can assist with gaining a deeper understanding of brain tissue structure and function.

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Application Note

Molecular Atlassing with MERSCOPE:

A New Spatial Transcriptomics Technique Accurately Reveals the Organization of The Mouse Brain Transcriptome

Building molecular atlases to fully understand the structure and function of each cell within the brain is now a key aspect of neuroscience research. The MERFISH Mouse Brain Receptor Map was generated by MERSCOPE and demonstrates how the platform can accurately generate a spatially resolved molecular atlas of the mouse brain transcriptome.

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Most comprehensive spatial analysis of neuronal biology at single-cell resolution

Vizgen's predesigned MERSCOPE PanNeuro Cell Type Panel 500 Gene (Mouse) for the MERSCOPE® Platform provides researchers with a curated list of 500 biologically relevant genes to enable cell typing and investigation of cellular functional states in the mouse brain.

Create a Mouse Brain Atlas

Distinguish molecular and cellular heterogeneity of the mouse brain using a highly sensitive, 500 gene panel with coverage of all major cell types and important biochemical pathways. The MERSCOPE PanNeuro Cell Type Predesigned Gene Panel (Mouse) provides the ability to identify cells and probe neuronal signaling and interactions at cellular and subcellular resolution with the sensitivity to detect changes at the single molecule level.

Figure 1: Spatial distribution of all cell clusters in one mouse coronal section. (left) and one mouse sagittal section (right) using the MERSCOPE PanNeuro Cell Type Panel.

PanNeuro Cell Type Panel Features

Comprehensive Coverage of Neurobiology

500 expertly curated genes enable the resolution of all major cell types and non-neuron subtypes as well as measure expression of key neural receptors, transmitters, and ion channels.

Single Molecule Sensitivity to Detect Low Expressors

Detect difficult-to-characterize lowly expressed genes such as with single-molecule sensitivity.

Robust, Reproducible Results

Highly reproducible data between technical replicates with strong correlation to RNA-Seq results.

Broad sample type compatibility

Proven performance in FFPE, Fresh frozen, fixed frozen, and cell culture sample types.

Figure: 2 The PanNeuro Cell Type Panel (Mouse) was constructed using The Mouse Brain Atlas1, published literature, and Vizgen published Mouse Brain dataset to build a comprehensive cell typing panel, providing the ability to identify cells, probe neuronal signaling, activity, and interactions at cellular and subcellular levels.

Designing gene panels that capture key marker genes for cell typing and investigation of cellular functional states can be difficult and time consuming. To address this need, we developed a 500-gene PanNeuro Cell Type Panel featuring a comprehensive list of genes specifically designed to identify all major cell types and established neuron subtypes in the mouse brain.

Insights Gained from MERSCOPE Data

Cellular Mapping of the Brain

MERSCOPE’s high sensitivity allows us to map gene expression by cell type and see the variation in the gene expression pattern of receptors within the mouse brain.

Figure 3: The variation in the gene expression pattern of eight different receptors between neuronal and non-neuronal cell types and their positions within the mouse brain are detectable by MERSCOPE.

Detect lowly expressing genes

We successfully detected multiple lowly expressed GPCRs including Oxtr, Tshr, and Insr that could be missed by other spatial transcriptomic platforms.

MERSCOPE is capable of a high 100nm resolution that enables users to see where RNA transcripts are located within a large 1cm2 tissue section and inside each cell.

Figure 4: MERSCOPE Data images showing an 8 RNA subset from a MERFISH measurement of 483 transcripts across a mouse brain coronal tissue section.

Highly reproducible MERFISH measurements

MERSCOPE generates highly reproducible MERFISH measurements between brain section replicates, resulting in high confidence in the data.

Figure 5: Correlation plots between the MERFISH measurements taken with MERSCOPE and bulk RNA-seq show that data generated by MERSOPE is highly quantitative and reproducible across large mouse brain tissue area.


­The MERSCOPE® Platform is a leading tool for building a whole brain atlas because it produces true spatial transcriptomic data for whole tissue sections down to the subcellular level. MERSCOPE enables researchers to harness the power of MERFISH technology for cellular mapping of the brain, functional mapping of the brain, and gaining deeper insights into neurological diseases.