Journal: bioRxiv

Article Title: MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

doi: 10.64898/2026.03.06.710199

Figure Lengend Snippet: Fresh frozen mouse brain sections were profiled with an 815-plex MERSCOPE Pan Neuro Panel and imaged on MERSCOPE platform to compare MERFISH 1.0 and MERFISH 2.0 chemistries. A) Sensitivity comparison between MERFISH (blue) and MERFISH 2.0 (red) measured as RNA transcript counts per 100 µm .Bars represent mean values across biological replicates (N=3). MERFISH 2.0 shows increased transcript detection and reduced variability relative to MERFISH 1.0. B ) Distribution of detected transcripts per cell for MERFISH 1.0 and MERFISH 2.0, shown as histograms of log10-transformed transcript counts per cell. MERFISH 2.0 exhibits higher transcript counts per cell. C ) UMAP visualization of major neuronal and non-neuronal cell populations identified using MERFISH 1.0 and MERFISH 2.0 data. The MERFISH 1.0 and MERFISH 2.0 data was combined for analysis and co-embedding in the UMAP. D) Relative abundance of annotated cell types detected with MERFISH 1.0 and MERFISH 2.0, shown as the percentage of total cells assigned to each cell type.

Article Snippet: Lastly, the sample was washed for 10 minutes with 5ml of Formamide Wash Buffer and then imaged on the MERSCOPE (Vizgen 10000001) and MERSCOPE Ultra system (Vizgen 10000108).

Techniques: Comparison, Transformation Assay

Journal: bioRxiv

Article Title: MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

doi: 10.64898/2026.03.06.710199

Figure Lengend Snippet: Fresh-frozen human brain sections were profiled using the 815-plex MERSCOPE Human Brain Panel and imaged on the MERSCOPE platform to compare MERFISH 1.0 and MERFISH 2.0 chemistries. A) Comparison of transcript detection between MERFISH 1.0 and MERFISH 2.0 on adjacent tissue slices. Scatter plot shows transcript counts detected by the two chemistries across the panel. B) Distribution of detected transcripts per cell for MERFISH 1.0 and MERFISH 2.0 shown as histograms of log10-transformed transcript counts per cell. MERFISH 2.0 shows increased transcript detection per cell. C-D) Correlation between bulk RNA-seq and MERFISH data with MERFISH 1.0 (C) or MERFISH 2.0 (D), demonstrating strong concordance between spatial and bulk measurements. E-F) Spatial heat map of transcript/cell across the tissue section for MERFISH 1.0 (E) and MERFISH 2.0 (F) chemistry illustrating increased transcript detection with MERFISH 2.0. G) Violin plot showing transcripts counts per cell across representative cell types identified in the human brain, including glutamatergic neurons, GABAegeric neurons, oligodendrocytes, astrocytes, vascular cells, and microglia cells. MERFISH 2.0 exhibits a broader dynamic range of transcript detection across cell types. H) Spatial distribution of representative marker genes with MERFISH 1.0 (top) and 2.0 (bottom) chemistry, including OLIG2, MOG and SOX10 with DAPI staining marking nuclei. MERFISH 2.0 shows substantially increased transcript counts for each marker gene.

Article Snippet: Lastly, the sample was washed for 10 minutes with 5ml of Formamide Wash Buffer and then imaged on the MERSCOPE (Vizgen 10000001) and MERSCOPE Ultra system (Vizgen 10000108).

Techniques: Comparison, Transformation Assay, RNA Sequencing, Marker, Staining

Journal: bioRxiv

Article Title: MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

doi: 10.64898/2026.03.06.710199

Figure Lengend Snippet: Archival fresh-frozen human brain sections with reduced RNA quality were profiled using the 815-plex MERSCOPE Human Brain Panel and imaged on the MERSCOPE platform to compare MERFISH 1.0 and MERFISH 2.0 chemistries. A) Sensitivity comparison between MERFISH 1.0 (blue) or MERFISH 2.0 (red), measured as RNA transcript counts per 100 µm². Bars represent mean values across biological replicates (n = 3). MERFISH 2.0 shows substantially increased transcript detection. B) Distribution of detected transcripts per cell for MERFISH 1.0 and MERFISH 2.0, shown as histograms of log10-transformed transcript counts per cell, demonstrating increased transcript detection with MERFISH 2.0. C) UMAP visualization of different cell types identified in human brain with MERFISH 1.0, with 10,463 cells pass QC. Left: clustering of cell types based on gene expression profiles. Right: spatial distribution of annotated cell types across the tissue section. D) UMAP visualization of cell populations identified in human brain with MERFISH 2.0, with 21,236 cells pass QC. Left: clustering of cell types. Right: spatial distribution of annotated cell types. MERFISH 2.0 recovers substantially more cells and improves detection of distinct cell populations. E) Absolute number of cells assigned to each cell-type cluster with MERFISH 1.0 and MERFISH 2.0 chemistry. F) Relative abundance of cell types detected with MERFISH 1.0 and MERFISH 2.0 chemistry, shown as the percentage of total cells assigned to each cluster. MERFISH 2.0 identifies a higher fraction of astrocytes and uniquely detects MGE interneurons that are not recovered with MERFISH 1.0.

Article Snippet: Lastly, the sample was washed for 10 minutes with 5ml of Formamide Wash Buffer and then imaged on the MERSCOPE (Vizgen 10000001) and MERSCOPE Ultra system (Vizgen 10000108).

Techniques: Comparison, Transformation Assay, Gene Expression