The MERSCOPE Platform from Vizgen is enabled by Multiplexed Error-Robust Fluorescence in-situ Hybridization (MERFISH). MERFISH is a spatial transcriptomics technology that expands the multiplexing capabilities of single molecule fluorescent in-situ hybridization (smFISH) via a combinatorial barcode coupled with sequential rounds of imaging. The technology enables detection of hundreds to thousands of single molecule targets at sub-cellular resolution. While MERFISH was designed to be compatible with fresh or fixed frozen tissues, Vizgen has demonstrated efficacy of the technology on FFPE tissue specimens.
Pros and cons
Pros:
- Commercial kit
- Single cell resolution
- High detection efficiency
- Formalin fixed, paraffin embedded (FFPE) tissue compatible
- Provides subcellular transcript localization information
- Compatible with histological staining including DAPI
- Protein co-detection is supported
Cons:
- A curated panel of usually a few hundred genes is required. However, Vizgen provides curated gene panels for neuroscience and oncology, as well as panel design services.
- Data size is harder to manage for larger tissue areas and number of samples. Not all spatial analysis methods can scale to hundreds of thousands to millions of cells.
Getting Started
Several MERFISH datasets have been generated on the MERSCOPE Platform
and are publicly available from Vizgen on their website. We provide
examples available for processing the output of various spatial
transcriptomics technologies into a SpatialFeatureExperiment(SFE)
object for use with Voyager in the vignette below.
The vignette provides technology specific notes for data downloaded
from Vizgen. Briefly, Vizgen provides cell metadata and the gene count
matrix as CSV files which can be read in quickly with the vroom
package. Cell segmentation data are provided as HDF5 files that are
delineated by field of view.
| Vignette | Colab Notebook | Description |
|---|---|---|
Create
a SFE object |
Colab Notebook | Download data, create SFE object, Vizgen/MERFISH
specific notes |
Analysis Workflows
The vignettes below demonstrate workflows that can be implemented
with Voyager using data generated with the MERFISH
technology. The publicly available MERFISH datasets profile hundreds of
genes in hundreds of thousands to millions of cells. Thus, the vignettes
linked below can provide some context on the capabilities of
Voyager for moderate to large datasets.
| Vignette | Colab Notebook | Description |
|---|---|---|
| MERFISH mouse liver analysis | Colab Notebook | Perform basic QC, compute Moran’s I, length scales of spatial autocorrelation, binning, variogram models, PCA for large datasets |
| MULTISPATI PCA and negative spatial autocorrelation | Colab Notebook | Run MULTISPATI PCA on MERFISH mouse liver dataset, and compare the results to those from non-spatial PCA |