CosMx Data Viewer

This viewer enables diverse views of SMI data. All results, from normalized gene expression values to cell type calls, have been generated by a NanoString analyst using our SMI analysis pipeline.

X-Y plot

Cell segmentation from the tissue morphology images—a composite image is displayed in the top-left corner of the viewer—assigned transcripts to individual cells and these cells are plotted in space as observed on the tissue.

Expression profile UMAP

Uniform Manifold Approximation and Projection (UMAP) is a non-linear dimension reduction technique which takes as input all of the transcripts detected for every cell and visualizes the results on the Cartesian plane.

Neighborhood UMAP

In this case UMAP is performed on a matrix characterizing the spatial context of each cell. Clustering on the expression of every cell results in cell type calling. In turn, the frequency of each cell type among each cell’s 200 closest neighbors is used to determine a spatial context for the cell.

Color by options

For each of the three types of plots above the cells can be colored in three different ways by selecting the drop-down menu under each plot. The first is by cell_type, an attribute assigned to each cell after semi-supervised clustering on the expression values. Cells may also be colored by their niche; this attribute is determined by a clustering algorithm on the spatial context neighborhood matrix described above. Finally, cells may also be colored by individual gene expression values.

Filtering

Filters may be applied on both the left and right plots by using the controls below them. Filters are based on either cell type or niche.

Zooming

Draw a rectangular marquee on either the left or right plot to zoom into that region of the plot. The corresponding cells on the other plot will be highlighted. Click outside the highlighted marquee to zoom back out.

Options

Expand the options tab on the sidebar to be able to change the point size or hide the legends on the plots.