CosMx Data Viewer

This viewer enables diverse views of SMI data. All results have been generated by a NanoString analyst using our SMI analysis pipeline.

X-Y plot

Cell segmentation from the tissue morphology images 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.

Color by options

For each of type of plot 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 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. 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.