Cell Selection, Comparison, and Heatmaps

Selecting Cells

Switch to the select cursor mode (dashed rectangle icon in the lower-left of the plot) and click-and-drag to draw a selection box around a group of cells.

Once cells are selected:

  • A histogram appears showing the distribution of metadata values within your selection.

  • If a gene is currently coloring the plot, a violin plot shows gene expression in the selected cells versus all other cells.

You can also select cells by metadata criteria using Edit > Find Cells.

Exporting Selected Cells

After selecting cells, go to Edit > Export to download the cell identifiers for use in your own analysis tools (e.g. Seurat or Scanpy).

Setting Background Cells

By default, violin plots compare your selected cells against all other cells in the dataset. You can define a custom comparison group:

  1. Select the cells you want as your background.

  2. Go to Tools > Set as background cells (or press b then s).

  3. Select a new group of cells — the violin plot will now compare against your defined background instead of all cells.

To clear the custom background, go to Tools > Reset background cells (or press b then r).

Split-Screen Comparison

The Cell Browser can split the main view into two side-by-side panes, allowing you to compare two different colorings simultaneously.

To enable split-screen:

  • Go to View > Split screen, or

  • Press t on your keyboard.

The currently active pane is outlined in black and its coloring is reflected in the legend. To change a pane’s coloring:

  1. Click the pane you want to modify (it will get the black outline).

  2. Change the annotation field or gene in the left sidebar.

Tip

When in split-screen mode, a “Show on both sides” checkbox appears under the Gene tab. Enable it to automatically color both panes with the same gene — particularly useful when comparing a spatial layout with a UMAP layout.

Expression Heatmap

If a dataset includes curated “dataset genes,” you can display an expression heatmap below the scatter plot:

  • Go to View > Heatmap to toggle it on.

  • The heatmap shows the expression of the dataset genes across the cluster labels visible in the scatter plot.

  • Click and drag the divider bar between the scatter plot and heatmap to resize.