Configuring Spatial Images

Navigate spatial image

• To zoom in and out, scroll with mouse or trackpad
• To move the plot and image, right click and drag, or with a trackpad, use two fingers to click and drag.

Adjust Spatial settings

To adjust spatial specific settings, click the gear icon in toolbar to the left of the spatial image. Click "Spatial view" to see the options.

• Scale bar - length in microns as a reference
• Minimap - the small display of the whole sample image, which indicates what part of the overall image you are viewing when zoomed in.
• Dynamic resolution (only for grid binned data) - the plot displays summarized data when zoomed out, and more detail as you zoom in. Turning this off will load and display all data at the actual resolution (ex 10µm bin).

Bin coloring - grid binned data

Navigate to Configure > Axes > Content > Data. Select an attribute to color the plot. For example:

• Leiden - color by cluster
• Expressed genes - color by the number of unique expressed transcripts
• Total count - the total number of transcripts expressed

Bin coloring - cell binned data

Navigate to Configure > Style > Color > Color by. Select an attribute to color the plot. For example:

• Leiden - color by cluster
• Expressed genes - color by the number of unique expressed transcripts
• Total count - the total number of transcripts expressed

For both cell and grid binned data you can choose to color the plots with data generated from other tasks by clicking the blue circle beside the dropdown menu and choosing the data from the mini task graph

Highlight a cluster across plots

All the data in the spatial report is linked. Click on a cluster in the pie graph to highlight only that cluster across all plots. To remove the selection, click just outside the pie graph.

Save Data Viewer session

Save a session of the data viewer with any changes you have made to plots by clicking the "save" button at the top right. If it is from the spatial report you will "save as" a new data viewer session. Later updates to data viewer sessions can be saved into the already existing session

That session can now be viewed from the Data Viewer page. You can navigate to the data viewer page by clicking the text at the top of the page.