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A basic example of a spatial data analysis, starting from the Single cell counts node, is shown below and is similar to a Single cell RNA-Seq analysis pipeline with the addition of the Spatial report task (shown) or Annotate Visium image task (not shown). 

Note that Single cell QA QA/QC has not been performed in this example, to visualize all spots (points) on the tissue image. Single cell QA/QC can be performed from the Single cell counts node with the filtered cells applied to the Single cell counts before the Filter features task. Click here for more information on Single cell QA/QC (see the pipeline in Figure 11). 

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Low-quality cells can be filtered out during the spatial data analysis using QA/QC and will not be viewed on the tissue image. Click here for more information on Single cell QA/QC. We will not perform Single cell QA/QC in this tutorial; this task would be invoked from the Single cell counts node and the Filter features task discussed below would be invoked from this output node (Filtered counts). 

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We can use these Cell attributes in analyses tasks such as Statistics (e.g. differential analysis comparisons) as well as to Style the visualizations in the Data Viewer. 

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