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• Click the newly created Single cell counts data node
• Click the Annotation/Metadata section in the toolbox
• Click Annotate Visium image
• Click on the Browse button to open the file browser and point to the file <project-name>_spatial.zip, created by the Space Ranger task
• Click Finish

Select the zipped image folder for each sample. The image zip file should contains 6 files including image files and tissue position text file with a scale factor json file. 

The setup page shows the sample table (one sample per row; Figure 8).

You can find the location of the <project-name>_spatial.zip file using the following steps. Select the Space Ranger task node (i.e. the rectangle) and then click on the Task Details (toolbox). Click on the Output files link to open the page with the list of files created by the Space Ranger task. Mouse over any of the files to see the directory in which the file is located. Figure 9 shows the path to the .zip file which is required for Annotate Visium image.

Figure 8. Mousing over a file on the Output files page shows a baloon with the file location

A new data node, Annotated counts, will be generated. 

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The Annotated counts node is Split by sample. This means that any tasks performed from this node will also be split by sample. Invoke tasks from the Single cell counts node to perform to not split by sample. 

Annotate Visium image task creates a new node, Annotated counts. Double click on the Annotated counts node to invoke the Data Viewer showing data points overlaid on top of the microscopy image (Figure 10).

Figure 9. Data Viewer session as a result of opening an Annotated counts data node. Each data point is a tissue spot

A new data node, Annotated counts, will be generated. 

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Output of annotate counts

When the task report of the annotated counts node is opened (or double click on the Annotated counts node), the images will be displayed in data viewer (Figure 4)

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