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The Space Ranger task output results in a Single cell counts node.
Annotate Visium image
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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).
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A new data node, Annotated counts, will be generated.
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 combine samples for analyses.
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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.
Data Viewer session as a result of opening an Annotated counts data node. Each data point is a tissue spot.
Proceed with analysis from the Single cell counts node. Click here to learn about viewing the multiple tissue images in the Data Viewer.
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