Obtain and add files to the project

Follow along to add files to your Xenium project: Add files to the project. 

Perform quality analysis / quality control and filtering

• Filter the data including control probes using the Filter features task 

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• task
• Choose Feature metadata filter
• Include the Gene Expression features

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• Click Finish

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• This results in a Filter features task (rectangle) and node (circle) results.
• Right click the circle to Rename data node to "Filtered to only gene expression". 

• Click the circular "Filtered to only gene expression" results node and select the Single cell QA/QC task from the context sensitive menu on the right. 

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• When the task completes it will be opaque and no longer transparent with a progress bar. 

This task does not produce a circular results node but instead a rectangle. Double click the opaque rectangle task to open and filter cells as described here. Apply the observation filter to the "Filtered to only gene expression" results node. This results in a "Filtered cells node". 

Normalize the data

• Select the "Filtered cells node" and choose the Normalization task from the Normalization and scaling drop-down in the task menu 

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• Click the Use recommended button to proceed with these settings
• Click Finish

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This results in a Normalized counts node as shown below in the pipeline. 

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