Process Xenium data

• Obtain and add files to the project

• Perform quality analysis / quality control and filtering

• Normalize the data

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

• Choose Feature metadata filter

• Include the Gene Expression features

• Click Finish

• 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

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

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

• Click the Use recommended button to proceed with these settings

• Click Finish

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

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