Process Xenium data
Obtain and add files to the project
Follow along to add files to your Xenium 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
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 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
This results in a Normalized counts node as shown below in the pipeline.
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