> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-xenium-data-analysis/process-xenium-data.md).

# Process Xenium data

* [Obtain and add files to the project](#obtain-and-add-files-to-the-project)
* [Perform quality analysis / quality control and filtering](#perform-quality-analysis--quality-control-and-filtering)
* [Normalize the data](#normalize-the-data)

## Obtain and add files to the project

Follow along to add files to your Xenium project: [Add files to the project](/partek/partek-flow/tutorials/10x-genomics-xenium-data-analysis/import-10x-genomics-xenium-analyzer-output.md).

## 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**

![](/files/GcMKgw6zoF5uoWxGy1ma)

* 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*"

![](/files/S5Ro4Eaw333uSYdcnHBz)

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

![](/files/XFEUcDjHuFxalOnglTD9)

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

![](/files/Ay2SMmlh0uQIf8fnl6JH)

Double click the opaque rectangle task to open and [filter cells as described here.](/partek/partek-flow/user-manual/task-menu/qa-qc/single-cell-qa-qc.md) 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

![](/files/Y6Q1qxHqSI40TvECbS3f)

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

![](/files/Czp3atA7exvSX7haL92g)

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

![](/files/M6itGeuWXcb3dIW4NJxA)

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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