# 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](https://help.connected.illumina.com/partek/partek-flow/tutorials/10x-genomics-xenium-data-analysis/import-10x-genomics-xenium-analyzer-output).

## 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**

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-199f80b9a113f5de73afe9e8a5ecc14b24b77db6%2Fimage2023-7-21_16-57-47.png?alt=media)

* 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*"

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8df94de116e4613bfa1e3127c3cf4fefe7d967b4%2Fimage2023-7-20_14-8-16.png?alt=media)

* 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

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-34112868cc08bd1457cf150deeca70dbc9711320%2Fimage2023-7-20_14-15-6.png?alt=media)

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

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-b2ce03379b610eb1759888964fa1cdf64da498dd%2Fimage2023-7-20_14-22-17.png?alt=media)

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

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-ee96b9ff78d469ae02a0bf2a45091af5b5a9958a%2Fimage2023-7-21_16-30-9.png?alt=media)

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

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-40e1d93be52448b5098501f967be47e0294f67de%2Fimage2023-7-21_16-38-33.png?alt=media)

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

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-50c78fcc7168738b3b13ff418dea3a5ae939db0c%2Fimage2023-7-21_16-36-5.png?alt=media)

## 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.