> 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/import-10x-genomics-xenium-analyzer-output.md).

# Import 10x Genomics Xenium Analyzer output

* [Obtain and add files to the project](#obtain-and-add-files-to-the-project)

## Obtain and add files to the project

The project includes [Human Breast Cancer (In Situ Replicate 1)](https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast) and [Human Breast Cancer (In Situ Replicate 2)](https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast) files in one project.

* Obtain the **Xenium Output Bundles** (Figure 1) for each sample.

![Figure 1. Obtain the Xenium Output Bundle on your machine](/files/Uvxqb1OHskrMwjXGPdZ8)

* Navigate the options to select **10x Genomics Xenium Output Bundle** as the file format for input. Choose to import **10x Genomics Xenium** for your project (Figure 2).

![Figure 2. Transfer files using the 10x Genomics Xenium importer](/files/3ASbdio8F4cIqm61pgFT)

* Click [**Transfer files**](/partek/partek-flow/user-manual/importing-data.md#navigating-the-file-browser-to-transfer-files-to-the-server) on the homepage, under settings, or during import.
* Click the blue **+ Add sample button** ![](/files/m4rooUgafEIGH8R98KlB)then use the green **Add sample** ![image2023-8-21\_12-7-17](/files/LfxK7ctIWZqXlmfixfLD) button to add each sample's Xenium output bundle folder. If you have not already transferred the folder to the server, this can be done using **Transfer files to the server**![image2023-8-21\_12-18-22](/files/XzofuvXdtMtN4n4Dk88U) (Figure 3).

<figure><img src="/files/Vra90OGwAL294b81sNuE" alt=""><figcaption><p>Figure 3. Transfer files using the 10x Genomics Xenium importer</p></figcaption></figure>

* You will need to **decompress** the Xenium Output Bundle zip file before they are uploaded to the server. After decompression, you can **drag and drop** the entire folder into the Transfer files dialog, all individual files in the folder will be listed in the Transfer files dialog after drag & drop, with no folder structure (Figure 4). The folder structure will be restored after upload is completed.

![Figure 4. Drag & drop unzipped Xenium Output Bundle folder into Transfer files dialog](/files/mCkEyNNZ3PfAmoo1gyvq)

* Once uploaded the folder to the server, navigate to the appropriate folder for each sample using **Add sample** ![image2023-8-21\_12-8-24](/files/LfxK7ctIWZqXlmfixfLD) (Figure 5).

The Xenium output bundle should be included for each sample (Figure 5). Each sample requires the whole sample folder or a folder containing these 6 files: cell\_feature\_matrix.h5, cells.csv.gz, cell\_boundaries.csv.gz, nucleus\_boundaries.csv.gz, transcripts.csv.gz, morphology\_focus.ome.tif. Once added, the *Cells* and *Features* values will update. You can choose an annotation file during import that matches what was used to generate the feature count.

Do not limit cells with a total read count since Xenium data is targeted to less features.

![Figure 5. Add Xenium output bundle](/files/R06UNTODRGT2rdZ00GTC)

Once the download completes, the sample table will appear in the *Metadata* tab, with one row per sample (Figure 6).

![Figure 6. Each sample should be present in the Metadata tab](/files/Iv7l27od2ETN20CfI2fd)

The sample table is pre-populated with one sample attributes: # Cells. Sample attributes can be added and edited manually by clicking *Manage* in the *Sample attributes* menu on the left. If a new attribute is added, click *Assign values* to assign samples to different groups. Alternatively, you can use the *Assign values from a file* option to assign sample attributes using a tab-delimited text file. For more information about sample attributes, see [here](/partek/partek-flow/tutorials/creating-and-analyzing-a-project/the-metadata-tab.md#sample-annotation). Cell attributes are found under Sample attributes and can be added by [publishing cell attributes to a project](/partek/partek-flow/user-manual/task-menu/annotation-metadata/publish-cell-attributes-to-project.md).

For this tutorial, we do not need to edit or change sample attributes.

## 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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