# 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](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-207b0109a672bf912bb0fcf68582506c9801d53f%2Fimage2023-7-19_16-15-55.png?alt=media) * 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](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-9da2b03ed6953ec317ed16238a8c4b9d46cbbf66%2Fimage2024-2-14_23-41-20.png?alt=media) * Click [**Transfer files**](https://help.connected.illumina.com/partek/user-manual/importing-data#navigating-the-file-browser-to-transfer-files-to-the-server) on the homepage, under settings, or during import. * Click the blue **+ Add sample button** ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-71bbe3445fdb7c2c03b603f90720c978f9c5c9da%2Fblue-add-sample-button.png?alt=media)then use the green **Add sample** ![image2023-8-21\_12-7-17](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c52044dce7545be93eecde9cd49c36d219e7b363%2Fgreen-add-sample-button.png?alt=media) 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](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-9ea047f932010e9124dec6e032b5e5d987a85337%2Ftransfer-files-to-the-server.png?alt=media) (Figure 3).

Figure 3. Transfer files using the 10x Genomics Xenium importer

* 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](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-0d3c19a8231f85ec17526f9111d3c1d3d07bcb62%2Fimage2024-2-14_12-27-46.png?alt=media) * Once uploaded the folder to the server, navigate to the appropriate folder for each sample using **Add sample** ![image2023-8-21\_12-8-24](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c52044dce7545be93eecde9cd49c36d219e7b363%2Fgreen-add-sample-button.png?alt=media) (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](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c2573c382829632982d23bae16b7275fde51ec33%2Fimage2024-2-14_23-37-43.png?alt=media) 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](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-05920c770aef96888eb141f294ea4bb357bab215%2Fimage2023-7-19_17-20-34.png?alt=media) 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](https://help.connected.illumina.com/partek/partek-flow/creating-and-analyzing-a-project/the-metadata-tab#sample-annotation). Cell attributes are found under Sample attributes and can be added by [publishing cell attributes to a project](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/annotation-metadata/publish-cell-attributes-to-project). 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.