Xenium Input Tutorial

Required files

Filename / pattern	Required	Format	Description
cells.parquet	Yes	Parquet	Cell-level statistics and coordinates
transcripts.parquet	Yes	Parquet	Transcript point coordinates
morphology.ome.tif/ morphology_focus.ome.tif	Yes	OME-TIFF	Morphology image
experiment.xenium	Yes	Xenium metadata	Platform metadata and file index
cell_feature_matrix.h5 / filtered_feature_cell_matrix.h5 / raw_feature_cell_matrix.h5 / filtered_feature_bc_matrix.h5 / raw_feature_bc_matrix.h5	No	H5	Alternative compatible matrix filenames that can be detected automatically

detail in Xenium Onboard Analysis Output Overview

Where these files come from

• Official download: directory exported from 10x Xenium Ranger output

• Public dataset: published studies and official 10x Genomics demonstration repositories

• Experimental output: complete sample directory delivered by the platform

Demo Walkthrough

run_type: xenium. In this tutorial, we use the public breast cancer dataset provided by 10x Genomics: Xenium Prime FFPE Human Breast Cancer

Before running Spatialsnake, create the project directory, download the Xenium output files from the dataset page, and place them under a single sample folder so that the directory matches the expected Xenium export structure.

Example setup:

mkdir -p project_root/data/breast_cancer
cd project_root/data/breast_cancer

curl -O https://s3-us-west-2.amazonaws.com/10x.files/samples/xenium/3.0.0/Xenium_Prime_Breast_Cancer_FFPE/Xenium_Prime_Breast_Cancer_FFPE_outs.zip
tar -xf Xenium_Prime_Breast_Cancer_FFPE_outs.zip

After download, the sample directory should match the layout shown below.

Example directory layout

project_root/
├── data/ (stores your raw data)
│   └── breast_cancer/
├── sample.txt (key sample description file)
├── results/ (stores analysis outputs)
└── <analysis_option>.yaml (optional configuration file)

data/
└── breast_cancer/
    ├── experiment.xenium
    ├── cells.parquet
    ├── transcripts.parquet
    ├── morphology.ome.tif
    └── cell_feature_matrix.h5
    └── ...

single_analysis:

sample_id input_path
breast_cancer data/breast_cancer

Make sure sample.txt is located in your current working directory.

spatialsnake single_analysis sample.txt xenium --option=integrate

Output structure after ingestion

results/
├── breast_cancer/
   └── integrate/
       ├── breast_cancer.zarr
       ├── total.png
       ├── total_umi_by_sample.png
       ├── total_genes_by_sample.png
       ├── genes_by_sample.png
       └── scatter.png

• Additional QC plots: the ingestion script writes five QC figures into the integrate directory.

You have now ingested your data into a zarr object. For the subsequent core analysis, please refer to Core Analysis Workflow. We recommend starting with the example dataset to gain hands-on experience with the basic core-analysis workflow. If you prefer to proceed directly with your own data, each step page begins with a concise summary of the essential parameters. Simply follow the tutorial to update the sample name and platform-specific parameters, then continue with the next step: Preprocessing. If you want to run multi-sample integration analysis, continue to Spatialsnake for multi-sample integration.