scHNSCC_325_MLN

Download 10x Xenium in situ data for this sample

Dataset Information

scHNDB ID

scHNSCC_325_MLN

Tissue Type

Lymph Node

Age

56

Gender

M

Position

Larynx

Clinical Stage

IV

Data download

10x Xenium in situ package: per-cell feature matrix (HDF5), cell and transcript tables, morphology OME-TIFF, and cell positions under spatial/ (default Xenium output names).

10X Xenium data package

Download

Package contents

Cell feature matrix

H5

cell_feature_matrix.h5

Per-cell probe counts in 10x HDF5 format (Xenium cell_feature_matrix).

Cells table

CSV.GZ

cells.csv.gz

Per-cell metrics and centroid coordinates (xenium output).

Transcripts

CSV.GZ

transcripts.csv.gz

Per-transcript calls with spatial locations (large file).

Morphology image

OME-TIFF

morphology.ome.tif

Multiresolution morphology (DAPI / tissue) in OME-TIFF.

Cell positions

CSV

spatial/cell_positions.csv

Cell centroids / polygon anchors in image space (under spatial/).

Usage Instructions

10x Xenium outputs: keep default file names in one folder (see Xenium Ranger and the Xenium file format overview). Seurat LoadXenium() reads that layout; in Python, load cell_feature_matrix.h5 with Scanpy and attach rows from cells.csv.gz (same row order as barcodes in the H5).

In R (Seurat):

library(Seurat)
data_dir <- "path/to/xenium_outs_folder"
obj <- LoadXenium(data.dir = data_dir)

In Python (Scanpy):

import scanpy as sc
import pandas as pd
adata = sc.read_10x_h5("path/to/cell_feature_matrix.h5")
adata.obs = pd.read_csv("path/to/cells.csv.gz")