stHNSCC_27

Download processed single-cell RNA-seq data for this sample

Dataset Information

scHNDB ID

stHNSCC_27

Tissue Type

Tumor

Age

65

Gender

M

Position

Oral Cavity

Clinical Stage

IV

Data download

Spatial ancillary files only: tissue spot coordinates, low-resolution H&E, and scale factors under spatial/ (layout for this cohort).

10X Raw Data Package

Download

Package contents

Tissue positions

CSV

spatial/tissue_positions_list.csv

Array coordinates linking spots to the tissue image.

H&E image (low resolution)

PNG

spatial/tissue_lowres_image.png

Low-resolution histology for this cohort (stHNSCC_20–27 layout).

Scale factors

JSON

spatial/scalefactors_json.json

Pixel ↔ spot scaling and related Visium metadata.

Usage Instructions

This package lists only Visium spatial/ assets (spot layout, low-resolution H&E, scale factors). It does not include a gene–spot expression matrix—use these files to align or visualize results together with expression data from the paired assay or another table.

In R:

pos <- read.csv("path/to/spatial/tissue_positions_list.csv", row.names = 1)
# Low-resolution image for overlay, e.g. png/jpeg reader + ggplot2::annotation_raster

In Python:

import pandas as pd
import matplotlib.pyplot as plt
pos = pd.read_csv("path/to/spatial/tissue_positions_list.csv")
im = plt.imread("path/to/spatial/tissue_lowres_image.png")  # if exported as PNG