Xenium — Human Breast Invasive Ductal Carcinoma (IDC, FFPE, full slide) 2D

Full whole-slide Xenium run of FFPE human breast tissue with invasive ductal carcinoma — the canonical Xenium reference dataset from Janesick et al. (Nat. Commun. 2023), profiled with a 280-gene custom human breast panel (~167k cells). Cell and nucleus boundaries are served as vector polygons, transcripts as points, and the DAPI morphology image as a raster pyramid. Tiled on the oden compute host.

Metadata

cells (tiled)	169,088 polygons
nuclei	169,083 polygons
transcripts	42,638,083 points
genes	541
resolution	0.2125 µm/px
image	35416×25778 px
zoom	0–9
tiles	94,700
size	4.01 GB

Provenance & reproducibility

Source: https://github.com/10XGenomics/janesick_nature_comms_2023_companion
License: CC BY 4.0
Cite: Janesick A, et al. High-resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis. Nat. Commun. 14, 8353 (2023). 10x Genomics Xenium; GEO GSE243275.

uv run python -m mudm_tools.converters.cli convert -f xenium -i data/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs -o tiles2d/xenium-breast-full  # tiled on oden
mudm 0.5.0 · mudm-tools 0.5.0
muDM: cells & nuclei → Polygon (featureClass cell/nucleus); transcripts → Point

Programmatic access

Raster tiles (PNG pyramid):

https://ngrf.mudm.io/tiles2d/xenium-breast-full/raster/{z}/{x}/{y}.png

Features (muDM tile-geometry Parquet, range-readable):

https://ngrf.mudm.io/tiles2d/xenium-breast-full/features.parquet/

Machine descriptors: tilejson.json · croissant.json · full access guide