Xenium — Human Brain Glioblastoma (GBM, FFPE, custom add-on) 2D

An FFPE human brain section affected by glioblastoma (GBM), the most aggressive and common primary malignant brain tumor in adults. It was assayed with the Xenium In Situ platform using a pre-designed gene panel plus a custom add-on. The tumor microenvironment lets users map malignant cells against surrounding neural and immune populations. Served as cell and nucleus boundary polygons, transcript points, and the DAPI raster.

Metadata

cells (tiled)	832,701 polygons
nuclei	824,909 polygons
transcripts	178,716,169 points
genes	541
resolution	0.2125 µm/px
image	53946×51043 px
zoom	0–9
tiles	247,981
size	16.11 GB

Provenance & reproducibility

Source: https://www.10xgenomics.com/datasets/ffpe-human-brain-cancer-data-with-human-immuno-oncology-profiling-panel-and-custom-add-on-1-standard
License: CC BY 4.0
Cite: 10x Genomics. FFPE Human Brain Cancer Data with Human Immuno-Oncology Profiling Panel and Custom Add-on (Xenium In Situ). Public dataset.

uv run python -m mudm_tools.converters.cli convert -f xenium -i data/Xenium_V1_Human_Brain_GBM_FFPE_outs -o tiles2d/xenium-brain-gbm  # tiled on oden
mudm 0.6.1 · mudm-tools 0.6.3
muDM: cells & nuclei → Polygon (featureClass cell/nucleus); transcripts → Point

Programmatic access

Raster tiles (PNG pyramid):

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

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

https://ngrf.mudm.io/tiles2d/xenium-brain-gbm/features.parquet/

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