Xenium — Mouse Brain (non-diseased, fresh-frozen, coronal) 2D

A non-diseased adult mouse brain, sectioned coronally from fresh-frozen tissue and profiled with the 10x Genomics Xenium Mouse Brain Gene Expression Panel (248 genes), which targets canonical neuronal, glial and regional marker genes across cortex, hippocampus, thalamus and other structures. This is one of 10x's reference fresh-frozen mouse-brain runs and serves as a non-diseased baseline alongside the Alzheimer's-model and replicate sections. The catalogue serves cell and nucleus boundaries as vector polygons, transcripts as points, and the DAPI morphology image as a raster pyramid.

Metadata

cells (tiled)	131,889 polygons
nuclei	131,903 polygons
transcripts	42,391,468 points
genes	541
resolution	0.2125 µm/px
image	48352×33135 px
zoom	0–9
tiles	144,281
size	4.09 GB

Provenance & reproducibility

Source: https://www.10xgenomics.com/datasets/fresh-frozen-mouse-brain-for-xenium-explorer-demo-1-standard
License: CC BY 4.0
Cite: 10x Genomics. Fresh Frozen Mouse Brain for Xenium Explorer Demo (Xenium). Public dataset.

uv run python -m mudm_tools.converters.cli convert -f xenium -i data/Xenium_V1_FF_Mouse_Brain_Coronal_outs -o tiles2d/xenium-mouse-brain-coronal  # 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-mouse-brain-coronal/raster/{z}/{x}/{y}.png

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

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

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