Xenium — Mouse Brain (TgCRND8 Alzheimer's model, FFPE, custom add-on, coronal, 17.9 months) 2D

A coronal brain section from a TgCRND8 mouse, an APP-transgenic model of Alzheimer's amyloidosis, was FFPE-prepared at the 17.9-month (aged, advanced-pathology) timepoint. It was profiled with the Xenium Mouse Brain Panel (248 genes) supplemented by a 99-gene custom add-on targeting activated microglia, astrocytes, and plaque-inducible genes. This run is part of a 10x Genomics time-course study of amyloid pathology in one hemisphere across ages. The catalogue serves cell and nucleus boundary polygons, transcript point features, and the DAPI nuclear raster.

Metadata

cells (tiled)	62,754 polygons
nuclei	62,762 polygons
transcripts	15,687,982 points
genes	541
resolution	0.2125 µm/px
image	31348×24864 px
zoom	0–8
tiles	77,141
size	1.65 GB

Provenance & reproducibility

Source: https://www.10xgenomics.com/datasets/xenium-in-situ-analysis-of-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard
License: CC BY 4.0
Cite: 10x Genomics. Xenium In Situ Analysis of Alzheimer's Disease Mouse Model Brain Coronal Sections from One Hemisphere Over a Time Course. Public dataset.

uv run python -m mudm_tools.converters.cli convert -f xenium -i data/Xenium_V1_FFPE_TgCRND8_17_9_months_outs -o tiles2d/xenium-mouse-ad-tgcrnd8-17-9mo  # 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-ad-tgcrnd8-17-9mo/raster/{z}/{x}/{y}.png

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

https://ngrf.mudm.io/tiles2d/xenium-mouse-ad-tgcrnd8-17-9mo/features.parquet/

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