10x Genomics Xenium Breast Cancer SpatialData with Chromium scRNA-seq Reference (CSAMA 2026)

SpatialData object containing a cropped, low-resolution representation of the 10x Genomics Xenium Prime FFPE Human Breast Cancer dataset. The object includes Xenium transcript coordinates, cell and nucleus segmentation boundaries, cell-level expression table, H&E image, and four immunofluorescence channels including DAPI. High-resolution image pyramids were removed to reduce file size.

Original dataset:
https://www.10xgenomics.com/datasets/xenium-prime-ffpe-human-breast-cancer

AnnData object containing reference breast cancer scRNA-seq data derived from the Janesick et al. Chromium dataset. Data processing followed the OSTA workflows.

Raw count matrix:
https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM7782698&format=file&file=GSM7782698%5Fcount%5Fraw%5Ffeature%5Fbc%5Fmatrix%2Eh5

Cell type annotations:
https://zenodo.org/records/10076046/files/Cell_Barcode_Type_Matrices.xlsx?download=1

Processing references:
https://github.com/lmweber/STexampleData/blob/devel/inst/scripts/make-data-Janesick-breastCancer-Chromium.R
https://lmweber.org/OSTA/pages/seq-deconvolution.html