Spatial assays#
The catalog currently holds 5114 datasets.
Each dataset loads as a SpatialData object whose elements (images, shapes, points, labels, tables) depend on the assay.
10x Genomics Visium captures the whole transcriptome on 55 µm spots. You get the H&E image, the spot shapes and an expression table.
4012 datasets in the catalog. Example: human pancreas
Visium HD reads the whole transcriptome on a gridded array, binned at 2, 8 or 16 µm
(the default table is square_008um). You get images, the bin shapes and one table per bin size.
134 datasets in the catalog. Example: human bone element
Xenium is a targeted in-situ panel with subcellular resolution. You get individual transcripts (points), cell and nucleus segmentation (shapes and labels), morphology images and a cell-by-gene table.
271 datasets in the catalog. Example: human kidney
Atera is a 10x preview platform that writes Xenium-format output, so it is read with the Xenium reader and yields the same kinds of elements.
2 datasets in the catalog. Example: human breast
The original Spatial Transcriptomics method (ST, Ståhl et al. 2016, Science) predates Visium. It profiles the whole transcriptome on 100 µm spots on ST 1k/2k arrays, giving images, spot shapes and a table.
552 datasets in the catalog. Example: mouse spinal cord
Other technologies
Merscope: 115 datasets. No description yet.
MERFISH: 10 datasets. No description yet.
spatial-CUT&Tag: 4 datasets. No description yet.
CosMx: 3 datasets. No description yet.
MALDI-MSI: 3 datasets. No description yet.
CODEX: 2 datasets. No description yet.
PhenoCyclerFusion1: 2 datasets. No description yet.
PhenoCyclerFusion2: 2 datasets. No description yet.
spatial-ATAC-seq: 2 datasets. No description yet.