Spatial assays#

The catalog currently holds 12159 datasets.

Each dataset loads as a SpatialData object whose elements (images, shapes, points, labels, tables) depend on the assay.

Visium

10x Genomics Visium captures the whole transcriptome on 55 µm spots. You get the H&E image, the spot shapes and an expression table.

4024 datasets in the catalog. Example: human pancreas

Visium HD

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.

156 datasets in the catalog. Example: human bone element

Xenium

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.

1234 datasets in the catalog. Example: human kidney

Atera

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

Spatial Transcriptomics

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

  • MIBI: 3372 datasets. No description yet.

  • Merscope: 778 datasets. No description yet.

  • IMC: 695 datasets. No description yet.

  • MALDI-MSI: 428 datasets. No description yet.

  • MERFISH: 420 datasets. No description yet.

  • PhenoCyclerFusion1: 251 datasets. No description yet.

  • StereoSeq: 110 datasets. No description yet.

  • DBiT-seq: 53 datasets. No description yet.

  • spatial-ATAC-RNA-seq: 30 datasets. No description yet.

  • spatial-CITE-seq: 24 datasets. No description yet.

  • spatial-CUT&Tag-RNA-seq: 9 datasets. No description yet.

  • spatial-CUT&Tag: 6 datasets. No description yet.

  • CODEX: 4 datasets. No description yet.

  • Spatial-Mux-seq: 4 datasets. No description yet.

  • CosMx: 3 datasets. No description yet.

  • PhenoCyclerFusion2: 2 datasets. No description yet.

  • spatial-ATAC-seq: 2 datasets. No description yet.