Tutorials

Notebooks tailored to showcase specific functionalities of the SpatialData ecosystem.

• Transformations and coordinate systems

• Deep learning example on image tiles

• Spatial query

• Annotating regions of interest with napari

• Use landmark annotations to align multiple -omics layers

• Integrate/aggregate signals across spatial layers

• Squidpy integration

Visualizations

Many different technologies can be visualised out-of-the-box. See below for a couple of examples. See the example datasets for additional technologies represented in SpatialData.

• Technology focus: 10x Genomics Visium

• Technology focus: MibiTOF

• Technology focus: MEFFISH

• Technology focus: COSMX