Tutorials

Tutorials#

Practical, task-oriented notebooks – what most users actually do with spatialrefinery. Each notebook is a narrated version of the equivalent script in scripts/, and ends with the plain command-line invocation if you’d rather run it as a batch job.

  1. Downloading Xenium data – fetch a 10x Genomics Xenium study’s raw asset bundle from a curl -O <url> manifest.

  2. Xenium to SpatialData zarr – convert a raw Xenium bundle into a SpatialData zarr store, with aligned H&E images and Visium-like pseudo-spots.

  3. Converting images to OME-TIFF – convert whole-slide/microscopy images to pyramidal OME-TIFF for fast, multi-resolution viewing.

  4. Nucleus segmentation to SpatialData zarr – segment nuclei in an H&E whole-slide image with InstanSeg and package the boundaries as a SpatialData zarr store.